WorldWideScience

Sample records for siberians reveals distinct

  1. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

    Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.

    2014-01-01

    ,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic......The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24...... that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans....

  2. Siberian Ginseng

    ... Some people use Siberian ginseng to improve athletic performance and the ability to do work. They also use it to treat sleep problems ( ... to reduce symptoms of chronic fatigue syndrome. Mental performance. Early ... in women experiencing mental stress. An inherited disorder that causes ...

  3. Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

    Dalli, Jesmond; Montero-Melendez, Trinidad; Norling, Lucy V; Yin, Xiaoke; Hinds, Charles; Haskard, Dorian; Mayr, Manuel; Perretti, Mauro

    2013-01-01

    Altered plasma neutrophil microparticle levels have recently been implicated in a number of vascular and inflammatory diseases, yet our understanding of their actions is very limited. Herein, we investigate the proteome of neutrophil microparticles in order to shed light on their biological actions. Stimulation of human neutrophils, either in suspension or adherent to an endothelial monolayer, led to the production of microparticles containing >400 distinct proteins with only 223 being shared by the two subsets. For instance, postadherent microparticles were enriched in alpha-2 macroglobulin and ceruloplasmin, whereas microparticles produced by neutrophils in suspension were abundant in heat shock 70 kDa protein 1. Annexin A1 and lactotransferrin were expressed in both microparticle subsets. We next determined relative abundance of these proteins in three types of human microparticle samples: healthy volunteer plasma, plasma of septic patients and skin blister exudates finding that these proteins were differentially expressed on neutrophil microparticles from these samples reflecting in part the expression profiles we found in vitro. Functional assessment of the neutrophil microparticles subsets demonstrated that in response to direct stimulation neutrophil microparticles produced reactive oxygen species and leukotriene B4 as well as locomoted toward a chemotactic gradient. Finally, we investigated the actions of the two neutrophil microparticles subsets described herein on target cell responses. Microarray analysis with human primary endothelial cells incubated with either microparticle subset revealed a discrete modulation of endothelial cell gene expression profile. These findings demonstrate that neutrophil microparticles are heterogenous and can deliver packaged information propagating the activation status of the parent cell, potentially exerting novel and fundamental roles both under homeostatic and disease conditions. PMID:23660474

  4. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

    Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

    2015-12-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

    Kendall, Michelle; Colijn, Caroline

    2016-10-01

    Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness.

    David P Hall

    Full Text Available Acute mountain sickness (AMS is a common problem among visitors at high altitude, and may progress to life-threatening pulmonary and cerebral oedema in a minority of cases. International consensus defines AMS as a constellation of subjective, non-specific symptoms. Specifically, headache, sleep disturbance, fatigue and dizziness are given equal diagnostic weighting. Different pathophysiological mechanisms are now thought to underlie headache and sleep disturbance during acute exposure to high altitude. Hence, these symptoms may not belong together as a single syndrome. Using a novel visual analogue scale (VAS, we sought to undertake a systematic exploration of the symptomatology of AMS using an unbiased, data-driven approach originally designed for analysis of gene expression. Symptom scores were collected from 292 subjects during 1110 subject-days at altitudes between 3650 m and 5200 m on Apex expeditions to Bolivia and Kilimanjaro. Three distinct patterns of symptoms were consistently identified. Although fatigue is a ubiquitous finding, sleep disturbance and headache are each commonly reported without the other. The commonest pattern of symptoms was sleep disturbance and fatigue, with little or no headache. In subjects reporting severe headache, 40% did not report sleep disturbance. Sleep disturbance correlates poorly with other symptoms of AMS (Mean Spearman correlation 0.25. These results challenge the accepted paradigm that AMS is a single disease process and describe at least two distinct syndromes following acute ascent to high altitude. This approach to analysing symptom patterns has potential utility in other clinical syndromes.

  7. Topic Modeling Reveals Distinct Interests within an Online Conspiracy Forum

    Colin Klein

    2018-02-01

    Full Text Available Conspiracy theories play a troubling role in political discourse. Online forums provide a valuable window into everyday conspiracy theorizing, and can give a clue to the motivations and interests of those who post in such forums. Yet this online activity can be difficult to quantify and study. We describe a unique approach to studying online conspiracy theorists which used non-negative matrix factorization to create a topic model of authors' contributions to the main conspiracy forum on Reddit.com. This subreddit provides a large corpus of comments which spans many years and numerous authors. We show that within the forum, there are multiple sub-populations distinguishable by their loadings on different topics in the model. Further, we argue, these differences are interpretable as differences in background beliefs and motivations. The diversity of the distinct subgroups places constraints on theories of what generates conspiracy theorizing. We argue that traditional “monological” believers are only the tip of an iceberg of commenters. Neither simple irrationality nor common preoccupations can account for the observed diversity. Instead, we suggest, those who endorse conspiracies seem to be primarily brought together by epistemological concerns, and that these central concerns link an otherwise heterogenous group of individuals.

  8. Two distinct microbial communities revealed in the sponge Cinachyrella

    Cuvelier, Marie L.; Blake, Emily; Mulheron, Rebecca; McCarthy, Peter J.; Blackwelder, Patricia; Thurber, Rebecca L. Vega; Lopez, Jose V.

    2014-01-01

    Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters. PMID:25408689

  9. Two distinct microbial communities revealed in the sponge Cinachyrella

    Marie Laure Cuvelier

    2014-11-01

    Full Text Available Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes, which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1 with low diversity (Shannon-Weiner index: 3.73 ± 0.22 and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25. Hosts’ 28S rDNA sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences present in low abundance or below detection limits (<0.07% in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5% and 22.4% of SG1 and SG2’s total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.

  10. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  11. Vibrio cholerae classical biotype strains reveal distinct signatures in Mexico.

    Alam, Munirul; Islam, M Tarequl; Rashed, Shah Manzur; Johura, Fatema-tuz; Bhuiyan, Nurul A; Delgado, Gabriela; Morales, Rosario; Mendez, Jose Luis; Navarro, Armando; Watanabe, Haruo; Hasan, Nur-A; Colwell, Rita R; Cravioto, Alejandro

    2012-07-01

    Vibrio cholerae O1 classical (CL) biotype caused the fifth and sixth pandemics, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the seventh pandemic in Asia in the 1970s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia and although it had never been reported from Latin America, V. cholerae CL and ET biotypes, including a hybrid ET, were found associated with areas of cholera endemicity in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from areas of cholera endemicity in Mexico between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and biotyping data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim-sulfamethoxazole, furazolidone, ampicillin, and gentamicin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all of the CL biotype strains although the Mexican strains differed from the Bangladeshi strains in 1 to 2 DNA bands. The difference was subtle but consistent, as confirmed by the subclustering patterns in the PFGE-based dendrogram, and can serve as a regional signature, suggesting the pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from Asia.

  12. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

    Kristina Kirschner

    2015-03-01

    Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

  13. Toward an implicit measure of emotions: ratings of abstract images reveal distinct emotional states.

    Bartoszek, Gregory; Cervone, Daniel

    2017-11-01

    Although implicit tests of positive and negative affect exist, implicit measures of distinct emotional states are scarce. Three experiments examined whether a novel implicit emotion-assessment task, the rating of emotion expressed in abstract images, would reveal distinct emotional states. In Experiment 1, participants exposed to a sadness-inducing story inferred more sadness, and less happiness, in abstract images. In Experiment 2, an anger-provoking interaction increased anger ratings. In Experiment 3, compared to neutral images, spider images increased fear ratings in spider-fearful participants but not in controls. In each experiment, the implicit task indicated elevated levels of the target emotion and did not indicate elevated levels of non-target negative emotions; the task thus differentiated among emotional states of the same valence. Correlations also supported the convergent and discriminant validity of the implicit task. Supporting the possibility that heuristic processes underlie the ratings, group differences were stronger among those who responded relatively quickly.

  14. Complete Mitochondrial Genomes of the Cherskii’s Sculpin and Siberian Taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

    Evgeniy S Balakirev

    2017-08-01

    Full Text Available The complete mitochondrial (mt genome is sequenced in 2 individuals of the Cherskii’s sculpin Cottus czerskii . A surprisingly high level of sequence divergence (10.3% has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027. At the same time, a surprisingly low level of divergence (1.4% has been detected between the GenBank C czerskii (KJ956027 and the Amur sculpin Cottus szanaga (KX762049, KX762050. We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii . Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1, bearing 2 introgressed fragments (≈0.9 kb [kilobase] from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis , submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550. Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

  15. Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.

    Balakirev, Evgeniy S; Saveliev, Pavel A; Ayala, Francisco J

    2017-01-01

    The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii . A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii . Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis , submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

  16. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata

    Closek, Collin J.

    2014-06-20

    Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD. © 2014 International Society for Microbial Ecology. All rights reserved.

  17. Siberian Moth: Potential New Pest

    Yuri Baranchikov; Michael Montgomery; Daniel Kucera

    1997-01-01

    The Siberian moth, Dendrolimus superans Butler (Family Lasiocampidae), is the most destructive defoliator of conifer forests in Northern Asia. Outbreaks defoliate millions of acres and occur at intervals of 8 to 11 years. The larvae feed on most conifers in the pine family, but outbreaks occur in fir, spruce, Siberian pine, and larch forests. The...

  18. Dynamic Changes in Amygdala Psychophysiological Connectivity Reveal Distinct Neural Networks for Facial Expressions of Basic Emotions.

    Diano, Matteo; Tamietto, Marco; Celeghin, Alessia; Weiskrantz, Lawrence; Tatu, Mona-Karina; Bagnis, Arianna; Duca, Sergio; Geminiani, Giuliano; Cauda, Franco; Costa, Tommaso

    2017-03-27

    The quest to characterize the neural signature distinctive of different basic emotions has recently come under renewed scrutiny. Here we investigated whether facial expressions of different basic emotions modulate the functional connectivity of the amygdala with the rest of the brain. To this end, we presented seventeen healthy participants (8 females) with facial expressions of anger, disgust, fear, happiness, sadness and emotional neutrality and analyzed amygdala's psychophysiological interaction (PPI). In fact, PPI can reveal how inter-regional amygdala communications change dynamically depending on perception of various emotional expressions to recruit different brain networks, compared to the functional interactions it entertains during perception of neutral expressions. We found that for each emotion the amygdala recruited a distinctive and spatially distributed set of structures to interact with. These changes in amygdala connectional patters characterize the dynamic signature prototypical of individual emotion processing, and seemingly represent a neural mechanism that serves to implement the distinctive influence that each emotion exerts on perceptual, cognitive, and motor responses. Besides these differences, all emotions enhanced amygdala functional integration with premotor cortices compared to neutral faces. The present findings thus concur to reconceptualise the structure-function relation between brain-emotion from the traditional one-to-one mapping toward a network-based and dynamic perspective.

  19. Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis.

    Zheng, Wenning; Tan, Mui Fern; Old, Lesley A; Paterson, Ian C; Jakubovics, Nicholas S; Choo, Siew Woh

    2017-06-07

    Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virulence genes. However, we observed subtle differences in genomic islands and prophages between the species. Comparative pathogenomics analysis identified S. sanguinis strains have genes encoding IgA proteases, mitogenic factor deoxyribonucleases, nickel/cobalt uptake and cobalamin biosynthesis. On the contrary, genomic islands of S. gordonii strains contain additional copies of comCDE quorum-sensing system components involved in genetic competence. Two distinct polysaccharide locus architectures were identified, one of which was exclusively present in S. gordonii strains. The first evidence of genes encoding the CylA and CylB system by the α-haemolytic S. gordonii is presented. This study provides new insights into the genetic distinctions between S. gordonii and S. sanguinis, which yields understanding of tooth surfaces colonization and contributions to dental plaque formation, as well as their potential roles in the pathogenesis of IE.

  20. Expression of cytokeratins in odontogenic jaw cysts: monoclonal antibodies reveal distinct variation between different cyst types.

    Hormia, M; Ylipaavalniemi, P; Nagle, R B; Virtanen, I

    1987-08-01

    Immunostaining with monoclonal antibodies was used to study and compare the cytokeratin content of odontogenic cysts and normal gingival epithelium. Two monoclonal antibodies, PKK2 and KA1, stained the whole epithelium in all cyst samples. In gingiva, PKK2 gave a suprabasal staining and KA1 reacted with all epithelial cell layers. Antibodies PKK1, KM 4.62 and KS 8.12 gave a heterogeneous staining in follicular and radicular cysts. In keratocysts and in gingiva PKK1 and KM 4.62 reacted mainly with basal cells and KS 8.12 gave a suprabasal staining. Antibodies reacting with the simple epithelial cytokeratin polypeptide No. 18 (PKK3, KS 18.18) recognized in gingiva only solitary cells compatible with Merkel cells. In a case of follicular ameloblastoma a distinct staining of tumor epithelium was revealed with these antibodies. In 2 follicular cysts, but not in other cyst types, a layer of cytokeratin 18-positive cells was revealed. KA5 and KK 8.60 antibodies, reacting exclusively with keratinizing epithelia, including normal gingiva, gave no reaction in radicular cysts, keratocysts and ameloblastoma. Two of the follicular cysts, were negative for PKK3 and KS 18.18, but reacted strongly with KA5 and KK 8.60. The present results show that odontogenic jaw cysts have distinct differences in their cytokeratin content. With the exception of some follicular cysts, they lack signs of keratinizing epithelial differentiation. Only follicular cysts appear to share with some types of ameloblastoma the expression of cytokeratin polypeptide No. 18.

  1. Serum and urine metabolomics study reveals a distinct diagnostic model for cancer cachexia

    Yang, Quan‐Jun; Zhao, Jiang‐Rong; Hao, Juan; Li, Bin; Huo, Yan; Han, Yong‐Long; Wan, Li‐Li; Li, Jie; Huang, Jinlu; Lu, Jin

    2017-01-01

    Abstract Background Cachexia is a multifactorial metabolic syndrome with high morbidity and mortality in patients with advanced cancer. The diagnosis of cancer cachexia depends on objective measures of clinical symptoms and a history of weight loss, which lag behind disease progression and have limited utility for the early diagnosis of cancer cachexia. In this study, we performed a nuclear magnetic resonance‐based metabolomics analysis to reveal the metabolic profile of cancer cachexia and establish a diagnostic model. Methods Eighty‐four cancer cachexia patients, 33 pre‐cachectic patients, 105 weight‐stable cancer patients, and 74 healthy controls were included in the training and validation sets. Comparative analysis was used to elucidate the distinct metabolites of cancer cachexia, while metabolic pathway analysis was employed to elucidate reprogramming pathways. Random forest, logistic regression, and receiver operating characteristic analyses were used to select and validate the biomarker metabolites and establish a diagnostic model. Results Forty‐six cancer cachexia patients, 22 pre‐cachectic patients, 68 weight‐stable cancer patients, and 48 healthy controls were included in the training set, and 38 cancer cachexia patients, 11 pre‐cachectic patients, 37 weight‐stable cancer patients, and 26 healthy controls were included in the validation set. All four groups were age‐matched and sex‐matched in the training set. Metabolomics analysis showed a clear separation of the four groups. Overall, 45 metabolites and 18 metabolic pathways were associated with cancer cachexia. Using random forest analysis, 15 of these metabolites were identified as highly discriminating between disease states. Logistic regression and receiver operating characteristic analyses were used to create a distinct diagnostic model with an area under the curve of 0.991 based on three metabolites. The diagnostic equation was Logit(P) = −400.53 – 481.88

  2. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  3. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

    Ang, Pei Woon; Soong, Richie; Loh, Marie; Liem, Natalia; Lim, Pei Li; Grieu, Fabienne; Vaithilingam, Aparna; Platell, Cameron; Yong, Wei Peng; Iacopetta, Barry

    2010-01-01

    Most previous studies of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA methylation profiling of CRC with the aim of characterizing CIMP subgroups. DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina GoldenGate ® methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological and molecular features including patient age, tumor site, microsatellite instability (MSI), methylation at a consensus panel of CpG islands and mutations in BRAF and KRAS. A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to as CIMP-low (CIMP-L, 21% of cases), CIMP-mid (CIMP-M, 14%) and CIMP-high (CIMP-H, 65%). In comparison to CIMP-L tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS and BRAF (P < 0.001). Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with the CIMP-H pathway of CRC rather than with distinct CIMP subgroups

  4. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

    Vaithilingam Aparna

    2010-05-01

    Full Text Available Abstract Background Most previous studies of the CpG island methylator phenotype (CIMP in colorectal cancer (CRC have been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA methylation profiling of CRC with the aim of characterizing CIMP subgroups. Methods DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina GoldenGate® methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological and molecular features including patient age, tumor site, microsatellite instability (MSI, methylation at a consensus panel of CpG islands and mutations in BRAF and KRAS. Results A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to as CIMP-low (CIMP-L, 21% of cases, CIMP-mid (CIMP-M, 14% and CIMP-high (CIMP-H, 65%. In comparison to CIMP-L tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS and BRAF (P Conclusions Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with the CIMP-H pathway of CRC rather than with distinct CIMP subgroups.

  5. A chimeric prokaryotic pentameric ligand–gated channel reveals distinct pathways of activation

    Schmandt, Nicolaus; Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.; Stein, Richard A.; Bonner, Ross; Talley, Lauren; Parker, Mark D.; Mchaourab, Hassane S.; Yee, Vivien C.; Lodowski, David T.

    2015-01-01

    Recent high resolution structures of several pentameric ligand–gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron–electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand–gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand–gated ion channel, which is activated by protons. We found that the chimera was independently gated by primary amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators. PMID:26415570

  6. The Brain–to–Pancreatic Islet Neuronal Map Reveals Differential Glucose Regulation From Distinct Hypothalamic Regions

    Rosario, Wilfredo; Singh, Inderroop; Wautlet, Arnaud; Patterson, Christa; Flak, Jonathan; Becker, Thomas C.; Ali, Almas; Tamarina, Natalia; Philipson, Louis H.; Enquist, Lynn W.; Myers, Martin G.

    2016-01-01

    The brain influences glucose homeostasis, partly by supplemental control over insulin and glucagon secretion. Without this central regulation, diabetes and its complications can ensue. Yet, the neuronal network linking to pancreatic islets has never been fully mapped. Here, we refine this map using pseudorabies virus (PRV) retrograde tracing, indicating that the pancreatic islets are innervated by efferent circuits that emanate from the hypothalamus. We found that the hypothalamic arcuate nucleus (ARC), ventromedial nucleus (VMN), and lateral hypothalamic area (LHA) significantly overlap PRV and the physiological glucose-sensing enzyme glucokinase. Then, experimentally lowering glucose sensing, specifically in the ARC, resulted in glucose intolerance due to deficient insulin secretion and no significant effect in the VMN, but in the LHA it resulted in a lowering of the glucose threshold that improved glucose tolerance and/or improved insulin sensitivity, with an exaggerated counter-regulatory response for glucagon secretion. No significant effect on insulin sensitivity or metabolic homeostasis was noted. Thus, these data reveal novel direct neuronal effects on pancreatic islets and also render a functional validation of the brain-to-islet neuronal map. They also demonstrate that distinct regions of the hypothalamus differentially control insulin and glucagon secretion, potentially in partnership to help maintain glucose homeostasis and guard against hypoglycemia. PMID:27207534

  7. The Brain-to-Pancreatic Islet Neuronal Map Reveals Differential Glucose Regulation From Distinct Hypothalamic Regions.

    Rosario, Wilfredo; Singh, Inderroop; Wautlet, Arnaud; Patterson, Christa; Flak, Jonathan; Becker, Thomas C; Ali, Almas; Tamarina, Natalia; Philipson, Louis H; Enquist, Lynn W; Myers, Martin G; Rhodes, Christopher J

    2016-09-01

    The brain influences glucose homeostasis, partly by supplemental control over insulin and glucagon secretion. Without this central regulation, diabetes and its complications can ensue. Yet, the neuronal network linking to pancreatic islets has never been fully mapped. Here, we refine this map using pseudorabies virus (PRV) retrograde tracing, indicating that the pancreatic islets are innervated by efferent circuits that emanate from the hypothalamus. We found that the hypothalamic arcuate nucleus (ARC), ventromedial nucleus (VMN), and lateral hypothalamic area (LHA) significantly overlap PRV and the physiological glucose-sensing enzyme glucokinase. Then, experimentally lowering glucose sensing, specifically in the ARC, resulted in glucose intolerance due to deficient insulin secretion and no significant effect in the VMN, but in the LHA it resulted in a lowering of the glucose threshold that improved glucose tolerance and/or improved insulin sensitivity, with an exaggerated counter-regulatory response for glucagon secretion. No significant effect on insulin sensitivity or metabolic homeostasis was noted. Thus, these data reveal novel direct neuronal effects on pancreatic islets and also render a functional validation of the brain-to-islet neuronal map. They also demonstrate that distinct regions of the hypothalamus differentially control insulin and glucagon secretion, potentially in partnership to help maintain glucose homeostasis and guard against hypoglycemia. © 2016 by the American Diabetes Association.

  8. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  9. Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions.

    Derenko, Miroslava; Malyarchuk, Boris; Denisova, Galina A; Wozniak, Marcin; Dambueva, Irina; Dorzhu, Choduraa; Luzina, Faina; Miścicka-Sliwka, Danuta; Zakharov, Ilia

    2006-01-01

    In order to investigate the genetic history of autochthonous South Siberian populations and to estimate the contribution of distinct patrilineages to their gene pools, we have analyzed 17 Y-chromosomal binary markers (YAP, RPS4Y(711), SRY-8299, M89, M201, M52, M170, 12f2, M9, M20, 92R7, SRY-1532, DYS199, M173, M17, Tat, and LLY22 g) in a total sample of 1,358 males from 14 ethnic groups of Siberia (Altaians-Kizhi, Teleuts, Shors, Tuvinians, Todjins, Tofalars, Sojots, Khakassians, Buryats, Evenks), Central/Eastern Asia (Mongolians and Koreans) and Eastern Europe (Kalmyks and Russians). Based on both, the distribution pattern of Y-chromosomal haplogroups and results on AMOVA analysis we observed the statistically significant genetic differentiation between the populations of Baikal and Altai-Sayan regions. We suggest that these regional differences can be best explained by different contribution of Central/Eastern Asian and Eastern European paternal lineages into gene pools of modern South Siberians. The population of the Baikal region demonstrates the prevalence of Central/Eastern Asian lineages, whereas in the populations of Altai and Sayan regions the highest paternal contribution resulted from Eastern European descent is revealed. Yet, our data on Y-chromosome STRs variation demonstrate the clear differences between the South Siberian and Eastern European R1a1-lineages with the evolutionary ages compatible with divergence time between these two regional groups.

  10. Siberian Pine Decline and Mortality in Southern Siberian Mountains

    Kharuk, V. I.; Im, S. T.; Oskorbin, P. A.; Petrov, I. A.; Ranson, K. J.

    2013-01-01

    The causes and resulting spatial patterns of Siberian pine mortality in eastern Kuznetzky Alatau Mountains, Siberia were analyzed based on satellite (Landsat, MODIS) and dendrochronology data. Climate variables studied included temperature, precipitation and Standardized Precipitation-Evapotranspiration Index (SPEI) drought index. Landsat data analysis showed that stand mortality was first detected in the year 2006 at an elevation of 650 m, and extended up to 900 m by the year 2012. Mortality was accompanied by a decrease in MODIS derived vegetation index (EVI).. The area of dead stands and the upper mortality line were correlated with increased drought. The uphill margin of mortality was limited by elevational precipitation gradients. Dead stands (i.e., >75% tree mortality) were located mainly on southern slopes. With respect to slope, mortality was observed within a 7 deg - 20 deg range with greatest mortality occurring on convex terrain. Tree radial incrementmeasurements correlate and were synchronous with SPEI (r sq = 0.37, r(sub s) = 80). Increasing synchrony between tree ring growth and SPEI indicates that drought has reduced the ecological niche of Siberian pine. The results also showed the primary role of drought stress on Siberian pine mortality. A secondary role may be played by bark beetles and root fungi attacks. The observed Siberian pine mortality is part of a broader phenomenon of "dark needle conifers" (DNC, i.e., Siberian pine, fir and spruce) decline and mortality in European Russia, Siberia, and the Russian Far East. All locations of DNC decline coincided with areas of observed drought increase. The results obtained are one of the first observations of drought-induced decline and mortality of DNC at the southern border of boreal forests. Meanwhile if model projections of increased aridity are correct DNC, within the southern part of its range may be replaced by drought-resistant Pinus silvestris and Larix sibirica.

  11. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    Herrera Sarrias, Marcela; Ziegler, Maren; Voolstra, Christian R.; Aranda, Manuel

    2017-01-01

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  12. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    Herrera Sarrias, Marcela

    2017-05-02

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  13. NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma

    Rocha, CM; Barros, AS; Goodfellow, BJ; Carreira, IM; Gomes, AA; Sousa, V; Bernardo, J; Carvalho, L; Gil, AM; Duarte, IF

    2015-01-01

    Lung tumour subtyping, particularly the distinction between adenocarcinoma (AdC) and squamous cell carcinoma (SqCC), is a critical diagnostic requirement. In this work, the metabolic signatures of lung carcinomas were investigated through (1)H NMR metabolomics, with a view to provide additional criteria for improved diagnosis and treatment planning. High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (NMR) spectroscopy was used to analyse matched tumour and adjacent control tissue...

  14. Genomic analyses of breast cancer progression reveal distinct routes of metastasis emergence

    Krøigård, Anne Bruun; Larsen, Martin Jakob; Brasch-Andersen, Charlotte

    2017-01-01

    receptor (ER)-positive breast cancer. Our data provide support for both linear and parallel progression towards metastasis. We report for the first time evidence of metastasis-to-metastasis seeding in breast cancer. Our results point to three distinct routes of metastasis emergence. This may have profound...... clinical implications and provides substantial novel molecular insights into the timing and mutational evolution of breast cancer metastasis....

  15. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

    Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

    2013-10-29

    Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

  16. Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

    Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

    2015-04-01

    The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits

  17. An overexpression screen of Toxoplasma gondii Rab-GTPases reveals distinct transport routes to the micronemes.

    Katrin Kremer

    2013-03-01

    Full Text Available The basic organisation of the endomembrane system is conserved in all eukaryotes and comparative genome analyses provides compelling evidence that the endomembrane system of the last common eukaryotic ancestor (LCEA is complex with many genes required for regulated traffic being present. Although apicomplexan parasites, causative agents of severe human and animal diseases, appear to have only a basic set of trafficking factors such as Rab-GTPases, they evolved unique secretory organelles (micronemes, rhoptries and dense granules that are sequentially secreted during invasion of the host cell. In order to define the secretory pathway of apicomplexans, we performed an overexpression screen of Rabs in Toxoplasma gondii and identified Rab5A and Rab5C as important regulators of traffic to micronemes and rhoptries. Intriguingly, we found that not all microneme proteins traffic depends on functional Rab5A and Rab5C, indicating the existence of redundant microneme targeting pathways. Using two-colour super-resolution stimulated emission depletion (STED we verified distinct localisations of independent microneme proteins and demonstrate that micronemal organelles are organised in distinct subsets or subcompartments. Our results suggest that apicomplexan parasites modify classical regulators of the endocytic system to carryout essential parasite-specific roles in the biogenesis of their unique secretory organelles.

  18. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Johnston, Josiah; Iser, Wendy B; Chow, David K; Goldberg, Ilya G; Wolkow, Catherine A

    2008-07-30

    Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  19. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Identifying Two Groups of Entitled Individuals: Cluster Analysis Reveals Emotional Stability and Self-Esteem Distinction.

    Crowe, Michael L; LoPilato, Alexander C; Campbell, W Keith; Miller, Joshua D

    2016-12-01

    The present study hypothesized that there exist two distinct groups of entitled individuals: grandiose-entitled, and vulnerable-entitled. Self-report scores of entitlement were collected for 916 individuals using an online platform. Model-based cluster analyses were conducted on the individuals with scores one standard deviation above mean (n = 159) using the five-factor model dimensions as clustering variables. The results support the existence of two groups of entitled individuals categorized as emotionally stable and emotionally vulnerable. The emotionally stable cluster reported emotional stability, high self-esteem, more positive affect, and antisocial behavior. The emotionally vulnerable cluster reported low self-esteem and high levels of neuroticism, disinhibition, conventionality, psychopathy, negative affect, childhood abuse, intrusive parenting, and attachment difficulties. Compared to the control group, both clusters reported being more antagonistic, extraverted, Machiavellian, and narcissistic. These results suggest important differences are missed when simply examining the linear relationships between entitlement and various aspects of its nomological network.

  1. Complete sequence analysis reveals two distinct poleroviruses infecting cucurbits in China.

    Xiang, Hai-ying; Shang, Qiao-xia; Han, Cheng-gui; Li, Da-wei; Yu, Jia-lin

    2008-01-01

    The complete RNA genomes of a Chinese isolate of cucurbit aphid-borne yellows virus (CABYV-CHN) and a new polerovirus tentatively referred to as melon aphid-borne yellows virus (MABYV) were determined. The entire genome of CABYV-CHN shared 89.0% nucleotide sequence identity with the French CABYV isolate. In contrast, nucleotide sequence identities between MABYV and CABYV and other poleroviruses were in the range of 50.7-74.2%, with amino acid sequence identities ranging from 24.8 to 82.9% for individual gene products. We propose that CABYV-CHN is a strain of CABYV and that MABYV is a member of a tentative distinct species within the genus Polerovirus.

  2. Distinctive anatomical and physiological features of migraine aura revealed by 18 years of recording

    Hansen, Jakob Møller; Baca, Serapio Michael; Vanvalkenburgh, Paul

    2013-01-01

    insight into basic aura mechanisms. An individual made detailed drawings of his visual percept of migraine aura in real time during more than 1000 attacks of migraine aura without headache over 18 years. Drawings were made in a consistent fashion documenting the shape and location of the aura wavefront...... originated centrally (within 10° eccentricity), but there were also other distinct sites of initiation in the visual field. Auras beginning centrally preferentially propagated first through lower nasal field (69-77% of all auras) before travelling to upper and temporal fields, on both sides. Some auras...... propagated from peripheral to central regions of the visual field-these typically followed the reverse path of those travelling in the opposite direction. The mean velocity of the perceived visual phenomenon did not differ between attacks starting peripherally and centrally. The estimated speed...

  3. Physical versus psychological social stress in male rats reveals distinct cardiovascular, inflammatory and behavioral consequences

    Padi, Akhila R.; Moffitt, Casey M.; Wilson, L. Britt; Wood, Christopher S.; Wood, Susan K.

    2017-01-01

    Repeated exposure to social stress can precipitate the development of psychosocial disorders including depression and comorbid cardiovascular disease. While a major component of social stress often encompasses physical interactions, purely psychological stressors (i.e. witnessing a traumatic event) also fall under the scope of social stress. The current study determined whether the acute stress response and susceptibility to stress-related consequences differed based on whether the stressor consisted of physical versus purely psychological social stress. Using a modified resident-intruder paradigm, male rats were either directly exposed to repeated social defeat stress (intruder) or witnessed a male rat being defeated. Cardiovascular parameters, behavioral anhedonia, and inflammatory cytokines in plasma and the stress-sensitive locus coeruleus were compared between intruder, witness, and control rats. Surprisingly intruders and witnesses exhibited nearly identical increases in mean arterial pressure and heart rate during acute and repeated stress exposures, yet only intruders exhibited stress-induced arrhythmias. Furthermore, re-exposure to the stress environment in the absence of the resident produced robust pressor and tachycardic responses in both stress conditions indicating the robust and enduring nature of social stress. In contrast, the long-term consequences of these stressors were distinct. Intruders were characterized by enhanced inflammatory sensitivity in plasma, while witnesses were characterized by the emergence of depressive-like anhedonia, transient increases in systolic blood pressure and plasma levels of tissue inhibitor of metalloproteinase. The current study highlights that while the acute cardiovascular responses to stress were identical between intruders and witnesses, these stressors produced distinct differences in the enduring consequences to stress, suggesting that witness stress may be more likely to produce long-term cardiovascular

  4. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Josiah Johnston

    2008-07-01

    Full Text Available Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  5. Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage

    van der Reijden, Wil A.; Brunner, Jorg; Bosch-Tijhof, Carolien J.; van Trappen, Stefanie; Rijnsburger, Martine C.; de Graaff, Marcel P. W.; van Winkelhoff, Arie J.; Cleenwerck, Ilse; de Vos, Paul

    2010-01-01

    The periodontal pathogen Aggregatibacter actinomycetemcomitans that comprises six serotypes (a-f), is often identified by PCR-based techniques targeting the 16S rRNA gene. In this study, 16S rRNA gene sequence analysis revealed an aberrant cluster of 19 strains within serotype e, denoted as serotype

  6. Indiana: Siberian Snake saves spin

    Anon.

    1990-01-15

    A team working at the Indiana University Cooler Ring has used a 'Siberian Snake' system to accelerate a spin-polarized proton beam through two depolarizing resonances with no loss of spin. The Michigan/lndiana/Brookhaven team under Alan Krisch overcame their first imperfection resonance hurdle at 108 MeV, and in a subsequent run vanquished a further resonance at 177 MeV.

  7. Indiana: Siberian Snake saves spin

    Anon.

    1990-01-01

    A team working at the Indiana University Cooler Ring has used a 'Siberian Snake' system to accelerate a spin-polarized proton beam through two depolarizing resonances with no loss of spin. The Michigan/lndiana/Brookhaven team under Alan Krisch overcame their first imperfection resonance hurdle at 108 MeV, and in a subsequent run vanquished a further resonance at 177 MeV

  8. Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis

    Zheng, Wenning; Tan, Mui Fern; Old, Lesley A.; Paterson, Ian C.; Jakubovics, Nicholas S.; Choo, Siew Woh

    2017-01-01

    Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virule...

  9. Internal Transcribed Spacer 1 (ITS1 based sequence typing reveals phylogenetically distinct Ascaris population

    Koushik Das

    2015-01-01

    Full Text Available Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1. Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis.

  10. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  11. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

    Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

    2011-07-01

    Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

  12. Molecular phylogenetics of the genus Costularia (Schoeneae, Cyperaceae) reveals multiple distinct evolutionary lineages.

    Larridon, Isabel; Bauters, Kenneth; Semmouri, Ilias; Viljoen, Jan-Adriaan; Prychid, Christina J; Muasya, A Muthama; Bruhl, Jeremy J; Wilson, Karen L; Senterre, Bruno; Goetghebeur, Paul

    2018-04-19

    We investigated the monophyly of Costularia (25 species), a genus of tribe Schoeneae (Cyperaceae) that illustrates a remarkable distribution pattern from southeastern Africa, over Madagascar, the Mascarenes and Seychelles, to Malesia and New Caledonia. A further species, Tetraria borneensis, has been suggested to belong to Costularia. Relationships and divergence times were inferred using an existing four marker phylogeny of Cyperaceae tribe Schoeneae expanded with newly generated sequence data mainly for Costularia s.l. species. Phylogenetic reconstruction was executed using Bayesian inference and maximum likelihood approaches. Divergence times were estimated using a relaxed molecular clock model, calibrated with fossil data. Based on our results, Tetraria borneensis is not related to the species of Costularia. Costularia s.l. is composed of four distinct evolutionary lineages. Two lineages, one including the type species, are part of the Oreobolus clade, i.e. a much reduced genus Costularia restricted to southeastern Africa, Madagascar, the Mascarenes and Seychelles, and a small endemic genus from New Caledonia for which a new genus Chamaedendron is erected based on Costularia subgenus Chamaedendron. The other two lineages are part of the Tricostularia clade, i.e. a separate single-species lineage from the Seychelles for which a new genus (Xyroschoenus) is described, and Costularia subgenus Lophoschoenus. For the latter, more research is needed to test whether they are congeneric with the species placed in the reticulate-sheathed Tetraria clade. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias

    Calin, George Adrian; Liu, Chang-Gong; Sevignani, Cinzia; Ferracin, Manuela; Felli, Nadia; Dumitru, Calin Dan; Shimizu, Masayoshi; Cimmino, Amelia; Zupo, Simona; Dono, Mariella; Dell'Aquila, Marie L.; Alder, Hansjuerg; Rassenti, Laura; Kipps, Thomas J.; Bullrich, Florencia; Negrini, Massimo; Croce, Carlo M.

    2004-01-01

    Little is known about the expression levels or function of micro-RNAs (miRNAs) in normal and neoplastic cells, although it is becoming clear that miRNAs play important roles in the regulation of gene expression during development [Ambros, V. (2003) Cell 113, 673–676; McManus, M. T. (2003) Semin. Cancer Biol. 13, 253–258]. We now report the genomewide expression profiling of miRNAs in human B cell chronic lymphocytic leukemia (CLL) by using a microarray containing hundreds of human precursor and mature miRNA oligonucleotide probes. This approach allowed us to identify significant differences in miRNome expression between CLL samples and normal CD5+ B cells; data were confirmed by Northern blot analyses and real-time RT-PCR. At least two distinct clusters of CLL samples can be identified that were associated with the presence or absence of Zap-70 expression, a predictor of early disease progression. Two miRNA signatures were associated with the presence or absence of mutations in the expressed Ig variableregion genes or with deletions at 13q14, respectively. These data suggest that miRNA expression patterns have relevance to the biological and clinical behavior of this leukemia. PMID:15284443

  14. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  15. Distinct neuronal coding schemes in memory revealed by selective erasure of fast synchronous synaptic transmission.

    Xu, Wei; Morishita, Wade; Buckmaster, Paul S; Pang, Zhiping P; Malenka, Robert C; Südhof, Thomas C

    2012-03-08

    Neurons encode information by firing spikes in isolation or bursts and propagate information by spike-triggered neurotransmitter release that initiates synaptic transmission. Isolated spikes trigger neurotransmitter release unreliably but with high temporal precision. In contrast, bursts of spikes trigger neurotransmission reliably (i.e., boost transmission fidelity), but the resulting synaptic responses are temporally imprecise. However, the relative physiological importance of different spike-firing modes remains unclear. Here, we show that knockdown of synaptotagmin-1, the major Ca(2+) sensor for neurotransmitter release, abrogated neurotransmission evoked by isolated spikes but only delayed, without abolishing, neurotransmission evoked by bursts of spikes. Nevertheless, knockdown of synaptotagmin-1 in the hippocampal CA1 region did not impede acquisition of recent contextual fear memories, although it did impair the precision of such memories. In contrast, knockdown of synaptotagmin-1 in the prefrontal cortex impaired all remote fear memories. These results indicate that different brain circuits and types of memory employ distinct spike-coding schemes to encode and transmit information. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. A mitochondrial analysis reveals distinct founder effect signatures in Canarian and Balearic goats.

    Ferrando, A; Manunza, A; Jordana, J; Capote, J; Pons, A; Pais, J; Delgado, T; Atoche, P; Cabrera, B; Martínez, A; Landi, V; Delgado, J V; Argüello, A; Vidal, O; Lalueza-Fox, C; Ramírez, O; Amills, M

    2015-08-01

    In the course of human migrations, domestic animals often have been translocated to islands with the aim of assuring food availability. These founder events are expected to leave a genetic footprint that may be recognised nowadays. Herewith, we have examined the mitochondrial diversity of goat populations living in the Canarian and Balearic archipelagos. Median-joining network analysis produced very distinct network topologies for these two populations. Indeed, a majority of Canarian goats shared a single ancestral haplotype that segregated in all sampled islands, suggesting a single founder effect followed by a stepping-stone pattern of diffusion. This haplotype also was present in samples collected from archaeological assemblies at Gran Canaria and Lanzarote, making evident its widespread distribution in ancient times. In stark contrast, goats from Majorca and Ibiza did not share any mitochondrial haplotypes, indicating the occurrence of two independent founder events. Furthermore, in Majorcan goats, we detected the segregation of the mitochondrial G haplogroup that has only been identified in goats from Egypt, Iran and Turkey. This finding suggests the translocation of Asian and/or African goats to Majorca, possibly as a consequence of the Phoenician and Carthaginian colonisations of this island. © 2015 Stichting International Foundation for Animal Genetics.

  17. Motor learning in childhood reveals distinct mechanisms for memory retention and re-learning.

    Musselman, Kristin E; Roemmich, Ryan T; Garrett, Ben; Bastian, Amy J

    2016-05-01

    Adults can easily learn and access multiple versions of the same motor skill adapted for different conditions (e.g., walking in water, sand, snow). Following even a single session of adaptation, adults exhibit clear day-to-day retention and faster re-learning of the adapted pattern. Here, we studied the retention and re-learning of an adapted walking pattern in children aged 6-17 yr. We found that all children, regardless of age, showed adult-like patterns of retention of the adapted walking pattern. In contrast, children under 12 yr of age did not re-learn faster on the next day after washout had occurred-they behaved as if they had never adapted their walking before. Re-learning could be improved in younger children when the adaptation time on day 1 was increased to allow more practice at the plateau of the adapted pattern, but never to adult-like levels. These results show that the ability to store a separate, adapted version of the same general motor pattern does not fully develop until adolescence, and furthermore, that the mechanisms underlying the retention and rapid re-learning of adapted motor patterns are distinct. © 2016 Musselman et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Gene expression profiling reveals distinct molecular signatures associated with the rupture of intracranial aneurysm.

    Nakaoka, Hirofumi; Tajima, Atsushi; Yoneyama, Taku; Hosomichi, Kazuyoshi; Kasuya, Hidetoshi; Mizutani, Tohru; Inoue, Ituro

    2014-08-01

    The rupture of intracranial aneurysm (IA) causes subarachnoid hemorrhage associated with high morbidity and mortality. We compared gene expression profiles in aneurysmal domes between unruptured IAs and ruptured IAs (RIAs) to elucidate biological mechanisms predisposing to the rupture of IA. We determined gene expression levels of 8 RIAs, 5 unruptured IAs, and 10 superficial temporal arteries with the Agilent microarrays. To explore biological heterogeneity of IAs, we classified the samples into subgroups showing similar gene expression patterns, using clustering methods. The clustering analysis identified 4 groups: superficial temporal arteries and unruptured IAs were aggregated into their own clusters, whereas RIAs segregated into 2 distinct subgroups (early and late RIAs). Comparing gene expression levels between early RIAs and unruptured IAs, we identified 430 upregulated and 617 downregulated genes in early RIAs. The upregulated genes were associated with inflammatory and immune responses and phagocytosis including S100/calgranulin genes (S100A8, S100A9, and S100A12). The downregulated genes suggest mechanical weakness of aneurysm walls. The expressions of Krüppel-like family of transcription factors (KLF2, KLF12, and KLF15), which were anti-inflammatory regulators, and CDKN2A, which was located on chromosome 9p21 that was the most consistently replicated locus in genome-wide association studies of IA, were also downregulated. We demonstrate that gene expression patterns of RIAs were different according to the age of patients. The results suggest that macrophage-mediated inflammation is a key biological pathway for IA rupture. The identified genes can be good candidates for molecular markers of rupture-prone IAs and therapeutic targets. © 2014 American Heart Association, Inc.

  19. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems

    Hook, Vivian; Bandeira, Nuno

    2015-12-01

    Neuropeptides regulate intercellular signaling as neurotransmitters of the central and peripheral nervous systems, and as peptide hormones in the endocrine system. Diverse neuropeptides of distinct primary sequences of various lengths, often with post-translational modifications, coordinate and integrate regulation of physiological functions. Mass spectrometry-based analysis of the diverse neuropeptide structures in neuropeptidomics research is necessary to define the full complement of neuropeptide signaling molecules. Human neuropeptidomics has notable importance in defining normal and dysfunctional neuropeptide signaling in human health and disease. Neuropeptidomics has great potential for expansion in translational research opportunities for defining neuropeptide mechanisms of human diseases, providing novel neuropeptide drug targets for drug discovery, and monitoring neuropeptides as biomarkers of drug responses. In consideration of the high impact of human neuropeptidomics for health, an observed gap in this discipline is the few published articles in human neuropeptidomics compared with, for example, human proteomics and related mass spectrometry disciplines. Focus on human neuropeptidomics will advance new knowledge of the complex neuropeptide signaling networks participating in the fine control of neuroendocrine systems. This commentary review article discusses several human neuropeptidomics accomplishments that illustrate the rapidly expanding diversity of neuropeptides generated by protease processing of pro-neuropeptide precursors occurring within the secretory vesicle proteome. Of particular interest is the finding that human-specific cathepsin V participates in producing enkephalin and likely other neuropeptides, indicating unique proteolytic mechanisms for generating human neuropeptides. The field of human neuropeptidomics has great promise to solve new mechanisms in disease conditions, leading to new drug targets and therapeutic agents for human

  20. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

    Weerachai Jaratlerdsiri

    Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

  1. Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation.

    Moore, Henna M; Bai, Baoyan; Boisvert, François-Michel; Latonen, Leena; Rantanen, Ville; Simpson, Jeremy C; Pepperkok, Rainer; Lamond, Angus I; Laiho, Marikki

    2011-10-01

    The nucleolus is a nuclear organelle that coordinates rRNA transcription and ribosome subunit biogenesis. Recent proteomic analyses have shown that the nucleolus contains proteins involved in cell cycle control, DNA processing and DNA damage response and repair, in addition to the many proteins connected with ribosome subunit production. Here we study the dynamics of nucleolar protein responses in cells exposed to stress and DNA damage caused by ionizing and ultraviolet (UV) radiation in diploid human fibroblasts. We show using a combination of imaging and quantitative proteomics methods that nucleolar substructure and the nucleolar proteome undergo selective reorganization in response to UV damage. The proteomic responses to UV include alterations of functional protein complexes such as the SSU processome and exosome, and paraspeckle proteins, involving both decreases and increases in steady state protein ratios, respectively. Several nonhomologous end-joining proteins (NHEJ), such as Ku70/80, display similar fast responses to UV. In contrast, nucleolar proteomic responses to IR are both temporally and spatially distinct from those caused by UV, and more limited in terms of magnitude. With the exception of the NHEJ and paraspeckle proteins, where IR induces rapid and transient changes within 15 min of the damage, IR does not alter the ratios of most other functional nucleolar protein complexes. The rapid transient decrease of NHEJ proteins in the nucleolus indicates that it may reflect a response to DNA damage. Our results underline that the nucleolus is a specific stress response organelle that responds to different damage and stress agents in a unique, damage-specific manner.

  2. The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

    Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E. (Cornell); (Pavia); (Lund); (Southern Research)

    2011-09-20

    Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

  3. DNA methylation analysis reveals distinct methylation signatures in pediatric germ cell tumors

    Amatruda, James F; Frazier, A Lindsay; Poynter, Jenny N; Ross, Julie A; Christensen, Brock; Fustino, Nicholas J; Chen, Kenneth S; Hooten, Anthony J; Nelson, Heather; Kuriger, Jacquelyn K; Rakheja, Dinesh

    2013-01-01

    Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy

  4. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

    2015-11-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Comparative Plasmodium gene overexpression reveals distinct perturbation of sporozoite transmission by profilin.

    Sato, Yuko; Hliscs, Marion; Dunst, Josefine; Goosmann, Christian; Brinkmann, Volker; Montagna, Georgina N; Matuschewski, Kai

    2016-07-15

    Plasmodium relies on actin-based motility to migrate from the site of infection and invade target cells. Using a substrate-dependent gliding locomotion, sporozoites are able to move at fast speed (1-3 μm/s). This motility relies on a minimal set of actin regulatory proteins and occurs in the absence of detectable filamentous actin (F-actin). Here we report an overexpression strategy to investigate whether perturbations of F-actin steady-state levels affect gliding locomotion and host invasion. We selected two vital Plasmodium berghei G-actin-binding proteins, C-CAP and profilin, in combination with three stage-specific promoters and mapped the phenotypes afforded by overexpression in all three extracellular motile stages. We show that in merozoites and ookinetes, additional expression does not impair life cycle progression. In marked contrast, overexpression of C-CAP and profilin in sporozoites impairs circular gliding motility and salivary gland invasion. The propensity for productive motility correlates with actin accumulation at the parasite tip, as revealed by combinations of an actin-stabilizing drug and transgenic parasites. Strong expression of profilin, but not C-CAP, resulted in complete life cycle arrest. Comparative overexpression is an alternative experimental genetic strategy to study essential genes and reveals effects of regulatory imbalances that are not uncovered from deletion-mutant phenotyping. © 2016 Sato et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  6. Live Imaging of Calcium Dynamics during Axon Degeneration Reveals Two Functionally Distinct Phases of Calcium Influx

    Yamagishi, Yuya; Tessier-Lavigne, Marc

    2015-01-01

    Calcium is a key regulator of axon degeneration caused by trauma and disease, but its specific spatial and temporal dynamics in injured axons remain unclear. To clarify the function of calcium in axon degeneration, we observed calcium dynamics in single injured neurons in live zebrafish larvae and tested the temporal requirement for calcium in zebrafish neurons and cultured mouse DRG neurons. Using laser axotomy to induce Wallerian degeneration (WD) in zebrafish peripheral sensory axons, we monitored calcium dynamics from injury to fragmentation, revealing two stereotyped phases of axonal calcium influx. First, axotomy triggered a transient local calcium wave originating at the injury site. This initial calcium wave only disrupted mitochondria near the injury site and was not altered by expression of the protective WD slow (WldS) protein. Inducing multiple waves with additional axotomies did not change the kinetics of degeneration. In contrast, a second phase of calcium influx occurring minutes before fragmentation spread as a wave throughout the axon, entered mitochondria, and was abolished by WldS expression. In live zebrafish, chelating calcium after the first wave, but before the second wave, delayed the progress of fragmentation. In cultured DRG neurons, chelating calcium early in the process of WD did not alter degeneration, but chelating calcium late in WD delayed fragmentation. We propose that a terminal calcium wave is a key instructive component of the axon degeneration program. SIGNIFICANCE STATEMENT Axon degeneration resulting from trauma or neurodegenerative disease can cause devastating deficits in neural function. Understanding the molecular and cellular events that execute axon degeneration is essential for developing treatments to address these conditions. Calcium is known to contribute to axon degeneration, but its temporal requirements in this process have been unclear. Live calcium imaging in severed zebrafish neurons and temporally controlled

  7. Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor.

    Alessandro Pandini

    Full Text Available Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM domains (amino-terminal (FliGN, middle (FliGM and FliGC as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6. FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM

  8. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

    Kevin M. Harlen

    2016-06-01

    Full Text Available Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II C-terminal domain (CTD and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7, we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

  9. Distinct Feedforward and Feedback Effects of Microstimulation in Visual Cortex Reveal Neural Mechanisms of Texture Segregation.

    Klink, P Christiaan; Dagnino, Bruno; Gariel-Mathis, Marie-Alice; Roelfsema, Pieter R

    2017-07-05

    The visual cortex is hierarchically organized, with low-level areas coding for simple features and higher areas for complex ones. Feedforward and feedback connections propagate information between areas in opposite directions, but their functional roles are only partially understood. We used electrical microstimulation to perturb the propagation of neuronal activity between areas V1 and V4 in monkeys performing a texture-segregation task. In both areas, microstimulation locally caused a brief phase of excitation, followed by inhibition. Both these effects propagated faithfully in the feedforward direction from V1 to V4. Stimulation of V4, however, caused little V1 excitation, but it did yield a delayed suppression during the late phase of visually driven activity. This suppression was pronounced for the V1 figure representation and weaker for background representations. Our results reveal functional differences between feedforward and feedback processing in texture segregation and suggest a specific modulating role for feedback connections in perceptual organization. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile

    Eng Alvin KH

    2008-10-01

    Full Text Available Abstract Background Overall gastric cancer survival remains poor mainly because there are no reliable methods for identifying highly curable early stage disease. Multi-protein profiling of gastric fluids, obtained from the anatomic site of pathology, could reveal diagnostic proteomic fingerprints. Methods Protein profiles were generated from gastric fluid samples of 19 gastric cancer and 36 benign gastritides patients undergoing elective, clinically-indicated gastroscopy using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry on multiple ProteinChip arrays. Proteomic features were compared by significance analysis of microarray algorithm and two-way hierarchical clustering. A second blinded sample set (24 gastric cancers and 29 clinically benign gastritides was used for validation. Results By significance analysyis of microarray, 60 proteomic features were up-regulated and 46 were down-regulated in gastric cancer samples (p Conclusion This simple and reproducible multimarker proteomic assay could supplement clinical gastroscopic evaluation of symptomatic patients to enhance diagnostic accuracy for gastric cancer and pre-malignant lesions.

  11. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  12. Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response.

    Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, Niranjan

    2013-11-01

    Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.

  13. Next generation sequencing reveals distinct fecal pollution signatures in aquatic sediments across gradients of anthropogenic influence

    Gian Marco Luna

    2016-11-01

    Full Text Available Aquatic sediments are the repository of a variety of anthropogenic pollutants, including bacteria of fecal origin, that reach the aquatic environment from a variety of sources. Although fecal bacteria can survive for long periods of time in aquatic sediments, the microbiological quality of sediments is almost entirely neglected when performing quality assessments of aquatic ecosystems. Here we investigated the relative abundance, patterns and diversity of fecal bacterial populations in two coastal areas in the Northern Adriatic Sea (Italy: the Po river prodelta (PRP, an estuarine area receiving significant contaminant discharge from one of the largest European rivers and the Lagoon of Venice (LV, a transitional environment impacted by a multitude of anthropogenic stressors. From both areas, several indicators of fecal and sewage contamination were determined in the sediments using Next Generation Sequencing (NGS of 16S rDNA amplicons. At both areas, fecal contamination was high, with fecal bacteria accounting for up to 3.96% and 1.12% of the sediment bacterial assemblages in PRP and LV, respectively. The magnitude of the fecal signature was highest in the PRP site, highlighting the major role of the Po river in spreading microbial contaminants into the adjacent coastal area. In the LV site, fecal pollution was highest in the urban area, and almost disappeared when moving to the open sea. Our analysis revealed a large number of fecal Operational Taxonomic Units (OTU, 960 and 181 in PRP and LV, respectively and showed a different fecal signature in the two areas, suggesting a diverse contribution of human and non-human sources of contamination. These results highlight the potential of NGS techniques to gain insights into the origin and fate of different fecal bacteria populations in aquatic sediments.

  14. Connectivity-based parcellation reveals distinct cortico-striatal connectivity fingerprints in Autism Spectrum Disorder.

    Balsters, Joshua H; Mantini, Dante; Wenderoth, Nicole

    2018-04-15

    Autism Spectrum Disorder (ASD) has been associated with abnormal synaptic development causing a breakdown in functional connectivity. However, when measured at the macro scale using resting state fMRI, these alterations are subtle and often difficult to detect due to the large heterogeneity of the pathology. Recently, we outlined a novel approach for generating robust biomarkers of resting state functional magnetic resonance imaging (RS-fMRI) using connectivity based parcellation of gross morphological structures to improve single-subject reproducibility and generate more robust connectivity fingerprints. Here we apply this novel approach to investigating the organization and connectivity strength of the cortico-striatal system in a large sample of ASD individuals and typically developed (TD) controls (N=130 per group). Our results showed differences in the parcellation of the striatum in ASD. Specifically, the putamen was found to be one single structure in ASD, whereas this was split into anterior and posterior segments in an age, IQ, and head movement matched TD group. An analysis of the connectivity fingerprints revealed that the group differences in clustering were driven by differential connectivity between striatum and the supplementary motor area, posterior cingulate cortex, and posterior insula. Our approach for analysing RS-fMRI in clinical populations has provided clear evidence that cortico-striatal circuits are organized differently in ASD. Based on previous task-based segmentations of the striatum, we believe that the anterior putamen cluster present in TD, but not in ASD, likely contributes to social and language processes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Improved flow cytometric assessment reveals distinct microvesicle (cell-derived microparticle signatures in joint diseases.

    Bence György

    Full Text Available INTRODUCTION: Microvesicles (MVs, earlier referred to as microparticles, represent a major type of extracellular vesicles currently considered as novel biomarkers in various clinical settings such as autoimmune disorders. However, the analysis of MVs in body fluids has not been fully standardized yet, and there are numerous pitfalls that hinder the correct assessment of these structures. METHODS: In this study, we analyzed synovial fluid (SF samples of patients with osteoarthritis (OA, rheumatoid arthritis (RA and juvenile idiopathic arthritis (JIA. To assess factors that may confound MV detection in joint diseases, we used electron microscopy (EM, Nanoparticle Tracking Analysis (NTA and mass spectrometry (MS. For flow cytometry, a method commonly used for phenotyping and enumeration of MVs, we combined recent advances in the field, and used a novel approach of differential detergent lysis for the exclusion of MV-mimicking non-vesicular signals. RESULTS: EM and NTA showed that substantial amounts of particles other than MVs were present in SF samples. Beyond known MV-associated proteins, MS analysis also revealed abundant plasma- and immune complex-related proteins in MV preparations. Applying improved flow cytometric analysis, we demonstrate for the first time that CD3(+ and CD8(+ T-cell derived SF MVs are highly elevated in patients with RA compared to OA patients (p=0.027 and p=0.009, respectively, after Bonferroni corrections. In JIA, we identified reduced numbers of B cell-derived MVs (p=0.009, after Bonferroni correction. CONCLUSIONS: Our results suggest that improved flow cytometric assessment of MVs facilitates the detection of previously unrecognized disease-associated vesicular signatures.

  16. Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties

    Mikeska, Ruth; Wacker, Roland; Arni, Raghuvir; Singh, Tej P.; Mikhailov, Albert; Gabdoulkhakov, Azat; Voelter, Wolfgang; Betzel, Christian

    2004-01-01

    The structures of mistletoe lectin I in complex with lactose and galactose reveal differences in binding by the two known sites in subdomains α1 and γ2 and suggest the presence of a third low-affinity site in subdomain β1. The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (R free = 23.6%) and 20.9 (R free = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML-I B-chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose-binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit β1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound

  17. Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

    Fernandes, Maria Cecilia; Dillon, Laura A L; Belew, Ashton Trey; Bravo, Hector Corrada; Mosser, David M; El-Sayed, Najib M

    2016-05-10

    Macrophages are mononuclear phagocytes that constitute a first line of defense against pathogens. While lethal to many microbes, they are the primary host cells of Leishmania spp. parasites, the obligate intracellular pathogens that cause leishmaniasis. We conducted transcriptomic profiling of two Leishmania species and the human macrophage over the course of intracellular infection by using high-throughput RNA sequencing to characterize the global gene expression changes and reprogramming events that underlie the interactions between the pathogen and its host. A systematic exclusion of the generic effects of large-particle phagocytosis revealed a vigorous, parasite-specific response of the human macrophage early in the infection that was greatly tempered at later time points. An analogous temporal expression pattern was observed with the parasite, suggesting that much of the reprogramming that occurs as parasites transform into intracellular forms generally stabilizes shortly after entry. Following that, the parasite establishes an intracellular niche within macrophages, with minimal communication between the parasite and the host cell later during the infection. No significant difference was observed between parasite species transcriptomes or in the transcriptional response of macrophages infected with each species. Our comparative analysis of gene expression changes that occur as mouse and human macrophages are infected by Leishmania spp. points toward a general signature of the Leishmania-macrophage infectome. Little is known about the transcriptional changes that occur within mammalian cells harboring intracellular pathogens. This study characterizes the gene expression signatures of Leishmania spp. parasites and the coordinated response of infected human macrophages as the pathogen enters and persists within them. After accounting for the generic effects of large-particle phagocytosis, we observed a parasite-specific response of the human macrophages early in

  18. Polymorphism Analysis of Ch1 and Ch2 Genes in the Siberian Cat

    Stefano Sartore

    2017-12-01

    Full Text Available Cats are usually spreaders of allergens that are critical for sensitive people; the Siberian cat is a breed supposed to be low level allergenic, according to some breeders’ statements. The sequence of the two genes, namely Ch1 and Ch2, that code for the allergen Fel d 1, the major allergen responsible for outbreaks of allergy symptoms, is not yet known in the Siberian cat, and finding this was the aim of our investigation. Notably, our work is the first survey of the genetic structure of these genes in Siberian cats. The comparison of the sequences of Siberian cats, non-Siberian cats, and sequences present in the National Center for Biotechnology Information database revealed a considerable number of mutations; some of those detected in the Siberian cat, due to their position in exon regions, could affect the Fel d 1 allergenic properties. Therefore, further investigations are recommended to assess if the identified mutations can be responsible for a reduced-allergen synthesis and can be used as markers for selection of low level allergenic cats.

  19. Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

    Cao, Huiluo

    2017-06-12

    Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome.Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the

  20. New practicable Siberian Snake schemes

    Steffen, K.

    1983-07-01

    Siberian Snake schemes can be inserted in ring accelerators for making the spin tune almost independent of energy. Two such schemes are here suggested which lend particularly well to practical application over a wide energy range. Being composed of horizontal and vertical bending magnets, the proposed snakes are designed to have a small maximum beam excursion in one plane. By applying in this plane a bending correction that varies with energy, they can be operated at fixed geometry in the other plane where most of the bending occurs, thus avoiding complicated magnet motion or excessively large magnet apertures that would otherwise be needed for large energy variations. The first of the proposed schemes employs a pair of standard-type Siberian Snakes, i.e. of the usual 1st and 2nd kind which rotate the spin about the longitudinal and the transverse horizontal axis, respectively. The second scheme employs a pair of novel-type snakes which rotate the spin about either one of the horizontal axes that are at 45 0 to the beam direction. In obvious reference to these axes, they are called left-pointed and right-pointed snakes. (orig.)

  1. First test of the Siberian Snake concept

    Krisch, A.D.

    1990-01-01

    Test results of the Siberian Snake concept at the Indiana University Cooler Ring are presented. The Siberian Snake is a clever and interesting concept for accelerating polarized protons to high energy. Thus it would be especially useful at TeV energies where there are thousands of depolarizing resonances. The Snake is the device which job is to rotate the proton's spin by 180 deg. every time the proton goes around the ring. The Snake's main element is the superconducting solenoid magnet. Examples of the Siberian Snake overcoming depolarizing resonances are presented. 6 refs.; 24 figs

  2. Single Particle Tracking reveals two distinct environments for CD4 receptors at the surface of living T lymphocytes

    Mascalchi, Patrice; Lamort, Anne Sophie; Salomé, Laurence; Dumas, Fabrice

    2012-01-01

    Highlights: ► We studied the diffusion of single CD4 receptors on living lymphocytes. ► This study reveals that CD4 receptors have either a random or confined diffusion. ► The dynamics of unconfined CD4 receptors was accelerated by a temperature raise. ► The dynamics of confined CD4 receptors was unchanged by a temperature raise. ► Our results suggest the existence of two different environments for CD4 receptors. -- Abstract: We investigated the lateral diffusion of the HIV receptor CD4 at the surface of T lymphocytes at 20 °C and 37 °C by Single Particle Tracking using Quantum Dots. We found that the receptors presented two major distinct behaviors that were not equally affected by temperature changes. About half of the receptors showed a random diffusion with a diffusion coefficient increasing upon raising the temperature. The other half of the receptors was permanently or transiently confined with unchanged dynamics on raising the temperature. These observations suggest that two distinct subpopulations of CD4 receptors with different environments are present at the surface of living T lymphocytes.

  3. Correlation of neural activity with behavioral kinematics reveals distinct sensory encoding and evidence accumulation processes during active tactile sensing.

    Delis, Ioannis; Dmochowski, Jacek P; Sajda, Paul; Wang, Qi

    2018-03-23

    Many real-world decisions rely on active sensing, a dynamic process for directing our sensors (e.g. eyes or fingers) across a stimulus to maximize information gain. Though ecologically pervasive, limited work has focused on identifying neural correlates of the active sensing process. In tactile perception, we often make decisions about an object/surface by actively exploring its shape/texture. Here we investigate the neural correlates of active tactile decision-making by simultaneously measuring electroencephalography (EEG) and finger kinematics while subjects interrogated a haptic surface to make perceptual judgments. Since sensorimotor behavior underlies decision formation in active sensing tasks, we hypothesized that the neural correlates of decision-related processes would be detectable by relating active sensing to neural activity. Novel brain-behavior correlation analysis revealed that three distinct EEG components, localizing to right-lateralized occipital cortex (LOC), middle frontal gyrus (MFG), and supplementary motor area (SMA), respectively, were coupled with active sensing as their activity significantly correlated with finger kinematics. To probe the functional role of these components, we fit their single-trial-couplings to decision-making performance using a hierarchical-drift-diffusion-model (HDDM), revealing that the LOC modulated the encoding of the tactile stimulus whereas the MFG predicted the rate of information integration towards a choice. Interestingly, the MFG disappeared from components uncovered from control subjects performing active sensing but not required to make perceptual decisions. By uncovering the neural correlates of distinct stimulus encoding and evidence accumulation processes, this study delineated, for the first time, the functional role of cortical areas in active tactile decision-making. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes.

    Gao, Fan-Xiang; Wang, Yang; Zhang, Qi-Ya; Mou, Cheng-Yan; Li, Zhi; Deng, Yuan-Sheng; Zhou, Li; Gui, Jian-Fang

    2017-07-24

    Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A + , candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A + , F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as "chemokine signaling pathway", "Toll-like receptor signaling pathway" and others, were remarkably much more than those from clone A + and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A + . In contrast to strong immune defense in resistant clone H, susceptible clone A + showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A + failed to resist virus offensive and evidently induced apoptosis or death. Our study is the first attempt to screen distinct resistances and

  5. Pyometra in a Siberian Polecat (Mustela eversmanni)

    Johnson, J.D.; Biggins, D.E.; Wrigley, R.H.; Mangone, B.A.; Wimsatt, J.

    1999-01-01

    A 2-year-old Siberian polecat (Mustela eversmanni) from a breeding colony presented for ultrasound evaluation for pregnancy. It was paired with a male for 2.75 months and had remained absent of pregnancy signs when it was anesthetized and clinically evaluated. Until this time, the animal had eaten well and shown no outward signs of debility. On palpation, the animal had a fluid-filled tubular structure in the caudal abdomen, consistent in location and size with the uterus. No sign of vaginal discharge was present. Ultrasonography revealed 10 fluid-filled evaginations (approximately 12 mm in diameter) of the uterine horns. A presumptive diagnosis of a fluid-filled reproductive tract and likely reproductive failure was made in light of the animal's history, its clinical signs, and the ultrasound findings. Euthanasia was performed because the animal was nonreproductive and might yield information relevant to the breeding colony as a whole. Necropsy of the polecat revealed a distended fluctuant uterus containing mildly odiferous, thick, yellow-green, purulent material. Histopathology confirmed the diagnosis of pyometra. A pure and heavy growth of Enterococcus fecalis was cultured from the uterine contents. In light of results from routine minimal inhibitory concentration antibiotic sensitivity screening, this isolate was resistant to all antibiotics tested in the standard teaching hospital screen.

  6. Pyometra in a Siberian Polecat (Mustela eversmanni).

    Johnson, Jay D.; Biggins, Dean E.; Wrigley, Robert H.; Mangone, Berney A.; Wimsatt, Jeffrey

    1999-11-01

    A 2-year-old Siberian polecat (Mustela eversmanni) from a breeding colony presented for ultrasound evaluation for pregnancy. It was paired with a male for 2.75 months and had remained absent of pregnancy signs when it was anesthetized and clinically evaluated. Until this time, the animal had eaten well and shown no outward signs of debility. On palpation, the animal had a fluid-filled tubular structure in the caudal abdomen, consistent in location and size with the uterus. No sign of vaginal discharge was present. Ultrasonography revealed 10 fluid-filled evaginations (approximately 12 mm in diameter) of the uterine horns. A presumptive diagnosis of a fluid-filled reproductive tract and likely reproductive failure was made in light of the animal's history, its clinical signs, and the ultrasound findings. Euthanasia was performed because the animal was nonreproductive and might yield information relevant to the breeding colony as a whole. Necropsy of the polecat revealed a distended fluctuant uterus containing mildly odiferous, thick, yellow-green, purulent material. Histopathology confirmed the diagnosis of pyometra. A pure and heavy growth of Enterococcus fecalis was cultured from the uterine contents. In light of results from routine minimal inhibitory concentration antibiotic sensitivity screening, this isolate was resistant to all antibiotics tested in the standard teaching hospital screen.

  7. Translational analysis of mouse and human placental protein and mRNA reveals distinct molecular pathologies in human preeclampsia.

    Cox, Brian; Sharma, Parveen; Evangelou, Andreas I; Whiteley, Kathie; Ignatchenko, Vladimir; Ignatchenko, Alex; Baczyk, Dora; Czikk, Marie; Kingdom, John; Rossant, Janet; Gramolini, Anthony O; Adamson, S Lee; Kislinger, Thomas

    2011-12-01

    Preeclampsia (PE) adversely impacts ~5% of pregnancies. Despite extensive research, no consistent biomarkers or cures have emerged, suggesting that different molecular mechanisms may cause clinically similar disease. To address this, we undertook a proteomics study with three main goals: (1) to identify a panel of cell surface markers that distinguish the trophoblast and endothelial cells of the placenta in the mouse; (2) to translate this marker set to human via the Human Protein Atlas database; and (3) to utilize the validated human trophoblast markers to identify subgroups of human preeclampsia. To achieve these goals, plasma membrane proteins at the blood tissue interfaces were extracted from placentas using intravascular silica-bead perfusion, and then identified using shotgun proteomics. We identified 1181 plasma membrane proteins, of which 171 were enriched at the maternal blood-trophoblast interface and 192 at the fetal endothelial interface with a 70% conservation of expression in humans. Three distinct molecular subgroups of human preeclampsia were identified in existing human microarray data by using expression patterns of trophoblast-enriched proteins. Analysis of all misexpressed genes revealed divergent dysfunctions including angiogenesis (subgroup 1), MAPK signaling (subgroup 2), and hormone biosynthesis and metabolism (subgroup 3). Subgroup 2 lacked expected changes in known preeclampsia markers (sFLT1, sENG) and uniquely overexpressed GNA12. In an independent set of 40 banked placental specimens, GNA12 was overexpressed during preeclampsia when co-incident with chronic hypertension. In the current study we used a novel translational analysis to integrate mouse and human trophoblast protein expression with human microarray data. This strategy identified distinct molecular pathologies in human preeclampsia. We conclude that clinically similar preeclampsia patients exhibit divergent placental gene expression profiles thus implicating divergent

  8. Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements.

    Olga V Viktorovskaya

    2016-08-01

    Full Text Available There are currently no vaccines or antivirals available for dengue virus infection, which can cause dengue hemorrhagic fever and death. A better understanding of the host pathogen interaction is required to develop effective therapies to treat DENV. In particular, very little is known about how cellular RNA binding proteins interact with viral RNAs. RNAs within cells are not naked; rather they are coated with proteins that affect localization, stability, translation and (for viruses replication.Seventy-nine novel RNA binding proteins for dengue virus (DENV were identified by cross-linking proteins to dengue viral RNA during a live infection in human cells. These cellular proteins were specific and distinct from those previously identified for poliovirus, suggesting a specialized role for these factors in DENV amplification. Knockdown of these proteins demonstrated their function as viral host factors, with evidence for some factors acting early, while others late in infection. Their requirement by DENV for efficient amplification is likely specific, since protein knockdown did not impair the cell fitness for viral amplification of an unrelated virus. The protein abundances of these host factors were not significantly altered during DENV infection, suggesting their interaction with DENV RNA was due to specific recruitment mechanisms. However, at the global proteome level, DENV altered the abundances of proteins in particular classes, including transporter proteins, which were down regulated, and proteins in the ubiquitin proteasome pathway, which were up regulated.The method for identification of host factors described here is robust and broadly applicable to all RNA viruses, providing an avenue to determine the conserved or distinct mechanisms through which diverse viruses manage the viral RNA within cells. This study significantly increases the number of cellular factors known to interact with DENV and reveals how DENV modulates and usurps

  9. A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation

    Shokat Kevan M

    2008-09-01

    Full Text Available Abstract Background Neurons assemble into a functional network through a sequence of developmental processes including neuronal polarization and synapse formation. In Caenorhabditis elegans, the serine/threonine SAD-1 kinase is essential for proper neuronal polarity and synaptic organization. To determine if SAD-1 activity regulates the establishment or maintenance of these neuronal structures, we examined its temporal requirements using a chemical-genetic method that allows for selective and reversible inactivation of its kinase activity in vivo. Results We generated a PP1 analog-sensitive variant of SAD-1. Through temporal inhibition of SAD-1 kinase activity we show that its activity is required for the establishment of both neuronal polarity and synaptic organization. However, while SAD-1 activity is needed strictly when neurons are polarizing, the temporal requirement for SAD-1 is less stringent in synaptic organization, which can also be re-established during maintenance. Conclusion This study reports the first temporal analysis of a neural kinase activity using the chemical-genetic system. It reveals that neuronal polarity and synaptic organization have distinct temporal requirements for SAD-1.

  10. Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters.

    Kumar, Vibhor; Rayan, Nirmala Arul; Muratani, Masafumi; Lim, Stefan; Elanggovan, Bavani; Xin, Lixia; Lu, Tess; Makhija, Harshyaa; Poschmann, Jeremie; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam

    2016-05-01

    Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers by performing 140 enhancer assays in human T cells. We tested 40 chromatin signatures on this unbiased enhancer set and identified H2BK20ac, a little-studied histone modification, as the most predictive mark of active enhancers. Notably, we detected a novel class of functionally distinct enhancers enriched in H2BK20ac but lacking H3K27ac, which was present in all examined cell lines and also in embryonic forebrain tissue. H2BK20ac was also unique in highlighting cell-type-specific promoters. In contrast, other acetylation marks were present in all active promoters, regardless of cell-type specificity. In stimulated microglial cells, H2BK20ac was more correlated with cell-state-specific expression changes than H3K27ac, with TGF-beta signaling decoupling the two acetylation marks at a subset of regulatory elements. In summary, our study reveals a previously unknown connection between histone acetylation and cell-type-specific gene regulation and indicates that H2BK20ac profiling can be used to uncover new dimensions of gene regulation. © 2016 Kumar et al.; Published by Cold Spring Harbor Laboratory Press.

  11. Long-term In Vivo Calcium Imaging of Astrocytes Reveals Distinct Cellular Compartment Responses to Sensory Stimulation.

    Stobart, Jillian L; Ferrari, Kim David; Barrett, Matthew J P; Stobart, Michael J; Looser, Zoe J; Saab, Aiman S; Weber, Bruno

    2018-01-01

    Localized, heterogeneous calcium transients occur throughout astrocytes, but the characteristics and long-term stability of these signals, particularly in response to sensory stimulation, remain unknown. Here, we used a genetically encoded calcium indicator and an activity-based image analysis scheme to monitor astrocyte calcium activity in vivo. We found that different subcellular compartments (processes, somata, and endfeet) displayed distinct signaling characteristics. Closer examination of individual signals showed that sensory stimulation elevated the number of specific types of calcium peaks within astrocyte processes and somata, in a cortical layer-dependent manner, and that the signals became more synchronous upon sensory stimulation. Although mice genetically lacking astrocytic IP3R-dependent calcium signaling (Ip3r2-/-) had fewer signal peaks, the response to sensory stimulation was sustained, suggesting other calcium pathways are also involved. Long-term imaging of astrocyte populations revealed that all compartments reliably responded to stimulation over several months, but that the location of the response within processes may vary. These previously unknown characteristics of subcellular astrocyte calcium signals provide new insights into how astrocytes may encode local neuronal circuit activity. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

    Kober, Daniel L.; Alexander-Brett, Jennifer M.; Karch, Celeste M.; Cruchaga, Carlos; Colonna, Marco; Holtzman, Michael J.; Brett, Thomas J. (WU-MED)

    2016-12-20

    Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.

  13. Complete Mitochondrial Genomes of the Cherskii’s Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

    Balakirev, Evgeniy S; Saveliev, Pavel A; Ayala, Francisco J

    2017-01-01

    The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii’s sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information. PMID:28890653

  14. Winter cloudiness variability over Northern Eurasia related to the Siberian High during 1966–2010

    Chernokulsky, Alexander; Mokhov, Igor I; Nikitina, Natalia

    2013-01-01

    This letter presents an assessment of winter cloudiness variability over Northern Eurasia regions related to the Siberian High intensity (SHI) variations during 1966–2010. An analysis of cloud fraction and the occurrence of different cloud types was carried out based on visual observations from almost 500 Russian meteorological stations. The moonlight criterion was implemented to reduce the uncertainty of night observations. The SHI was defined based on sea-level pressure fields from different reanalyses. We found a statistically significant negative correlation of cloud cover with the SHI over central and southern Siberia and the southern Urals with regression coefficients around 3% hPa −1 for total cloud fraction (TCF) for particular stations near the Siberian High center. Cross-wavelet analysis of TCF and SHI revealed a long-term relationship between cloudiness and the Siberian High. Generally, the Siberian High intensification by 1 hPa leads to a replacement of one overcast day with one day without clouds, which is associated mainly with a decrease in precipitating and stratiform clouds. These changes point to a positive feedback between cloudiness and the Siberian High. (letter)

  15. Optogenetic Inhibition Reveals Distinct Roles for Basolateral Amygdala Activity at Discrete Time Points during Risky Decision Making.

    Orsini, Caitlin A; Hernandez, Caesar M; Singhal, Sarthak; Kelly, Kyle B; Frazier, Charles J; Bizon, Jennifer L; Setlow, Barry

    2017-11-29

    Decision making is a multifaceted process, consisting of several distinct phases that likely require different cognitive operations. Previous work showed that the basolateral amygdala (BLA) is a critical substrate for decision making involving risk of punishment; however, it is unclear how the BLA is recruited at different stages of the decision process. To this end, the current study used optogenetics to inhibit the BLA during specific task phases in a model of risky decision making (risky decision-making task) in which rats choose between a small, "safe" reward and a large reward accompanied by varying probabilities of footshock punishment. Male Long-Evans rats received intra-BLA microinjections of viral vectors carrying either halorhodopsin (eNpHR3.0-mCherry) or mCherry alone (control) followed by optic fiber implants and were trained in the risky decision-making task. Laser delivery during the task occurred during intertrial interval, deliberation, or reward outcome phases, the latter of which was further divided into the three possible outcomes (small, safe; large, unpunished; large, punished). Inhibition of the BLA selectively during the deliberation phase decreased choice of the large, risky outcome (decreased risky choice). In contrast, BLA inhibition selectively during delivery of the large, punished outcome increased risky choice. Inhibition had no effect during the other phases, nor did laser delivery affect performance in control rats. Collectively, these data indicate that the BLA can either inhibit or promote choice of risky options, depending on the phase of the decision process in which it is active. SIGNIFICANCE STATEMENT To date, most behavioral neuroscience research on neural mechanisms of decision making has used techniques that preclude assessment of distinct phases of the decision process. Here we show that optogenetic inhibition of the BLA has opposite effects on choice behavior in a rat model of risky decision making, depending on the phase

  16. Culture, characteristics and chromosome complement of Siberian tiger fibroblasts for nuclear transfer.

    Song, Jimei; Hua, Song; Song, Kai; Zhang, Yong

    2007-01-01

    Tiger (Panthera tigris Linnaeus, 1758) is a characteristic species of Asia, which is in severe danger. Siberian tiger (Panthera tigris altaica) is the largest one of the five existent tiger subspecies. It is extremely endangered. One new way for tiger protection and rescue is to study interspecies cloning. But there is few research data about Siberian tiger. In this study, we cultured Siberian tiger fibroblasts in vitro, analyzed their biological characteristics, chromosomes, and cell cycles, to provide not only nuclear donors with good morphology, normal biological characteristics, and chromosome quantity for tiger interspecies cloning, but also reliable data for further studying Siberian tiger. The results indicated that Siberian tiger ear fibroblasts can be successfully obtained by tissue culture either with or without overnight cold digestion, the cultured cells were typical fibroblasts with normal morphology, growth curve, and chromosome quantity; G0/G1 percentage increased and S percentage decreased with the confluence of cells. G0/G1 and S stage rate was significantly different between 40-50% and 80-90%, 95-100% confluence; there is no distinct difference between 80-90% and 95-100% confluence. The cells at the same density (80-90% confluence) were treated with or without 0.5% serum starving, GO/G1 rate of the former was higher than the latter, but the difference was not significant. GO/G1 proportion of 95-100% confluence was slightly higher than serum starving (80-90% confluence), but no significant difference. Therefore, the Siberian tiger fibroblasts we cultured in vitro can be used as donor cells, and the donor cells do not need to be treated with normal serum starvation during nuclear transfer; if we will just consider the rate of the G0/G1 stage cells, serum starvation can be replaced by confluence inhibition when cultured cells were more than 80-90% confluence.

  17. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

    Kevin A Wilkinson

    2008-04-01

    Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further

  18. Large-scale expression analysis reveals distinct microRNA profiles at different stages of human neurodevelopment.

    Brandon Smith

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are short non-coding RNAs predicted to regulate one third of protein coding genes via mRNA targeting. In conjunction with key transcription factors, such as the repressor REST (RE1 silencing transcription factor, miRNAs play crucial roles in neurogenesis, which requires a highly orchestrated program of gene expression to ensure the appropriate development and function of diverse neural cell types. Whilst previous studies have highlighted select groups of miRNAs during neural development, there remains a need for amenable models in which miRNA expression and function can be analyzed over the duration of neurogenesis. PRINCIPAL FINDINGS: We performed large-scale expression profiling of miRNAs in human NTera2/D1 (NT2 cells during retinoic acid (RA-induced transition from progenitors to fully differentiated neural phenotypes. Our results revealed dynamic changes of miRNA patterns, resulting in distinct miRNA subsets that could be linked to specific neurodevelopmental stages. Moreover, the cell-type specific miRNA subsets were very similar in NT2-derived differentiated cells and human primary neurons and astrocytes. Further analysis identified miRNAs as putative regulators of REST, as well as candidate miRNAs targeted by REST. Finally, we confirmed the existence of two predicted miRNAs; pred-MIR191 and pred-MIR222 associated with SLAIN1 and FOXP2, respectively, and provided some evidence of their potential co-regulation. CONCLUSIONS: In the present study, we demonstrate that regulation of miRNAs occurs in precise patterns indicative of their roles in cell fate commitment, progenitor expansion and differentiation into neurons and glia. Furthermore, the similarity between our NT2 system and primary human cells suggests their roles in molecular pathways critical for human in vivo neurogenesis.

  19. Distinct genetic diversity of Oncomelania hupensis, intermediate host of Schistosoma japonicum in mainland China as revealed by ITS sequences.

    Qin Ping Zhao

    Full Text Available BACKGROUND: Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which causes schistosomiasis endemic in the Far East, and especially in mainland China. O. hupensis largely determines the parasite's geographical range. How O. hupensis's genetic diversity is distributed geographically in mainland China has never been well examined with DNA sequence data. METHODOLOGY/PRINCIPAL FINDINGS: In this study we investigate the genetic variation among O. hupensis from different geographical origins using the combined complete internal transcribed spacer 1 (ITS1 and ITS2 regions of nuclear ribosomal DNA. 165 O. hupensis isolates were obtained in 29 localities from 7 provinces across mainland China: lake/marshland and hill regions in Anhui, Hubei, Hunan, Jiangxi and Jiangsu provinces, located along the middle and lower reaches of Yangtze River, and mountainous regions in Sichuan and Yunnan provinces. Phylogenetic and haplotype network analyses showed distinct genetic diversity and no shared haplotypes between populations from lake/marshland regions of the middle and lower reaches of the Yangtze River and populations from mountainous regions of Sichuan and Yunnan provinces. The genetic distance between these two groups is up to 0.81 based on Fst, and branch time was estimated as 2-6 Ma. As revealed in the phylogenetic tree, snails from Sichuan and Yunnan provinces were also clustered separately. Geographical separation appears to be an important factor accounting for the diversification of the two groups of O. hupensis in mainland China, and probably for the separate clades between snails from Sichuan and Yunnan provinces. In lake/marshland and hill regions along the middle and lower reaches of the Yangtze River, three clades were identified in the phylogenetic tree, but without any obvious clustering of snails from different provinces. CONCLUSIONS: O. hupensis in mainland China may have considerable genetic diversity, and a more

  20. Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae1[OPEN

    Uebler, Joseph B.; Liu, Xiaoxiao

    2017-01-01

    Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato (Solanum lycopersicum), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3ʹ, and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petunia axillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris, tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris, PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3ʹ position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3ʹ position in tomato, is absent in P. axillaris. Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis. PMID:28701351

  1. Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae.

    Nadakuduti, Satya Swathi; Uebler, Joseph B; Liu, Xiaoxiao; Jones, A Daniel; Barry, Cornelius S

    2017-09-01

    Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato ( Solanum lycopersicum ), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3', and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petunia axillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris , tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris , PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3' position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3' position in tomato, is absent in P. axillaris Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  2. Crustal structure of the Siberian craton and the West Siberian basin

    Cherepanova, Yulia; Artemieva, Irina; Thybo, Hans

    2013-01-01

    We present a digital model SibCrust of the crustal structure of the Siberian craton (SC) and the West Siberian basin (WSB), based on all seismic profiles published since 1960 and sampled with a nominal interval of 50. km. Data quality is assessed and quantitatively assigned to each profile based...... and ~. 6.2-6.6. km/s in parts of the WSB and SC. Exceptionally high basement Vp velocities (6.8-7.0. km/s) at the northern border between the SC and the WSB indicate the presence of magmatic intrusions and are proposed to mark the source zone of the Siberian LIP. The cratonic crust generally consists...

  3. Comparative transcriptome analysis reveals distinct ethylene-independent regulation of ripening in response to low temperature in kiwifruit.

    Asiche, William O; Mitalo, Oscar W; Kasahara, Yuka; Tosa, Yasuaki; Mworia, Eric G; Owino, Willis O; Ushijima, Koichiro; Nakano, Ryohei; Yano, Kentaro; Kubo, Yasutaka

    2018-03-21

    Kiwifruit are classified as climacteric since exogenous ethylene (or its analogue propylene) induces rapid ripening accompanied by ethylene production under positive feedback regulation. However, most of the ripening-associated changes (Phase 1 ripening) in kiwifruit during storage and on-vine occur largely in the absence of any detectable ethylene. This ripening behavior is often attributed to basal levels of system I ethylene, although it is suggested to be modulated by low temperature. To elucidate the mechanisms regulating Phase 1 ripening in kiwifruit, a comparative transcriptome analysis using fruit continuously exposed to propylene (at 20 °C), and during storage at 5 °C and 20 °C was conducted. Propylene exposure induced kiwifruit softening, reduction of titratable acidity (TA), increase in soluble solids content (SSC) and ethylene production within 5 days. During storage, softening and reduction of TA occurred faster in fruit at 5 °C compared to 20 °C although no endogenous ethylene production was detected. Transcriptome analysis revealed 3761 ripening-related differentially expressed genes (DEGs), of which 2742 were up-regulated by propylene while 1058 were up-regulated by low temperature. Propylene exclusively up-regulated 2112 DEGs including those associated with ethylene biosynthesis and ripening such as AcACS1, AcACO2, AcPL1, AcXET1, Acβ-GAL, AcAAT, AcERF6 and AcNAC7. Similarly, low temperature exclusively up-regulated 467 DEGS including AcACO3, AcPL2, AcPMEi, AcADH, Acβ-AMY2, AcGA2ox2, AcNAC5 and AcbZIP2 among others. A considerable number of DEGs such as AcPG, AcEXP1, AcXET2, Acβ-AMY1, AcGA2ox1, AcNAC6, AcMADS1 and AcbZIP1 were up-regulated by either propylene or low temperature. Frequent 1-MCP treatments failed to inhibit the accelerated ripening and up-regulation of associated DEGs by low temperature indicating that the changes were independent of ethylene. On-vine kiwifruit ripening proceeded in the absence of any detectable

  4. Wildfires in Siberian Mountain Forest

    Kharuk, V.; Ponomarev, E. I.; Antamoshkina, O.

    2017-12-01

    The annual burned area in Russia was estimated as 0.55 to 20 Mha with >70% occurred in Siberia. We analyzed Siberian wildfires distribution with respect to elevation, slope steepness and exposure. In addition, wildfires temporal dynamic and latitudinal range were analyzed. We used daily thermal anomalies derived from NOAA/AVHRR and Terra/MODIS satellites (1990-2016). Fire return intervals were (FRI) calculated based on the dendrochronology analysis of samples taken from trees with burn marks. Spatial distribution of wildfires dependent on topo features: relative burned area increase with elevation increase (ca. 1100 m), switching to following decrease. The wildfires frequency exponentially decreased within lowlands - highlands transition. Burned area is increasing with slope steepness increase (up to 5-10°). Fire return intervals (FRI) on the southfacing slopes are about 30% longer than on the north facing. Wildfire re-occurrence is decreasing exponentially: 90% of burns were caused by single fires, 8.5% by double fires, 1% burned three times, and on about 0.05% territory wildfires occurred four times (observed period: 75 yr.). Wildfires area and number, as well as FRI, also dependent on latitude: relative burned area increasing exponentially in norward direction, whereas relative fire number is exponentially decreasing. FRI increases in the northward direction: from 80 years at 62°N to 200 years at the Arctic Circle, and to 300 years at the northern limit of closed forests ( 71+°N). Fire frequency, fire danger period and FRI are strongly correlated with incoming solar radiation (r = 0.81 - 0.95). In 21-s century, a positive trend of wildfires number and area observed in mountain areas in all Siberia. Thus, burned area and number of fires in Siberia are significantly increased since 1990th (R2 =0.47, R2 =0.69, respectively), and that increase correlated with air temperatures and climate aridity increases. However, wildfires are essential for supporting fire

  5. Methane from the East Siberian Arctic shelf

    Petrenko...[], Vasilii V.; Etheridge, David M.

    2010-01-01

    In their Report “Extensive methane venting to the atmosphere from sediments of the East Siberian Arctic Shelf” (5 March, p. 1246), N. Shakhova et al. write that methane (CH4) release resulting from thawing Arctic permafrost “is a likely positive feedback to climate warming.” They add...

  6. Transcranial magnetic stimulation reveals two functionally distinct stages of motor cortex involvement during perception of emotional body language

    Borgomaneri, Sara; Gazzola, Valeria; Avenanti, Alessio

    Studies indicate that perceiving emotional body language recruits fronto-parietal regions involved in action execution. However, the nature of such motor activation is unclear. Using transcranial magnetic stimulation (TMS) we provide correlational and causative evidence of two distinct stages of

  7. fMRI Reveals Distinct CNS Processing during Symptomatic and Recovered Complex Regional Pain Syndrome in Children

    Lebel, A.; Becerra, L.; Wallin, D.; Moulton, E. A.; Morris, S.; Pendse, G.; Jasciewicz, J.; Stein, M.; Aiello-Lammens, M.; Grant, E.; Berde, C.; Borsook, D.

    2008-01-01

    Complex regional pain syndrome (CRPS) in paediatric patients is clinically distinct from the adult condition in which there is often complete resolution of its signs and symptoms within several months to a few years. The ability to compare the symptomatic and asymptomatic condition in the same individuals makes this population interesting for the…

  8. Transcranial magnetic stimulation reveals two functionally distinct stages of motor cortex involvement during perception of emotional body language

    Borgomaneri, S.; Gazzola, V.; Avenanti, A.

    2015-01-01

    Studies indicate that perceiving emotional body language recruits fronto-parietal regions involved in action execution. However, the nature of such motor activation is unclear. Using transcranial magnetic stimulation (TMS) we provide correlational and causative evidence of two distinct stages of

  9. Variability and ecology of Siberian larch species

    Abaimov, A.P.; Milyutin, L.I. [Russian Academy of Sciences, Krasnoyarsk (Russian Federation). Sukachev Inst. of Forest, Siberian Branch; Lesinski, J.A.; Martinsson, Owe [Swedish Univ. of Agricultural Sciences, Umeaa (Sweden). Dept. of Silviculture

    1998-12-31

    There are at least four larch taxons distinguished in Siberia that occupy almost 37 percent of the the Russian forests. The natural distribution of the taxons is clinal from the west to the east with L. sibirica Ledeb. in the west followed by L. x czekanowskii Szafer, L. gmelinii Rupr. and L. cajanderi Mayr. L. sibirica and L. x czekanowskii are phytocenosis builders only at the northern timberline and in the South-Siberian mountains whereas L. gmelinii and L. cajanderi are the main species over the vast territory within and beyond the permafrost zone of East Siberia. Due to large variety of growing conditions, the main features of the larch forests in terms of age structure and growth rates are also enormously variable. Thanks to specific life strategies with respect to seed dispersion patterns and very high adaptability to fires that often affect Siberian forests, these larch species regenerate very well being only seldom temporary replaced by Betula sp. forming secondary forest associations. Larch forests of different categories (protective and commercial) are exploited and regenerated in the same way as it is applied for Scots pine in Siberia. There is a growing interest in Siberian larch species among researchers and practitioners from abroad, mainly due to their fast growth and excellent wood properties. Some attempts of introducing Siberian larch species as commercial plantations have already been initiated in western countries. However, the knowledge of botanical, ecological and silvicultural features of Siberian larch species is rather poor outside of Russia. Because of its economic importance for Russian forestry the Siberian larch species have been comprehensively studied for many years and many papers as well as a number of monographs have been published, most of them in Russian. The large Russian expertise concerning regionalisation of seed sources, seed crop and quality, seed orchards, seedling production in nurseries and silvicultural practices in

  10. Chemical analysis of bioactive substances in seven siberian Saussurea species

    Avdeeva, Elena; Reshetov, Yaroslav; Shurupova, Margarita; Zibareva, Larisa; Borisova, Evgeniia; Belousov, Mikhail

    2017-11-01

    Main groups of biologically active substances of seven siberian Saussurea species (S. controversa DC., S. latifolia Ledeb., S. parviflora (Poir.) DC., S. frolowii Ledeb, S. amara (L.) DC., S. salicifolia (L.) DC. and S. daurica Adams) have been studied using paper, thin-layer, performance liquid chromatography, IR spectroscopy, spectrophotometry and mass spectrometry with inductively coupled plasma. Siberian Saussurea species have a rich elemental composition and contain a variety of phenolic compounds, amino acids, polysaccharides. The majority of polysaccharides are accumulated by S. controversa, S. salicifolia and S. frolowii. These plants contain a significant amount of calcium that may be a species characteristic. All plants contain quercetin and its glycosides, in some species luteolin, kaempferol, glycosides of apigenin and myricetin were revealed. Phenolic acids with predominant content of caffeic, chlorogenic and cinnamic acids were found in all the species. The maximum amount of phenolic acids and flavonoids was determined in the grass of S. latifolia, S. controversa and S. daurica. Characteristic absorption bands of lactone carbonyl of sesquiterpenoids in IR spectrum found in S. latifolia, S. controversa, S. daurica, S. amara and S. salicifolia. HPLC / UV analysis showed that peaks with absorption maxima of 242-246 nm due to the presence of α,β-unsaturated ketone group in the structure of ecdysteroids were found in S. salicifolia, S. controversa, S. daurica and S. latifolia.

  11. A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics

    Sadanandam, Anguraj; Wullschleger, Stephan; Lyssiotis, Costas A.; Grötzinger, Carsten; Barbi, Stefano; Bersani, Samantha; Körner, Jan; Wafy, Ismael; Mafficini, Andrea; Lawlor, Rita T.; Simbolo, Michele; Asara, John M.; Bläker, Hendrik; Cantley, Lewis C.; Wiedenmann, Bertram; Scarpa, Aldo; Hanahan, Douglas

    2016-01-01

    Seeking to assess the representative and instructive value of an engineered mouse model of pancreatic neuroendocrine tumors (PanNET) for its cognate human cancer, we profiled and compared mRNA and miRNA transcriptomes of tumors from both. Mouse PanNET tumors could be classified into two distinctive subtypes, well-differentiated islet/insulinoma tumors (IT) and poorly differentiated tumors associated with liver metastases, dubbed metastasis-like primary (MLP). Human PanNETs were independently classified into these same two subtypes, along with a third, specific gene mutation–enriched subtype. The MLP subtypes in human and mouse were similar to liver metastases in terms of miRNA and mRNA transcriptome profiles and signature genes. The human/mouse MLP subtypes also similarly expressed genes known to regulate early pancreas development, whereas the IT subtypes expressed genes characteristic of mature islet cells, suggesting different tumorigenesis pathways. In addition, these subtypes exhibit distinct metabolic profiles marked by differential pyruvate metabolism, substantiating the significance of their separate identities. SIGNIFICANCE This study involves a comprehensive cross-species integrated analysis of multi-omics profiles and histology to stratify PanNETs into subtypes with distinctive characteristics. We provide support for the RIP1-TAG2 mouse model as representative of its cognate human cancer with prospects to better understand PanNET heterogeneity and consider future applications of personalized cancer therapy. PMID:26446169

  12. [Identification and production of monoclonal antibody of Siberian tiger's immunoglobulin].

    Zhang, Yaonglong; Zhang, Duanling; Zhou, Ming; Xue, Yuan; Hua, Yuping; Ma, Jianzhang

    2010-03-01

    To purify immunoglobulin (Ig) of Siberian Tiger and prepare monoclonal antibody (mAb) against the Ig,which can be used to develop immunological diagnostic kits for diagnosing infectious disease in Siberian Tiger. The Ig of Siberian tigers was purified with saturated ammonium sulfate combined with recombinant Protein G. The C57BL/6 mice were immunized with the purified Ig. Spleno-cytes of the mice immunized were collected and fused with the mouse myeloma cell line (Sp2/0-Ag14). The positive hybridoma clones were selected by ELISA and were identified by western blot. The sandwich ELISA was used to detect immunocompetence of the purified Ig and the mAb. We obtained three mouse hybridoma clones that produced mAbs against Ig of Siberian Tiger. The derived McAbs could recognize Ig heavy chain of Siberian Tiger specifically. The biological activity of the Ig and obtained McAbs also could be identified by detecting the antibody induced by panleukopenia virus (FPV-HLJ) vaccine in Siberian Tiger. The antibody also would be useful for assess the vaccine efficacy against the infectious disease on the Siberian Tiger. Protein G can be used in Ig purification of Siberian Tiger. The obtained McAbs from the hybridoma ADT11 in this study owned strong ability to bind Ig of Siberian Tiger and have a stable immunocompetence. They can be used to develop diagnostic methods for detecting infectious disease in Siberian Tiger and vaccine research.

  13. Metabolomics reveals distinct, antibody-independent, molecular signatures of MS, AQP4-antibody and MOG-antibody disease.

    Jurynczyk, Maciej; Probert, Fay; Yeo, Tianrong; Tackley, George; Claridge, Tim D W; Cavey, Ana; Woodhall, Mark R; Arora, Siddharth; Winkler, Torsten; Schiffer, Eric; Vincent, Angela; DeLuca, Gabriele; Sibson, Nicola R; Isabel Leite, M; Waters, Patrick; Anthony, Daniel C; Palace, Jacqueline

    2017-12-06

    The overlapping clinical features of relapsing remitting multiple sclerosis (RRMS), aquaporin-4 (AQP4)-antibody (Ab) neuromyelitis optica spectrum disorder (NMOSD), and myelin oligodendrocyte glycoprotein (MOG)-Ab disease mean that detection of disease specific serum antibodies is the gold standard in diagnostics. However, antibody levels are not prognostic and may become undetectable after treatment or during remission. Therefore, there is still a need to discover antibody-independent biomarkers. We sought to discover whether plasma metabolic profiling could provide biomarkers of these three diseases and explore if the metabolic differences are independent of antibody titre. Plasma samples from 108 patients (34 RRMS, 54 AQP4-Ab NMOSD, and 20 MOG-Ab disease) were analysed by nuclear magnetic resonance spectroscopy followed by lipoprotein profiling. Orthogonal partial-least squares discriminatory analysis (OPLS-DA) was used to identify significant differences in the plasma metabolite concentrations and produce models (mathematical algorithms) capable of identifying these diseases. In all instances, the models were highly discriminatory, with a distinct metabolite pattern identified for each disease. In addition, OPLS-DA identified AQP4-Ab NMOSD patient samples with low/undetectable antibody levels with an accuracy of 92%. The AQP4-Ab NMOSD metabolic profile was characterised by decreased levels of scyllo-inositol and small high density lipoprotein particles along with an increase in large low density lipoprotein particles relative to both RRMS and MOG-Ab disease. RRMS plasma exhibited increased histidine and glucose, along with decreased lactate, alanine, and large high density lipoproteins while MOG-Ab disease plasma was defined by increases in formate and leucine coupled with decreased myo-inositol. Despite overlap in clinical measures in these three diseases, the distinct plasma metabolic patterns support their distinct serological profiles and confirm that these

  14. Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components.

    Lu, Qiaosheng; Wierzbicki, Sara; Krasilnikov, Andrey S; Schmitt, Mark E

    2010-03-01

    RNase MRP is a ribonucleoprotein endoribonuclease found in three cellular locations where distinct substrates are processed: the mitochondria, the nucleolus, and the cytoplasm. Cytoplasmic RNase MRP is the nucleolar enzyme that is transiently relocalized during mitosis. Nucleolar RNase MRP (NuMRP) was purified to homogeneity, and we extensively purified the mitochondrial RNase MRP (MtMRP) to a single RNA component identical to the NuMRP RNA. Although the protein components of the NuMRP were identified by mass spectrometry successfully, none of the known NuMRP proteins were found in the MtMRP preparation. Only trace amounts of the core NuMRP protein, Pop4, were detected in MtMRP by Western blot. In vitro activity of the two enzymes was compared. MtMRP cleaved only mitochondrial ORI5 substrate, while NuMRP cleaved all three substrates. However, the NuMRP enzyme cleaved the ORI5 substrate at sites different than the MtMRP enzyme. In addition, enzymatic differences in preferred ionic strength confirm these enzymes as distinct entities. Magnesium was found to be essential to both enzymes. We tested a number of reported inhibitors including puromycin, pentamidine, lithium, and pAp. Puromycin inhibition suggested that it binds directly to the MRP RNA, reaffirming the role of the RNA component in catalysis. In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity.

  15. Comparative genomic analysis of the Lipase3 gene family in five plant species reveals distinct evolutionary origins.

    Wang, Dan; Zhang, Lin; Hu, JunFeng; Gao, Dianshuai; Liu, Xin; Sha, Yan

    2018-04-01

    Lipases are physiologically important and ubiquitous enzymes that share a conserved domain and are classified into eight different families based on their amino acid sequences and fundamental biological properties. The Lipase3 family of lipases was reported to possess a canonical fold typical of α/β hydrolases and a typical catalytic triad, suggesting a distinct evolutionary origin for this family. Genes in the Lipase3 family do not have the same functions, but maintain the conserved Lipase3 domain. There have been extensive studies of Lipase3 structures and functions, but little is known about their evolutionary histories. In this study, all lipases within five plant species were identified, and their phylogenetic relationships and genetic properties were analyzed and used to group them into distinct evolutionary families. Each identified lipase family contained at least one dicot and monocot Lipase3 protein, indicating that the gene family was established before the split of dicots and monocots. Similar intron/exon numbers and predicted protein sequence lengths were found within individual groups. Twenty-four tandem Lipase3 gene duplications were identified, implying that the distinctive function of Lipase3 genes appears to be a consequence of translocation and neofunctionalization after gene duplication. The functional genes EDS1, PAD4, and SAG101 that are reportedly involved in pathogen response were all located in the same group. The nucleotide diversity (Dxy) and the ratio of nonsynonymous to synonymous nucleotide substitutions rates (Ka/Ks) of the three genes were significantly greater than the average across the genomes. We further observed evidence for selection maintaining diversity on three genes in the Toll-Interleukin-1 receptor type of nucleotide binding/leucine-rich repeat immune receptor (TIR-NBS LRR) immunity-response signaling pathway, indicating that they could be vulnerable to pathogen effectors.

  16. The De Long Trough: a newly discovered glacial trough on the East Siberian continental margin

    M. O'Regan

    2017-09-01

    Full Text Available Ice sheets extending over parts of the East Siberian continental shelf have been proposed for the last glacial period and during the larger Pleistocene glaciations. The sparse data available over this sector of the Arctic Ocean have left the timing, extent and even existence of these ice sheets largely unresolved. Here we present new geophysical mapping and sediment coring data from the East Siberian shelf and slope collected during the 2014 SWERUS-C3 expedition (SWERUS-C3: Swedish – Russian – US Arctic Ocean Investigation of Climate-Cryosphere-Carbon Interactions. The multibeam bathymetry and chirp sub-bottom profiles reveal a set of glacial landforms that include grounding zone formations along the outer continental shelf, seaward of which lies a  >  65 m thick sequence of glacio-genic debris flows. The glacial landforms are interpreted to lie at the seaward end of a glacial trough – the first to be reported on the East Siberian margin, here referred to as the De Long Trough because of its location due north of the De Long Islands. Stratigraphy and dating of sediment cores show that a drape of acoustically laminated sediments covering the glacial deposits is older than ∼ 50 cal kyr BP. This provides direct evidence for extensive glacial activity on the Siberian shelf that predates the Last Glacial Maximum and most likely occurred during the Saalian (Marine Isotope Stage (MIS 6.

  17. Comparative linkage meta-analysis reveals regionally-distinct, disparate genetic architectures: application to bipolar disorder and schizophrenia.

    Brady Tang

    2011-04-01

    Full Text Available New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for "missing heritability." However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS, alternative approaches robust to detection of low-frequency (1-5% MAF and rare (<1% variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods--GSMA and MSP--applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA may be used to optimize low-frequency and rare variant discovery in the modern genomic era.

  18. Transcranial magnetic stimulation reveals two functionally distinct stages of motor cortex involvement during perception of emotional body language.

    Borgomaneri, Sara; Gazzola, Valeria; Avenanti, Alessio

    2015-09-01

    Studies indicate that perceiving emotional body language recruits fronto-parietal regions involved in action execution. However, the nature of such motor activation is unclear. Using transcranial magnetic stimulation (TMS) we provide correlational and causative evidence of two distinct stages of motor cortex engagement during emotion perception. Participants observed pictures of body expressions and categorized them as happy, fearful or neutral while receiving TMS over the left or right motor cortex at 150 and 300 ms after picture onset. In the early phase (150 ms), we observed a reduction of excitability for happy and fearful emotional bodies that was specific to the right hemisphere and correlated with participants' disposition to feel personal distress. This 'orienting' inhibitory response to emotional bodies was also paralleled by a general drop in categorization accuracy when stimulating the right but not the left motor cortex. Conversely, at 300 ms, greater excitability for negative, positive and neutral movements was found in both hemispheres. This later motor facilitation marginally correlated with participants' tendency to assume the psychological perspectives of others and reflected simulation of the movement implied in the neutral and emotional body expressions. These findings highlight the motor system's involvement during perception of emotional bodies. They suggest that fast orienting reactions to emotional cues--reflecting neural processing necessary for visual perception--occur before motor features of the observed emotional expression are simulated in the motor system and that distinct empathic dispositions influence these two neural motor phenomena. Implications for theories of embodied simulation are discussed.

  19. Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage.

    Russell, Scott D; Gou, Xiaoping; Wong, Chui E; Wang, Xinkun; Yuan, Tong; Wei, Xiaoping; Bhalla, Prem L; Singh, Mohan B

    2012-08-01

    Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  20. Transgenic Mouse Lines Subdivide External Segment of the Globus Pallidus (GPe) Neurons and Reveal Distinct GPe Output Pathways

    Mastro, Kevin J.; Bouchard, Rachel S.; Holt, Hiromi A. K.

    2014-01-01

    Cell-type diversity in the brain enables the assembly of complex neural circuits, whose organization and patterns of activity give rise to brain function. However, the identification of distinct neuronal populations within a given brain region is often complicated by a lack of objective criteria to distinguish one neuronal population from another. In the external segment of the globus pallidus (GPe), neuronal populations have been defined using molecular, anatomical, and electrophysiological criteria, but these classification schemes are often not generalizable across preparations and lack consistency even within the same preparation. Here, we present a novel use of existing transgenic mouse lines, Lim homeobox 6 (Lhx6)–Cre and parvalbumin (PV)–Cre, to define genetically distinct cell populations in the GPe that differ molecularly, anatomically, and electrophysiologically. Lhx6–GPe neurons, which do not express PV, are concentrated in the medial portion of the GPe. They have lower spontaneous firing rates, narrower dynamic ranges, and make stronger projections to the striatum and substantia nigra pars compacta compared with PV–GPe neurons. In contrast, PV–GPe neurons are more concentrated in the lateral portions of the GPe. They have narrower action potentials, deeper afterhyperpolarizations, and make stronger projections to the subthalamic nucleus and parafascicular nucleus of the thalamus. These electrophysiological and anatomical differences suggest that Lhx6–GPe and PV–GPe neurons participate in different circuits with the potential to contribute to different aspects of motor function and dysfunction in disease. PMID:24501350

  1. Complete identification of E-selectin ligands on neutrophils reveals distinct functions of PSGL-1, ESL-1, and CD44.

    Hidalgo, Andrés; Peired, Anna J; Wild, Martin; Vestweber, Dietmar; Frenette, Paul S

    2007-04-01

    The selectins and their ligands are required for leukocyte extravasation during inflammation. Several glycoproteins have been suggested to bind to E-selectin in vitro, but the complete identification of its physiological ligands has remained elusive. Here, we showed that E-selectin ligand-1 (ESL-1), P-selectin glycoprotein ligand-1 (PSGL-1), and CD44 encompassed all endothelial-selectin ligand activity on neutrophils by using gene- and RNA-targeted loss of function. PSGL-1 played a major role in the initial leukocyte capture, whereas ESL-1 was critical for converting initial tethers into steady slow rolling. CD44 controlled rolling velocity and mediated E-selectin-dependent redistribution of PSGL-1 and L-selectin to a major pole on slowly rolling leukocytes through p38 signaling. These results suggest distinct and dynamic contributions of these three glycoproteins in selectin-mediated neutrophil adhesion and signaling.

  2. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance

    Elliott Ferris

    2018-03-01

    Full Text Available The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ∼33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.

  3. Modeling autosomal recessive cutis laxa type 1C in mice reveals distinct functions for Ltbp-4 isoforms

    Bultmann-Mellin, Insa; Conradi, Anne; Maul, Alexandra C

    2015-01-01

    Recent studies have revealed an important role for LTBP-4 in elastogenesis. Its mutational inactivation in humans causes autosomal recessive cutis laxa type 1C (ARCL1C), which is a severe disorder caused by defects of the elastic fiber network. Although the human gene involved in ARCL1C has been ...

  4. Hydrogeology of the West Siberian Basin

    Foley, M.G.; Bradley, D.J.; Cole, C.R.

    1996-01-01

    Nuclear fuel cycle activities of the former Soviet Union (FSU) have resulted in extensive radioactive contaminant releases to the environment in western Siberia. We are developing three-dimensional numerical models of the hydrogeology and potential contaminant migration in the West Siberian Basin. We have assumed that ground-water flow in the West Siberian Basin is topographically driven, with recharge to the basin occurring in the highlands on the west, east, and south, and internal discharge localized in numerous river valleys and lakes that ultimately discharge north to the ocean. We are modeling the regional hydrogeology as three-dimensional, steady-state, saturated flow that is recharged from above. We acquired topographic, geologic, hydrostratigraphic, hydrogeologic, and water-balance data for the West Siberian Basin and constructed a regional water table. We correlated and combined 70 different rock types derived from published descriptions of West Siberian Basin rocks into 17 rock types appropriate for assignment of hydrogeologic properties on the basis of spatial heterogeneity and constituent (i.e., sand, silt, and clay) diversity. Examination of resulting three-dimensional assemblages of rock types showed that they were consistent with published and inferred paleogeography and depositional processes. Calibrating the basin's moisture balance (i.e., recharge and discharge) to the derived water table determined plausible input parameter values for unknowns such as hydraulic conductivities. The general directions of calculated ground-water flow suggest that major rivers act as discharge areas, with upwelling below the rivers extending down into the basement rocks, and that ground-water divides that penetrate the entire thickness of the model are evident between major rivers

  5. Trouble Upstairs: Reconstructing Permian-Triassic Climate during Siberian Traps Magmatism

    Black, B. A.; Neely, R. R., III; Lamarque, J. F.; Elkins-Tanton, L. T.; Mills, M. J.

    2014-12-01

    The eruption of large igneous provinces can transfer significant masses of volatiles from Earth's interior to the atmosphere. What are the consequences of this degassing for habitability and extinction? In this presentation, we consider this question in the context of Siberian Traps magmatism, which has been shown to overlap within geochronologic uncertainty with catastrophic deterioration of Permian-Triassic marine and terrestrial ecosystems. To investigate the impacts of endogenic gases on climate, atmospheric chemistry, and ocean circulation, we conducted a series of numerical experiments with a comprehensive global model for the Permian-Triassic. Our simulations predict the intensity and distribution of acid rain and ozone depletion, with implications for terrestrial biota. We further explore feedbacks between sulfur emissions, transient cooling, and shifts in ocean circulation. We suggest that Siberian Traps magmatism may have triggered several distinct kill mechanisms in the oceans and on land, contributing to a complex combined pattern of environmental stress and latest Permian ecological failure.

  6. Climate constraints for siberian moth distribution in Europe

    Yuri Baranchikov; Nadezda Tschebakova; Elena Parfenova; Natalia. Kirichenko

    2010-01-01

    A simplistic bioclimatic model of the Siberian moth Dendrolimus sibiricus Tschtvrk. (Lepidoptera: Lasiocampidae) is based on the moth's basic biological requirements, expressed through summer thermal conditions...

  7. Cambrian trilobites with Siberian affinities, southwestern Alaska

    Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

    1985-02-01

    Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

  8. Paleomagnetism of Siberian Trap Intrusions: Implications for the Timing and Intensity of the Magmatic Activity

    Latyshev, Anton; Veselovskiy, Roman; Mirsayanova, Elina; Ulyahina, Polina

    2016-04-01

    Large Igneous Provinces (LIPs) are the areas of the exceptional interest due to associated Cu-Ni-Pt deposits, problems of the causal link between volcanic hazards and mass extinctions, and questions about mantle plume dynamics. High-precise U-Pb and 40Ar/39Ar dating determined the duration of the main phase of the most voluminous Siberian Trap province formation as 1-2 Ma (Kamo et al., 2003; Reichow et al., 2008). Recent paleomagnetic investigations demonstrated the predominance of pulsating volcanic activity during LIPs formation (Chenet et al., 2009; Pavlov et al., 2015). We perform the results of detailed paleomagnetic study of intrusive complexes from Tunguska syncline and Angara-Taseeva depression (Siberian Trap province). Our data taken together with the previous paleomagnetic results from trap intrusions revealed two different styles of magmatic activity. In the central part of Tunguska syncline emplacement of was rather even without sharp bursts. Local intrusive events coeval to volcanic eruptions took place within spatially limited areas. In contrast, in the periphery of Tunguska syncline several short and powerful peaks of magmatic activity happened on the background of weak prolonged magmatism. These events resulted in huge Padunsky, Tulunsky and some other sills in the southern part of the Siberian platform. According to our paleomagnetic data, the duration of such pulses did not exceed 10-100 thousand years. Taking into account our paleomagnetic data and recent U-Pb ages for Siberian trap intrusions from (Burgess, Bowring, 2015), it is possible to correlate intrusive complexes with the volcanic section. In particular, formation the largest Tulunsky and Padunsky sills happened right after the termination of the main phase of Permian-Triassic volcanic activity on the Siberian platform. This work was supported by grants RFBR # 16-35-60114 and 15-35-20599 and Ministry of Education and Science of the Russian Federation (grant 14.Z50.31.0017).

  9. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

    Statham, Mark J; Murdoch, James; Janecka, Jan; Aubry, Keith B; Edwards, Ceiridwen J; Soulsbury, Carl D; Berry, Oliver; Wang, Zhenghuan; Harrison, David; Pearch, Malcolm; Tomsett, Louise; Chupasko, Judith; Sacks, Benjamin N

    2014-10-01

    Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva. © 2014 John Wiley & Sons Ltd.

  10. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance.

    Ferris, Elliott; Abegglen, Lisa M; Schiffman, Joshua D; Gregg, Christopher

    2018-03-06

    The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ∼33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  11. Regional inactivations of primate ventral prefrontal cortex reveal two distinct mechanisms underlying negative bias in decision making.

    Clarke, Hannah F; Horst, Nicole K; Roberts, Angela C

    2015-03-31

    Dysregulation of the orbitofrontal and ventrolateral prefrontal cortices is implicated in anxiety and mood disorders, but the specific contributions of each region are unknown, including how they gate the impact of threat on decision making. To address this, the effects of GABAergic inactivation of these regions were studied in marmoset monkeys performing an instrumental approach-avoidance decision-making task that is sensitive to changes in anxiety. Inactivation of either region induced a negative bias away from punishment that could be ameliorated with anxiolytic treatment. However, whereas the effects of ventrolateral prefrontal cortex inactivation on punishment avoidance were seen immediately, those of orbitofrontal cortex inactivation were delayed and their expression was dependent upon an amygdala-anterior hippocampal circuit. We propose that these negative biases result from deficits in attentional control and punishment prediction, respectively, and that they provide the basis for understanding how distinct regional prefrontal dysregulation contributes to the heterogeneity of anxiety disorders with implications for cognitive-behavioral treatment strategies.

  12. Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol

    Kwon, Hyock Joo; Abi-Mosleh, Lina; Wang, Michael L.; Deisenhofer, Johann; Goldstein, Joseph L.; Brown, Michael S.; Infante, Rodney E.; (UTSMC)

    2010-09-21

    LDL delivers cholesterol to lysosomes by receptor-mediated endocytosis. Exit of cholesterol from lysosomes requires two proteins, membrane-bound Niemann-Pick C1 (NPC1) and soluble NPC2. NPC2 binds cholesterol with its isooctyl side chain buried and its 3{beta}-hydroxyl exposed. Here, we describe high-resolution structures of the N-terminal domain (NTD) of NPC1 and complexes with cholesterol and 25-hydroxycholesterol. NPC1(NTD) binds cholesterol in an orientation opposite to NPC2: 3{beta}-hydroxyl buried and isooctyl side chain exposed. Cholesterol transfer from NPC2 to NPC1(NTD) requires reorientation of a helical subdomain in NPC1(NTD), enlarging the opening for cholesterol entry. NPC1 with point mutations in this subdomain (distinct from the binding subdomain) cannot accept cholesterol from NPC2 and cannot restore cholesterol exit from lysosomes in NPC1-deficient cells. We propose a working model wherein after lysosomal hydrolysis of LDL-cholesteryl esters, cholesterol binds NPC2, which transfers it to NPC1(NTD), reversing its orientation and allowing insertion of its isooctyl side chain into the outer lysosomal membranes.

  13. OCT2, SSX and SAGE1 reveal the phenotypic heterogeneity of spermatocytic seminoma reflecting distinct subpopulations of spermatogonia

    Lim, Jasmine; Goriely, Anne; Turner, Gareth Dh

    2011-01-01

    in the normal adult testis. We analysed the expression pattern of OCT2, SSX2-4, and SAGE1 in 36 SS cases and four intratubular SS (ISS) as well as a series of normal testis samples throughout development. We describe for the first time two different types of SS characterized by OCT2 or SSX2-4 immunoexpression......, whilst SAGE1 was exclusively present in a subset of post-pubertal germ cells, most likely B spermatogonia. The presence of OCT2 and SSX2-4 in distinct subsets of germ cells implies that these markers represent germ cells at different maturation stages. Analysis of SAGE1 and SSX2-4 in ISS showed spatial...... differences suggesting ongoing maturation of germ cells during progression of SS tumourigenesis. We conclude that the expression pattern of OCT2, SSX2-4, and SAGE1 supports the origin of SS from spermatogonia and provides new evidence for heterogeneity of this tumour, potentially linked either to the cellular...

  14. Saturation Mutagenesis of the HIV-1 Envelope CD4 Binding Loop Reveals Residues Controlling Distinct Trimer Conformations.

    Maria Duenas-Decamp

    2016-11-01

    Full Text Available The conformation of HIV-1 envelope (Env glycoprotein trimers is key in ensuring protection against waves of neutralizing antibodies generated during infection, while maintaining sufficient exposure of the CD4 binding site (CD4bs for viral entry. The CD4 binding loop on Env is an early contact site for CD4 while penetration of a proximal cavity by CD4 triggers Env conformational changes for entry. The role of residues in the CD4 binding loop in regulating the conformation of the trimer and trimer association domain (TAD was investigated using a novel saturation mutagenesis approach. Single mutations identified, resulted in distinct trimer conformations affecting CD4bs exposure, the glycan shield and the TAD across diverse HIV-1 clades. Importantly, mutations that improve access to the CD4bs without exposing the immunodominant V3 loop were identified. The different trimer conformations identified will affect the specificity and breadth of nabs elicited in vivo and are important to consider in design of Env immunogens for vaccines.

  15. Integrative omic analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

    Gage eKoehler

    2015-10-01

    Full Text Available To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative omic approaches were applied to Fragaria × ananassa Duch. ‘Korona’. Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1 to 10 days of cold (2°C exposure. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine, pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold.Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.

  16. Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.

    Fonseca, Emanuella Maria Barreto; Scorsato, Valéria; Dos Santos, Marcelo Leite; Júnior, Atilio Tomazini; Tada, Susely Ferraz Siqueira; Dos Santos, Clelton Aparecido; de Toledo, Marcelo Augusto Szymanski; de Souza, Anete Pereira; Polikarpov, Igor; Aparicio, Ricardo

    2017-04-01

    Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.

  17. Multiple analytical approaches reveal distinct gene-environment interactions in smokers and non smokers in lung cancer.

    Rakhshan Ihsan

    Full Text Available Complex disease such as cancer results from interactions of multiple genetic and environmental factors. Studying these factors singularly cannot explain the underlying pathogenetic mechanism of the disease. Multi-analytical approach, including logistic regression (LR, classification and regression tree (CART and multifactor dimensionality reduction (MDR, was applied in 188 lung cancer cases and 290 controls to explore high order interactions among xenobiotic metabolizing genes and environmental risk factors. Smoking was identified as the predominant risk factor by all three analytical approaches. Individually, CYP1A1*2A polymorphism was significantly associated with increased lung cancer risk (OR = 1.69;95%CI = 1.11-2.59,p = 0.01, whereas EPHX1 Tyr113His and SULT1A1 Arg213His conferred reduced risk (OR = 0.40;95%CI = 0.25-0.65,p<0.001 and OR = 0.51;95%CI = 0.33-0.78,p = 0.002 respectively. In smokers, EPHX1 Tyr113His and SULT1A1 Arg213His polymorphisms reduced the risk of lung cancer, whereas CYP1A1*2A, CYP1A1*2C and GSTP1 Ile105Val imparted increased risk in non-smokers only. While exploring non-linear interactions through CART analysis, smokers carrying the combination of EPHX1 113TC (Tyr/His, SULT1A1 213GG (Arg/Arg or AA (His/His and GSTM1 null genotypes showed the highest risk for lung cancer (OR = 3.73;95%CI = 1.33-10.55,p = 0.006, whereas combined effect of CYP1A1*2A 6235CC or TC, SULT1A1 213GG (Arg/Arg and betel quid chewing showed maximum risk in non-smokers (OR = 2.93;95%CI = 1.15-7.51,p = 0.01. MDR analysis identified two distinct predictor models for the risk of lung cancer in smokers (tobacco chewing, EPHX1 Tyr113His, and SULT1A1 Arg213His and non-smokers (CYP1A1*2A, GSTP1 Ile105Val and SULT1A1 Arg213His with testing balance accuracy (TBA of 0.6436 and 0.6677 respectively. Interaction entropy interpretations of MDR results showed non-additive interactions of tobacco chewing with

  18. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia

    Kerr, Peter J.; Cattadori, Isabella M.; Fitch, Adam; Geber, Adam; Liu, June; Sim, Derek G.; Boag, Brian; Ghedin, Elodie

    2017-01-01

    The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954–1955) and between 2008–2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms. PMID:28253375

  19. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

    Peter J Kerr

    2017-03-01

    Full Text Available The co-evolution of myxoma virus (MYXV and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955 and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release Lausanne strain. Inferred virulence ranged from highly virulent (grade 1 to highly attenuated (grade 5. Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.

  20. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

    Kerr, Peter J; Cattadori, Isabella M; Rogers, Matthew B; Fitch, Adam; Geber, Adam; Liu, June; Sim, Derek G; Boag, Brian; Eden, John-Sebastian; Ghedin, Elodie; Read, Andrew F; Holmes, Edward C

    2017-03-01

    The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955) and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.

  1. Three distinct Holocene intervals of stalagmite deposition and nondeposition revealed in NW Madagascar, and their paleoclimate implications

    Riavo Gilbertinie Voarintsoa, Ny; Railsback, Loren Bruce; Brook, George Albert; Wang, Lixin; Kathayat, Gayatri; Cheng, Hai; Li, Xianglei; Edwards, Richard Lawrence; Rakotondrazafy, Amos Fety Michel; Olga Madison Razanatseheno, Marie

    2017-12-01

    Petrographic features, mineralogy, and stable isotopes from two stalagmites, ANJB-2 and MAJ-5, respectively from Anjohibe and Anjokipoty caves, allow distinction of three intervals of the Holocene in NW Madagascar. The Malagasy early Holocene (between ca. 9.8 and 7.8 ka) and late Holocene (after ca. 1.6 ka) intervals (MEHI and MLHI, respectively) record evidence of stalagmite deposition. The Malagasy middle Holocene interval (MMHI, between ca. 7.8 and 1.6 ka) is marked by a depositional hiatus of ca. 6500 years. Deposition of these stalagmites indicates that the two caves were sufficiently supplied with water to allow stalagmite formation. This suggests that the MEHI and MLHI intervals may have been comparatively wet in NW Madagascar. In contrast, the long-term depositional hiatus during the MMHI implies it was relatively drier than the MEHI and the MLHI. The alternating wet-dry-wet conditions during the Holocene may have been linked to the long-term migrations of the Intertropical Convergence Zone (ITCZ). When the ITCZ's mean position is farther south, NW Madagascar experiences wetter conditions, such as during the MEHI and MLHI, and when it moves north, NW Madagascar climate becomes drier, such as during the MMHI. A similar wet-dry-wet succession during the Holocene has been reported in neighboring locations, such as southeastern Africa. Beyond these three subdivisions, the records also suggest wet conditions around the cold 8.2 ka event, suggesting a causal relationship. However, additional Southern Hemisphere high-resolution data will be needed to confirm this.

  2. MICHIGAN/INDIANA: Siberian Snakes strike again

    Anon.

    1993-01-01

    Full text: Siberian snakes are showing themselves to be even more deadly than expected in killing their prey, the depolarizing resonances which would make it very difficult to accelerate polarized protons to TeV energies at accelerators such as the Tevatron, UNK, LHC, and SSC. The snake concept was proposed in the mid-1970s by Siberians Yaroslav Derbenev and Anatoly Kondratenko at Novosibirsk, but the snakes lay almost dormant until Owen Chamberlain, Ernest Courant, Alan Krisch, and the late Kent Terwilliger organized the 1985 Superconducting Supercollider (SSC) polarized beam workshop in Ann Arbor, which highlighted the need to test the concept. The idea is to rotate the spin through 180° on each turn in the ring. With such successive spin flips, the depolarizing effects seen in one turn should be cancelled by an equal and opposite perturbation on the subsequent turn. The new Cooler Ring at the Indiana University Cyclotron Facility then seemed an excellent test site for these eager but untested serpents. The Michigan/lndiana/Brookhaven team led by Krisch constructed the world's first snake and found that it could easily overcome its initial enemy, the imperfection depolarizing resonances caused by ring magnet imperfections (January/February 1990, page 20). In the next few years the growing team of ''herpetologists'' showed that Siberian snakes could overcome all kinds of depolarizing resonances, including the intrinsic kind (caused by the vertical betatron oscillations which keep the beam focused) and the synchrotron resonances (caused by synchrotron oscillations in energy). The team also discovered a new type of snake that was inadvertently built into the cooling section. This socalled type-3 snake rotates the spin around the vertical direction. A full type-1 snake (such as the team's superconducting solenoid magnet) rotates the spin by 180° around the beam direction; a type-2 snake rotates the spin around the radial direction

  3. Molecular diversity of poleroviruses infecting cucurbit crops in four countries reveals the presence of members of six distinct species.

    Knierim, D; Tsai, W S; Maiss, E; Kenyon, L

    2014-06-01

    When 66 cucurbit samples with yellowing symptoms from fields in Mali, the Philippines, Thailand and Uzbekistan were screened by RT-PCR using universal polerovirus primers, 21 were identified as harboring polerovirus RNA. When these 21 samples were screened with specific primers for the known cucurbit-infecting poleroviruses, suakwa aphid-borne yellows virus and a recombinant strain of cucurbit aphid-borne yellows virus were detected for the first time in the Philippines and Thailand. However, seven polerovirus-positive samples did not react with any of the known species-specific primers. Sequencing of 1.4-kb universal polerovirus RT-PCR products revealed the presence of two poleroviruses that had not been described previously. These viruses, from Mali and Thailand, were provisionally named pepo aphid-borne yellows virus and luffa aphid-borne yellows virus, respectively.

  4. Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

    Cristina eTakacs-vesbach

    2013-05-01

    Full Text Available The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal ‘filamentous streamer’ communities (~40 Mbp per site, which targeted three different groups of Aquificales found in Yellowstone National Park (YNP. Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae populations, whereas the circumneutral pH (6.5 - 7.8 sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae. Thermocrinis (Aquificaceae populations were found primarily in the circumneutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl. The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl CoA synthetase (Ccs and citryl CoA lyase (Ccl. All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2 have resulted in niche specialization among members of the Aquificales.

  5. Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus.

    Woo, Patrick C Y; Lau, Susanna K P; Lam, Carol S F; Tsang, Alan K L; Hui, Suk-Wai; Fan, Rachel Y Y; Martelli, Paolo; Yuen, Kwok-Yung

    2014-01-01

    While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (CoVs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (Tursiops aduncus), which we named bottlenose dolphin CoV (BdCoV) HKU22. All the three BdCoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1 × 10(3) to 1 × 10(5) copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of BdCoV HKU22. Complete genome sequencing and comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all CoVs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (Ks) to the number of nonsynonymous substitutions per nonsynonymous site (Ka) in multiple regions of the genome, especially the S gene (Ka/Ks ratio, 2.5), indicated that BdCoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species, Cetacean coronavirus, in Gammacoronavirus, to include BdCoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird CoVs represent another species, Avian coronavirus, in Gammacoronavirus.

  6. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

    Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

    2018-01-01

    Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more

  7. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

    Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

    2018-01-01

    Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

  8. Lipidomic profiling reveals distinct differences in plasma lipid composition in healthy, prediabetic, and type 2 diabetic individuals

    Zhong, Huanzi; Fang, Chao; Fan, Yanqun; Lu, Yan; Wen, Bo; Ren, Huahui; Hou, Guixue; Yang, Fangming; Xie, Hailiang; Jie, Zhuye; Peng, Ye; Ye, Zhiqiang; Wu, Jiegen; Zi, Jin; Zhao, Guoqing; Chen, Jiayu; Bao, Xiao; Hu, Yihe; Gao, Yan; Zhang, Jun; Yang, Huanming; Wang, Jian; Madsen, Lise; Kristiansen, Karsten

    2017-01-01

    Abstract The relationship between dyslipidemia and type 2 diabetes mellitus (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized. Liquid chromatography coupled to tandem mass spectrometry was applied to detect the global lipidome in the fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects, and 98 individuals with normal glucose tolerance (NGT). Both qualitative and quantitative analyses revealed a gradual change in plasma lipid features with T2D patients exhibiting characteristics close to those of prediabetic individuals, whereas they differed significantly from individuals with NGT. We constructed and validated a random forest classifier with 28 lipidomic features that effectively discriminated T2D from NGT or prediabetes. Most of the selected features significantly correlated with diabetic clinical indices. Hydroxybutyrylcarnitine was positively correlated with fasting plasma glucose, 2-hour postprandial glucose, glycated hemoglobin, and insulin resistance index (HOMA-IR). Lysophosphatidylcholines such as lysophosphatidylcholine (18:0), lysophosphatidylcholine (18:1), and lysophosphatidylcholine (18:2) were all negatively correlated with HOMA-IR. The altered plasma lipidome in Chinese T2D and prediabetic subjects suggests that lipid features may play a role in the pathogenesis of T2D and that such features may provide a basis for evaluating risk and monitoring disease development. PMID:28505362

  9. Azadirachtin(A) distinctively modulates subdomain 2 of actin - novel mechanism to induce depolymerization revealed by molecular dynamics study.

    Pravin Kumar, R; Roopa, L; Sudheer Mohammed, M M; Kulkarni, Naveen

    2016-12-01

    Azadirachtin(A) (AZA), a potential insecticide from neem, binds to actin and induces depolymerization in Drosophila. AZA binds to the pocket same as that of Latrunculin A (LAT), but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP-ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA-induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilized the interactions between subdomain 2 of one actin and subdomains 1 and 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n + 2. However, the specific triggering point for the separation of the subunits was the destabilization of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n + 2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.

  10. Molecular characterization of HCV in a Swedish county over 8 years (2002–2009 reveals distinct transmission patterns

    Josefine Ederth

    2016-02-01

    Full Text Available Background: Hepatitis C virus (HCV is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county. The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission. Methods: Molecular analyses of serum samples from 91% (N=557 of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL was used to analyze trends over time. Results: The most prevalent subtypes were 1a (38% and 3a (34%. Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs. Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered, while the 1a sequences formed smaller clusters (19% of the sequences clustered, possibly suggesting different epidemics. Conclusion: We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.

  11. Use of a molecular genetic platform technology to produce human Wnt proteins reveals distinct local and distal signaling abilities.

    Jennifer L Green

    Full Text Available Functional and mechanistic studies of Wnt signaling have been severely hindered by the inaccessibility of bioactive proteins. To overcome this long-standing barrier, we engineered and characterized a panel of Chinese hamster ovary (CHO cell lines with inducible transgenes encoding tagged and un-tagged human WNT1, WNT3A, WNT5A, WNT7A, WNT11, WNT16 or the soluble Wnt antagonist Fzd8CRD, all integrated into an identical genomic locus. Using a quantitative real-time bioluminescence assay, we show that cells expressing WNT1, 3A and 7A stimulate Wnt/beta-catenin reporter activity, while the other WNT expressing cell lines interfere with this activation. Additionally, in contrast to WNT3A, WNT1 only exhibits activity when cell-associated, and thus only signals to neighboring cells. The reporter assay also revealed a rapid decline of Wnt activity at 37°C, indicating that Wnt activity is highly labile. These engineered cell lines will reduce the cost of making and purifying Wnt proteins and serve as a continuous, reliable and regulatable source of Wnts to research laboratories around the world.

  12. Genome-wide transcriptional profiling reveals two distinct outcomes in central Nervous system infections of rabies virus

    Daiting eZhang

    2016-05-01

    Full Text Available Rabies remains a major public health concern in many developing countries. The precise neuropathogenesis of rabies is unknown, though it is hypothesized to be due to neuronal death or dysfunction. Mice that received intranasal inoculation of an attenuated rabies virus (RABV strain HEP-Flury exhibited subtle clinical signs, and eventually recovered, which is different from the fatal encephalitis caused by the virulent RABV strain CVS-11. To understand the neuropathogenesis of rabies and the mechanisms of viral clearance, we applied RNA sequencing (RNA-Seq to compare the brain transcriptomes of normal mice versus HEP-Flury or CVS-11 intranasally inoculated mice. Our results revealed that both RABV strains altered positively and negatively the expression levels of many host genes, including genes associated with innate and adaptive immunity, inflammation and cell death. It is found that HEP-Flury infection can activate the innate immunity earlier through the RIG-I/MDA-5 signaling, and the innate immunity pre-activated by HEP-Flury or Newcastle disease virus (NDV infection can effectively prevent the CVS-11 to invade central nervous system (CNS, but fails to clear the CVS-11 after its entry into the CNS. In addition, following CVS-11 infection, genes implicated in cell adhesion, blood vessel morphogenesis and coagulation were mainly up-regulated, while the genes involved in synaptic transmission and ion transport were significantly down-regulated. On the other hand, several genes involved in the MHC class II-mediated antigen presentation pathway were activated to a greater extent after the HEP-Flury infection as compared with the CVS-11 infection suggesting that the collaboration of CD4+ T cells and MHC class II-mediated antigen presentation is critical for the clearance of attenuated RABV from the CNS. The differentially regulated genes reported here are likely to include potential therapeutic targets for expanding the postexposure treatment window

  13. Quantitative Imaging of Cholinergic Interneurons Reveals a Distinctive Spatial Organization and a Functional Gradient across the Mouse Striatum.

    Miriam Matamales

    Full Text Available Information processing in the striatum requires the postsynaptic integration of glutamatergic and dopaminergic signals, which are then relayed to the output nuclei of the basal ganglia to influence behavior. Although cellularly homogeneous in appearance, the striatum contains several rare interneuron populations which tightly modulate striatal function. Of these, cholinergic interneurons (CINs have been recently shown to play a critical role in the control of reward-related learning; however how the striatal cholinergic network is functionally organized at the mesoscopic level and the way this organization influences striatal function remains poorly understood. Here, we systematically mapped and digitally reconstructed the entire ensemble of CINs in the mouse striatum and quantitatively assessed differences in densities, spatial arrangement and neuropil content across striatal functional territories. This approach demonstrated that the rostral portion of the striatum contained a higher concentration of CINs than the caudal striatum and that the cholinergic content in the core of the ventral striatum was significantly lower than in the rest of the regions. Additionally, statistical comparison of spatial point patterns in the striatal cholinergic ensemble revealed that only a minor portion of CINs (17% aggregated into cluster and that they were predominantly organized in a random fashion. Furthermore, we used a fluorescence reporter to estimate the activity of over two thousand CINs in naïve mice and found that there was a decreasing gradient of CIN overall function along the dorsomedial-to-ventrolateral axis, which appeared to be independent of their propensity to aggregate within the striatum. Altogether this work suggests that the regulation of striatal function by acetylcholine across the striatum is highly heterogeneous, and that signals originating in external afferent systems may be principally determining the function of CINs in the

  14. Photoperiod Regulates vgf-Derived Peptide Processing in Siberian Hamsters.

    Barbara Noli

    Full Text Available VGF mRNA is induced in specific hypothalamic areas of the Siberian hamster upon exposure to short photoperiods, which is associated with a seasonal decrease in appetite and weight loss. Processing of VGF generates multiple bioactive peptides, so the objective of this study was to determine the profile of the VGF-derived peptides in the brain, pituitary and plasma from Siberian hamsters, and to establish whether differential processing might occur in the short day lean state versus long day fat. Antisera against short sequences at the C- or N- termini of proVGF, as well as against NERP-1, TPGH and TLQP peptides, were used for analyses of tissues, and both immunohistochemistry and enzyme linked immunosorbent assay (ELISA coupled with high-performance liquid (HPLC or gel chromatography were carried out. VGF peptide immunoreactivity was found within cortex cholinergic perikarya, in multiple hypothalamic nuclei, including those containing vasopressin, and in pituitary gonadotrophs. ELISA revealed that exposure to short day photoperiod led to a down-regulation of VGF immunoreactivity in the cortex, and a less pronounced decrease in the hypothalamus and pituitary, while the plasma VGF levels were not affected by the photoperiod. HPLC and gel chromatography both confirmed the presence of multiple VGF-derived peptides in these tissues, while gel chromatography showed the presence of the VGF precursor in all tissues tested except for the cortex. These observations are consistent with the view that VGF-derived peptides have pleiotropic actions related to changing photoperiod, possibly by regulating cholinergic systems in the cortex, vasopressin hypothalamic pathways, and the reproductive axis.

  15. Helical Siberian snakes using dipole magnets

    Wienands, U.

    1990-09-01

    A family of multi-twist transverse-field spin rotators using discrete bending magnets is described that can be used as Siberian snakes. By varying the number of twists, snakes with quite small excursions can be constructed at only a small penalty in the overall field integral. Examples for a 1/4-twist snake and a 3-twist snake are presented, the first suitable for a very high energy machine and the second for use in the proposed TRIUMF Kaon Factory. (Author) (3 refs.)

  16. Siberian Snakes in high-energy accelerators

    Mane, S R; Shatunov, Yu M; Yokoya, K

    2005-01-01

    We review modern techniques to accelerate spin-polarized beams to high energy and to preserve their polarization in storage rings. Crucial to the success of such work is the use of so-called Siberian Snakes. We explain these devices and the reason for their necessity. Closely related to Snakes is the concept of 'spin rotators'. The designs and merits of several types of Snakes and spin rotators are examined. Theoretical work with Snakes and spin rotators, and experimental results from several storage rings, are reviewed, including the so-called Snake resonances. (topical review)

  17. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  18. Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history.

    Kovalev, S Y; Mukhacheva, T A

    2017-11-01

    Tick-borne encephalitis is widespread in Eurasia and transmitted by Ixodes ticks. Classification of its causative agent, tick-borne encephalitis virus (TBEV), includes three subtypes, namely Far-Eastern, European, and Siberian (TBEV-Sib), as well as a group of 886-84-like strains with uncertain taxonomic status. TBEV-Sib is subdivided into three phylogenetic lineages: Baltic, Asian, and South-Siberian. A reason to reconsider TBEV-Sib classification was the analysis of 186 nucleotide sequences of an E gene fragment submitted to GenBank during the last two years. Within the South-Siberian lineage, we have identified a distinct group with prototype strains Aina and Vasilchenko as an individual lineage named East-Siberian. The analysis of reclassified lineages has promoted a new model of the evolutionary history of TBEV-Sib lineages and TBEV-Sib as a whole. Moreover, we present arguments supporting separation of 886-84-like strains into an individual TBEV subtype, which we propose to name Baikalian (TBEV-Bkl). Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Beam polarization during a Siberian snake turn-on

    Anferov, Vladimir A.

    1999-01-01

    Installing Siberian snakes in a circular proton accelerator allows one to overcome all spin depolarizing resonances even at very high energies. However, Siberian snake application at low energies is technically rather difficult. Turning snake on at some energy during acceleration would allow using Siberian snakes even in rings with low injection energies. It is shown that the beam polarization would be preserved during the snake ramp, provided that the snake is turned on in more than ten turns, and the energy is set near a half-integer Gγ

  20. ACCELERATION OF POLARIZED BEAMS USING MULTIPLE STRONG PARTIAL SIBERIAN SNAKES

    ROSER, T.; AHRENS, L.; BAI, M.

    2004-01-01

    Acceleration of polarized protons in the energy range of 5 to 25 GeV is particularly difficult since depolarizing spin resonances are strong enough to cause significant depolarization but full Siberian snakes cause intolerably large orbit excursions. Using a 20-30% partial Siberian snake both imperfection and intrinsic resonances can be overcome. Such a strong partial Siberian snake was designed for the Brookhaven AGS using a dual pitch helical superconducting dipole. Multiple strong partial snakes are also discussed for spin matching at beam injection and extraction

  1. North Atlantic Origin of Interdecadal variability of Siberian High

    Kim, Seon-Hwa; Sung, Mi-Kyung; Kim, Baek-Min

    2017-04-01

    We suggest that the changes in the mean atmospheric circulation structure in the North Atlantic Ocean upstream region of Eurasian continent play an important role in the interdecadal variability of Siberian High (SH) through the modulation of Ural blocking frequency. Previous studies suggested that the interdecadal variability of SH is partly explained by the Arctic Oscillation. However, in this study, we emphasize the role of 'Warm Arctic and Cold Eurasia (WACE)', which is the second mode of winter surface air temperature variability over Eurasia. We show that the correlation between SH and WACE is high in general compared to that between SH and AO. However, the correlation between SH and WACE does not always exhibit high constant value. It shows a distinctive interdecadal fluctuation in the correlation. We found that this fluctuation in the correlation is due to the interdecadal fluctuation of the continental trough over the North Atlantic and the resultant strengthening of in-situ atmospheric baroclinicity. This accompanies changes in the transient vorticity flux divergence which leads to the downstream wave development and anomalous anticyclonic flow near Ural region. Obviously, the existence of anticyclonic flow over Ural region helps more frequent occurrence of Ural blocking and it is shown that this condition favors positive WACE event, which links to an intensified SH.

  2. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.

    2015-01-01

    organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10ºC. Multivariate statistical analysis of the bacterial diversity data (DNA......The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78º......N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable...

  3. Construction of cDNA library and preliminary analysis of expressed sequence tags from Siberian tiger

    Liu, Chang-Qing; Lu, Tao-Feng; Feng, Bao-Gang; Liu, Dan; Guan, Wei-Jun; Ma, Yue-Hui

    2010-01-01

    In this study we successfully constructed a full-length cDNA library from Siberian tiger, Panthera tigris altaica, the most well-known wild Animal. Total RNA was extracted from cultured Siberian tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.30×106 pfu/ml and 1.62×109 pfu/ml respectively. The proportion of recombinants from unamplified library was 90.5% and average length of exogenous inserts was 1.13 kb. A total of 282 individual ESTs with sizes ranging from 328 to 1,142bps were then analyzed the BLASTX score revealed that 53.9% of the sequences were classified as strong match, 38.6% as nominal and 7.4% as weak match. 28.0% of them were found to be related to enzyme/catalytic protein, 20.9% ESTs to metabolism, 13.1% ESTs to transport, 12.1% ESTs to signal transducer/cell communication, 9.9% ESTs to structure protein, 3.9% ESTs to immunity protein/defense metabolism, 3.2% ESTs to cell cycle, and 8.9 ESTs classified as novel genes. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genomic research of Siberian tigers. PMID:20941376

  4. [HYGIENIC ASSESSMENT OF WORKING CONDITIONS AND HEALTH OF EMPLOYEES OF THE "SIBERIAN LIFT CO., LTD."].

    Rodkin, V P; Usatov, A N

    2015-01-01

    There was carried out a hygienic assessment of the working conditions and health of employees of the "Siberian Lift Co., Ltd.". When studying occupational factors on workplaces intensity, the temperature radiation, natural and artificial lighting, and also the content of chemicals they were revealed to fail to answer to the hygienic specifications. It is established that in 82% of employees the class of working conditions was detected as admissible (2) and in 18%--harmful (3.1 and 3.2). Results of the performed periodic medical examination of employees of the "Siberian Lift Co., Ltd.". It is testified that 6.14% out of them are persistently unfit of the work with harmful and (or) dangerous substances and occupational factors also. 4.68% of employees demand an additional examination. 11,70% of workers need for out-patient examination and treatment. Sanatorium treatment is required for 1 (0.29%) the person. 4,68% of employees of the "Siberian Lift Co., Ltd." need dispensary supervision. There are suggested measures for the improvement of working conditions and health of the employees.

  5. Optogenetic activation of CA1 pyramidal neurons at the dorsal and ventral hippocampus evokes distinct brain-wide responses revealed by mouse fMRI.

    Norio Takata

    Full Text Available The dorsal and ventral hippocampal regions (dHP and vHP are proposed to have distinct functions. Electrophysiological studies have revealed intra-hippocampal variances along the dorsoventral axis. Nevertheless, the extra-hippocampal influences of dHP and vHP activities remain unclear. In this study, we compared the spatial distribution of brain-wide responses upon dHP or vHP activation and further estimate connection strengths between the dHP and the vHP with corresponding extra-hippocampal areas. To achieve this, we first investigated responses of local field potential (LFP and multi unit activities (MUA upon light stimulation in the hippocampus of an anesthetized transgenic mouse, whose CA1 pyramidal neurons expressed a step-function opsin variant of channelrhodopsin-2 (ChR2. Optogenetic stimulation increased hippocampal LFP power at theta, gamma, and ultra-fast frequency bands, and augmented MUA, indicating light-induced activation of CA1 pyramidal neurons. Brain-wide responses examined using fMRI revealed that optogenetic activation at the dHP or vHP caused blood oxygenation level-dependent (BOLD fMRI signals in situ. Although activation at the dHP induced BOLD responses at the vHP, the opposite was not observed. Outside the hippocampal formation, activation at the dHP, but not the vHP, evoked BOLD responses at the retrosplenial cortex (RSP, which is in line with anatomical evidence. In contrast, BOLD responses at the lateral septum (LS were induced only upon vHP activation, even though both dHP and vHP send axonal fibers to the LS. Our findings suggest that the primary targets of dHP and vHP activation are distinct, which concurs with attributed functions of the dHP and RSP in spatial memory, as well as of the vHP and LS in emotional responses.

  6. Revealing the distinct habitat ranges and hybrid zone of genetic sub-populations within Pseudo-nitzschia pungens (Bacillariophyceae) in the West Pacific area.

    Kim, Jin Ho; Wang, Pengbin; Park, Bum Soo; Kim, Joo-Hwan; Patidar, Shailesh Kumar; Han, Myung-Soo

    2018-03-01

    Genetic sub-populations (clades) of cosmopolitan marine diatom Pseudo-nitzschia pungens might have distinct habitats, and their hybrid zone is suspected in higher latitude area of the West Pacific area, however, it is still unrevealed because of technical difficulties and lack of evidences in natural environments. The aim of this study is to investigate the habitat characteristics of each clade of P. pungens on geographical distribution with the habitat temperature ranges of each clade and to reveal their hybrid zone in the West Pacific area. We employed the 137 number of nucleotide sequences of P. pungens and its sampling data (spatial and temporal scale) originated from the West Pacific area, and used field application of qPCR assay for intra-specific level of P. pungens. Only two genotypes, clade I and III, were identified in the West Pacific area. Clade I was distributed from 39 to 32.3°N, and clade III were from 1.4 to 34.4°N. The estimated habitat temperature for the clade I and clade III ranges were 8.1-26.9 °C and 24.2-31.2 °C, respectively. The latitudinal distributions and temperature ranges of each clade were significantly different. The qPCR assay employed, and results suggested that the hybrid zone for clade I and III has been observed in the southern Korean coasts, and clade III might be introduced from the Southern Pacific area. The cell abundances of clade III were strongly related with the higher seawater temperature and warm current force. This study has defined distinct habitat characteristics of genetically different sub-populations of P. pungens, and revealed its hybrid zone in natural environment for the first time. We also provided strong evidences about dispersion of the population of clade III to higher latitude in the West Pacific area. Copyright © 2018. Published by Elsevier B.V.

  7. Functional C1q is present in the skin mucus of Siberian sturgeon (Acipenser baerii).

    Fan, Chunxin; Wang, Jian; Zhang, Xuguang; Song, Jiakun

    2015-01-01

    The skin mucus of fish acts as the first line of self-protection against pathogens in the aquatic environment and comprises a number of innate immune components. However, the presence of the critical classical complement component C1q, which links the innate and adaptive immune systems of mammalians, has not been explored in a primitive actinopterygian fish. In this study, we report that C1q is present in the skin mucus of the Siberian sturgeon (Acipenser baerii). The skin mucus was able to inhibit the growth of Escherichia coli. The bacteriostatic activity of the skin mucus was reduced by heating and by pre-incubation with EDTA or mouse anti-human C1q antibody. We also detected C1q protein in skin mucus using the western blot procedure and isolated a cDNA that encodes the Siberian sturgeon C1qC, which had 44.7-51.4% identity with C1qCs in teleosts and tetrapods. A phylogenetic analysis revealed that Siberian sturgeon C1qC lies at the root of the actinopterygian branch and is separate from the tetrapod branch. The C1qC transcript was expressed in many tissues as well as in skin. Our data indicate that C1q is present in the skin mucus of the Siberian sturgeon to protect against water-borne bacteria, and the C1qC found in the sturgeon may represent the primitive form of teleost and tetrapod C1qCs. © 2014 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  8. Siberian snakes for the Fermilab Main Injector

    Anferov, V.A.; Baiod, R.; Courant, E.D.

    1993-01-01

    Appropriate Siberian snakes were designed to maintain the proton beam polarization during acceleration in the Fermilab Main Injector from 8 to 150 GeV. Various snake designs were investigated to find one fitting into the 14 m straight section spaces with the required spin rotation axis and the minimum orbit excursion. The authors studied both cold and warm discrete magnet snakes as well as warm snakes with helical magnets. For the warm discrete magnet snake, obtaining small orbit excursions required a nearly longitudinal snake axis, while axes near ±45 degrees are needed when using two snakes in a ring. The authors found acceptable snakes either by using superconducting magnets or by using warm magnets with a helical dipole field

  9. Field of a helical Siberian Snake

    Luccio, A. [Brookhaven National Lab., Upton, NY (United States)

    1995-02-01

    To preserve the spin polarization of a beam of high energy protons in a circular accelerator, magnets with periodic magnetic field, called Siberian Snakes are being used. Recently, it was proposed to build Siberian Snakes with superconducting helical dipoles. In a helical, or twisted dipole, the magnetic field is perpendicular to the axis of the helix and rotates around it as one proceeds along the magnet. In an engineering study of a 4 Tesla helical snake, the coil geometry is derived, by twisting, from the geometry of a cosine superconducting dipole. While waiting for magnetic measurement data on such a prototype, an analytical expression for the field of the helice is important, to calculate the particle trajectories and the spin precession in the helix. This model will also allow to determine the optical characteristics of the snake, as an insertion in the lattice of the accelerator. In particular, one can calculate the integrated multipoles through the magnet and the equivalent transfer matrix. An expression for the field in the helix body, i.e., excluding the fringe field was given in a classical paper. An alternate expression can be found by elaborating on the treatment of the field of a transverse wiggler obtained under the rather general conditions that the variables are separable. This expression exactly satisfies Maxwell`s div and curl equations for a stationary field, {del} {center_dot} B = 0, {del} x B = 0. This approach is useful in that it will allow one to use much of the work already done on the problem of inserting wigglers and undulators in the lattice of a circular accelerator.

  10. Complete mitochondrial genome of a wild Siberian tiger.

    Sun, Yujiao; Lu, Taofeng; Sun, Zhaohui; Guan, Weijun; Liu, Zhensheng; Teng, Liwei; Wang, Shuo; Ma, Yuehui

    2015-01-01

    In this study, the complete mitochondrial genome of Siberian tiger (Panthera tigris altaica) was sequenced, using muscle tissue obtained from a male wild tiger. The total length of the mitochondrial genome is 16,996 bp. The genome structure of this tiger is in accordance with other Siberian tigers and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes, and 1 control region.

  11. Siberian larch at the western edge of its area

    Kishchenko Ivan Tarasovich

    2015-06-01

    In the vertical structure of phytocenoses with Siberian larch up to 4 plant tiers are formed: the 1st and 2nd tier of the forest stand; the 3rd - grassy and shrubby; the 4th - mossy. The last two layers are usually developed very moderately, floristically poor and are noted for strong mosaic. There is no undergrowth. The reliable undergrowth of conifers is completely absent. Resumption of Siberian larch stopped 50-60 years ago.

  12. "European" race-specific metacentrics in East Siberian common shrews (Sorex araneus): a description of two new chromosomal races, Irkutsk and Zima.

    Pavlova, Svetlana V; Borisov, Sergei A; Timoshenko, Alexander F; Sheftel, Boris I

    2017-01-01

    Karyotype studies of common shrews in the vicinity of Lake Baikal (Irkutsk Region, Eastern Siberia) resulted in the description of two new chromosomal races of Sorex araneus Linnaeus, 1758 (Lypotyphla, Mammalia), additional to 5 races formerly found in Siberia. In the karyotypes of 12 specimens from 3 locations, the polymorphism of metacentric and acrocentric chromosomes of the Robertsonian type was recorded and two distinct groups of karyotypes interpreted as the chromosomal races were revealed. They are geographically distant and described under the racial names Irkutsk (Ir) and Zima (Zi). Karyotypes of both races were characterized by species-specific (the same for all 74 races known so far) metacentric autosomes af, bc, tu and jl , and the typical sex chromosome system - XX/XY 1 Y 2 . The race-specific arm chromosome combinations include three metacentrics and four acrocentrics in the Irkutsk race ( gk, hi, nq, m, o, p, r ) and four metacentrics and two acrocentrics in the Zima race ( gm, hi, ko, nq, p, r ). Within the races, individuals with polymorphic chromosomes were detected ( g/m, k/o, n/q, p/r ). The presence of the specific metacentric gk allowed us to include the Irkutsk race into the Siberian Karyotypic Group (SKG), distributed in surrounding regions. The Zima race karyotype contained two metacentrics, gm and ko , which have been never found in the Siberian part of the species range, but appear as the common feature of chromosomal races belonging to the West European Karyotypic Group (WEKG). Moreover, the metacentrics of that karyotype are almost identical to the Åkarp race (except the heterozygous pair p/r ) locally found in the southern Sweden. One of two Siberian races described here for the first time, the Zima race, occurs in an area considerably distant from Europe and shares the common metacentrics ( gm, hi, ko ) with races included in WEKG. This fact may support a hypothesis of independent formation of identical arm chromosome combinations

  13. Neomycin damage and regeneration of hair cells in both mechanoreceptor and electroreceptor lateral line organs of the larval Siberian sturgeon (Acipenser baerii).

    Fan, Chunxin; Zou, Sha; Wang, Jian; Zhang, Bo; Song, Jiakun

    2016-05-01

    The lateral line found in some amphibians and fishes has two distinctive classes of sensory organs: mechanoreceptors (neuromasts) and electroreceptors (ampullary organs). Hair cells in neuromasts can be damaged by aminoglycoside antibiotics and they will regenerate rapidly afterward. Aminoglycoside sensitivity and the capacity for regeneration have not been investigated in ampullary organs. We treated Siberian sturgeon (Acipenser baerii) larvae with neomycin and observed loss and regeneration of sensory hair cells in both organs by labeling with DASPEI and scanning electron microscopy (SEM). The numbers of sensory hair cells in both organs were reduced to the lowest levels at 6 hours posttreatment (hpt). New sensory hair cells began to appear at 12 hpt and were regenerated completely in 7 days. To reveal the possible mechanism for ampullary hair cell regeneration, we analyzed cell proliferation and the expression of neural placodal gene eya1 during regeneration. Both cell proliferation and eya1 expression were concentrated in peripheral mantle cells and both increased to the highest level at 12 hpt, which is consistent with the time course for regeneration of the ampullary hair cells. Furthermore, we used Texas Red-conjugated gentamicin in an uptake assay following pretreatment with a cation channel blocker (amiloride) and found that entry of the antibiotic was suppressed in both organs. Together, our results indicate that ampullary hair cells in Siberian sturgeon larvae can be damaged by neomycin exposure and they can regenerate rapidly. We suggest that the mechanisms for aminoglycoside uptake and hair cell regeneration are conserved for mechanoreceptors and electroreceptors. J. Comp. Neurol. 524:1443-1456, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  14. Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

    Malone, Kerri M.; Rue-Albrecht, Kévin; Magee, David A.; Conlon, Kevin; Schubert, Olga T.; Nalpas, Nicolas C.; Browne, John A.; Smyth, Alicia; Gormley, Eamonn; Aebersold, Ruedi; MacHugh, David E.; Gordon, Stephen V.

    2018-01-01

    Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection. PMID:29557774

  15. Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus.

    Teng, Jade L L; Huang, Yi; Tse, Herman; Chen, Jonathan H K; Tang, Ying; Lau, Susanna K P; Woo, Patrick C Y

    2014-10-20

    Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the "sanguinis group." As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the "mitis group." On the basis of the findings, we propose a novel group, named "sinensis group," to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-01-01

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

  17. Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

    King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

    2006-12-01

    Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

  18. Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models

    Brad A. Friedman

    2018-01-01

    Full Text Available Microglia, the CNS-resident immune cells, play important roles in disease, but the spectrum of their possible activation states is not well understood. We derived co-regulated gene modules from transcriptional profiles of CNS myeloid cells of diverse mouse models, including new tauopathy model datasets. Using these modules to interpret single-cell data from an Alzheimer’s disease (AD model, we identified microglial subsets—distinct from previously reported “disease-associated microglia”—expressing interferon-related or proliferation modules. We then analyzed whole-tissue RNA profiles from human neurodegenerative diseases, including a new AD dataset. Correcting for altered cellular composition of AD tissue, we observed elevated expression of the neurodegeneration-related modules, but also modules not implicated using expression profiles from mouse models alone. We provide a searchable, interactive database for exploring gene expression in all these datasets (http://research-pub.gene.com/BrainMyeloidLandscape. Understanding the dimensions of CNS myeloid cell activation in human disease may reveal opportunities for therapeutic intervention.

  19. Two distinct mtDNA lineages of the blue crab reveal large-scale population structure in its native Atlantic distribution

    Alaniz Rodrigues, Marcos; Dumont, Luiz Felipe Cestari; dos Santos, Cléverson Rannieri Meira; D'Incao, Fernando; Weiss, Steven; Froufe, Elsa

    2017-10-01

    For the first time, a molecular approach was used to evaluate the phylogenetic structure of the disjunct native American distribution of the blue crab Callinectes sapidus. Population structure was investigated by sequencing 648bp of the Cytochrome oxidase subunit 1 (COI), in a total of 138 sequences stemming from individual samples from both the northern and southern hemispheres of the Western Atlantic distribution of the species. A Bayesian approach was used to construct a phylogenetic tree for all samples, and a 95% confidence parsimony network was created to depict the relationship among haplotypes. Results revealed two highly distinct lineages, one containing all samples from the United States and some from Brazil (lineage 1) and the second restricted to Brazil (lineage 2). In addition, gene flow (at least for females) was detected among estuaries at local scales and there is evidence for shared haplotypes in the south. Furthermore, the findings of this investigation support the contemporary introduction of haplotypes that have apparently spread from the south to the north Atlantic.

  20. A comparative study on Ca content and distribution in two Gesneriaceae species reveals distinctive mechanisms to cope with high rhizospheric soluble calcium

    Wenlong eLi

    2014-11-01

    Full Text Available Excessive Ca is toxic to plants thus significantly affects plant growth and species distribution in Ca-rich karst areas. To understand how plants survive high Ca soil, laboratory experiments were established to compare the physiological responses and internal Ca distribution in organ, tissue, cell and intracellular levels under different Ca levels for Lysionotus pauciflorus and Boea hygrometrica, two karst habitant Gesneriaceae species in Southwest China. In the controlled condition, L. pauciflorus could survive as high as 200 mM rhizospheric soluble Ca, attributed to a series of physiological responses and preferential storage that limited Ca accumulation in chloroplasts of palisade cells. In contrast, B. hygrometrica could survive only 20 mM rhizospheric soluble Ca, but accumulated a high level of internal Ca in both palisade and spongy cells without disturbance on photosynthetic activity. By phenotype screening of transgenic plants expressing high Ca-inducible genes from B. hygrometrica, the expression of BhDNAJC2 in A. thaliana was found to enhance plant growth and photosynthesis under high soluble Ca stress. BhDNAJC2 encodes a recently reported heat shock protein (HSP 40 family DnaJ-domain protein. The Ca-resistant phenotype of BhDNAJC2 highlights the important role of chaperone-mediated protein quality control in Ca tolerance in B. hygrometrica. Taken together, our results revealed that distinctive mechanisms were employed in the two Gesneriaceae karst habitants to cope with a high Ca environment.

  1. Genome-wide analysis of cold adaptation in indigenous Siberian populations.

    Alexia Cardona

    Full Text Available Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66-69 Mb contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA and vascular smooth muscle contraction (PRKG1. By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

  2. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

    Lemieux Claude

    2006-02-01

    Full Text Available Abstract Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae, in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR featuring an inverted rRNA operon and a small single-copy (SSC region containing 14 genes normally found in the large single-copy (LSC region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of

  3. Numerical studies of Siberian snakes and spin rotators for RHIC

    Luccio, A.

    1995-01-01

    For the program of polarized protons in RHIC, two Siberian snakes and four spin rotators per ring will be used. The Snakes will produce a complete spin flip. Spin Rotators, in pairs, will rotate the spin from the vertical direction to the horizontal plane at a given insertion, and back to the vertical after the insertion. Snakes, 180 degrees apart and with their axis of spin precession at 90 degrees to each other, are an effective means to avoid depolarization of the proton beam in traversing resonances. Classical snakes and rotators are made with magnetic solenoids or with a sequence of magnetic dipoles with fields alternately directed in the radial and vertical direction. Another possibility is to use helical magnets, essentially twisted dipoles, in which the field, transverse the axis of the magnet, continuously rotates as the particles proceed along it. After some comparative studies, the authors decided to adopt for RHIC an elegant solution with four helical magnets both for the snakes and the rotators proposed by Shatunov and Ptitsin. In order to simplify the construction of the magnets and to minimize cost, four identical super conducting helical modules will be used for each device. Snakes will be built with four right-handed helices. Spin rotators with two right-handed and two left-handed helices. The maximum field will be limited to 4 Tesla. While small bore helical undulators have been built for free electron lasers, large super conducting helical magnets have not been built yet. In spite of this difficulty, this choice is dictated by some distinctive advantages of helical over more conventional transverse snakes/rotators: (i) the devices are modular, they can be built with arrangements of identical modules, (ii) the maximum orbit excursion in the magnet is smaller, (iii) orbit excursion is independent from the separation between adjacent magnets, (iv) they allow an easier control of the spin rotation and the orientation of the spin precession axis

  4. Distinct steps of neural induction revealed by Asterix, Obelix and TrkC, genes induced by different signals from the organizer.

    Sonia Pinho

    2011-04-01

    Full Text Available The amniote organizer (Hensen's node can induce a complete nervous system when grafted into a peripheral region of a host embryo. Although BMP inhibition has been implicated in neural induction, non-neural cells cannot respond to BMP antagonists unless previously exposed to a node graft for at least 5 hours before BMP inhibitors. To define signals and responses during the first 5 hours of node signals, a differential screen was conducted. Here we describe three early response genes: two of them, Asterix and Obelix, encode previously undescribed proteins of unknown function but Obelix appears to be a nuclear RNA-binding protein. The third is TrkC, a neurotrophin receptor. All three genes are induced by a node graft within 4-5 hours but they differ in the extent to which they are inducible by FGF: FGF is both necessary and sufficient to induce Asterix, sufficient but not necessary to induce Obelix and neither sufficient nor necessary for induction of TrkC. These genes are also not induced by retinoic acid, Noggin, Chordin, Dkk1, Cerberus, HGF/SF, Somatostatin or ionomycin-mediated Calcium entry. Comparison of the expression and regulation of these genes with other early neural markers reveals three distinct "epochs", or temporal waves, of gene expression accompanying neural induction by a grafted organizer, which are mirrored by specific stages of normal neural plate development. The results are consistent with neural induction being a cascade of responses elicited by different signals, culminating in the formation of a patterned nervous system.

  5. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  6. Whole-genome sequence of a novel Chinese cyprinid herpesvirus 3 isolate reveals the existence of a distinct European genotype in East Asia.

    Li, Wei; Lee, Xuezhu; Weng, Shaoping; He, Jianguo; Dong, Chuanfu

    2015-02-25

    Cyprinid herpesvirus 3 (CyHV3), also known as koi herpesvirus (KHV), can be subdivided primarily into European and Asian genotypes, which are represented by CyHV3-U or CyHV3-I and CyHV3-J, respectively. In this study, the whole genome sequence of a novel Chinese CyHV3 isolate (GZ11) was determined and annotated. CyHV3-GZ11 genome was found to contain 295,119 nucleotides with 52.9% G/C content, which is highly similar to those of published CyHV3-U, CyHV3-I, and CyHV3-J strains. With reference to CyHV3-U, CyHV3-I, and CyHV3-J, CyHV3-GZ11 was also classified into 164 open reading frames (ORF), which include eight repeated ORFs. On the basis of the 12 alloherpeviruses core genes, results from phylogenetic analysis showed that CyHV3-GZ11 had closer evolutionary relationships with CyHV3-U and CyHV3-I than with CyHV3/KHV-J, which were also supported by genome wide-based single nucleotide substitution analysis and the use of a series of developed molecular markers. This study was the first to reveal the presence of a distinct European CyHV3 genotype in East and Southeast Asia at a whole genome level, which will evoke new insights on exploring the origin, evolution, and epidemiology of the virus. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.

    Chen, Yaozong; Li, Tin Lok; Lin, Xingbang; Li, Xin; Li, Xiang David; Guo, Zhihong

    2017-07-21

    o -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins*

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-01

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. PMID:27927989

  9. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins.

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-20

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. 5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells.

    Krzysztof Poterlowicz

    2017-09-01

    Full Text Available Mammalian genomes contain several dozens of large (>0.5 Mbp lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene

  11. Characterization of a siberian virus isolated from a patient with progressive chronic tick-borne encephalitis.

    Gritsun, T S; Frolova, T V; Zhankov, A I; Armesto, M; Turner, S L; Frolova, M P; Pogodina, V V; Lashkevich, V A; Gould, E A

    2003-01-01

    A strain of Tick-borne encephalitis virus designated Zausaev (Za) was isolated in Siberia from a patient who died of a progressive (2-year) form of tick-borne encephalitis 10 years after being bitten by a tick. The complete genomic sequence of this virus was determined, and an attempt was made to correlate the sequence with the biological characteristics of the virus. Phylogenetic analysis demonstrated that this virus belongs to the Siberian subtype of Tick-borne encephalitis virus. Comparison of Za virus with two related viruses, a Far Eastern isolate, Sofjin, and a Siberian isolate, Vasilchenko, revealed differences among the three viruses in pathogenicity for Syrian hamsters, cytopathogenicity for PS cells, plaque morphology, and the electrophoretic profiles of virus-specific nonstructural proteins. Comparative amino acid alignments revealed 10 individual amino acid substitutions in the Za virus polyprotein sequence that were different from those of other tick-borne flaviviruses. Notably, the dimeric form of the Za virus NS1 protein migrated in polyacrylamide gels as a heterogeneous group of molecules with a significantly higher electrophoretic mobility than those of the Sofjin and Vasilchenko viruses. Two amino acid substitutions, T(277)-->V and E(279)-->G, within the NS1 dimerization domain are probably responsible for the altered oligomerization of Za virus NS1. These studies suggest that the patient from whom Za virus was isolated died due to increased pathogenicity of the latent virus following spontaneous mutagenesis.

  12. Accretionary Tectonics of Rock Complexes in the Western Margin of the Siberian Craton

    Likhanov, I. I.; Nozhkin, A. D.; Savko, K. A.

    2018-01-01

    The geological, geochemical, and isotope-geochronological evidence of the events at the final stage of the Neoproterozoic history of the Yenisei Range is considered (beginning from the formation of fragments of the oceanic crust in the region and their accretion to the Siberian Craton until the postaccretionary stage of crustal tension and onset of the Caledonian orogeny). Based on an analysis of new data on the petrogeochemical composition, age, and geodynamic nature of the formation of contrasting rocks in the composition of tectonic mélange of the Near-Yenisei (Prieniseiskaya) regional shear zone, we have found the chronological sequence of events that marks the early stages of the Paleoasian Ocean evolution in the zone of its junction with the Siberian Craton. These events are documented by the continental marginal, ophiolitic, and island-arc geological complexes, each of which has different geochemical features. The most ancient structures are represented by fragments of oceanic crust and island arcs from the Isakovka terrane (700-620 Ma). The age of glaucophane-schist metamorphic units that formed in the paleosubduction zone corresponds to the time interval of 640-620 Ma. The formation of high-pressure tectonites in the suture zone, about 600 Ma in age, marks the finishing stage of accretion of the Isakovka block to the western margin of the Siberian Craton. The final events in the early history of the Asian Paleoocean were related to the formation of Late Vendian riftogenic amygdaloidal basalts (572 ± 6.5 Ma) and intrusion of postcollisional leucogranites of the Osinovka massif (550-540 Ma), which intruded earlier fragments of the oceanic crust in the Isakovka terrane. These data allow us to refine the Late Precambrian stratigraphic scheme in the northwestern Trans-Angarian part of the Yenisei Range and the evolutionary features of the Sayan-Yenisei accretionary belt. The revealed Late Neoproterozoic landmarks of the evolution of the Isakovka terrane are

  13. Aging in the Soviet Union: A West Siberian Perspective.

    Demitri, Shimkin

    1989-01-01

    Presents ethnographic observations on the aged and aging from six months' residence in Siberian industrial city. Describes interactions with medical personnel and reviews scanty literature in Soviet Union. Notes integration of aged in families and respect given to older persons. Discusses problems of elderly caused by hard living conditions,…

  14. The problem of radiative depolarization in the 'Siberian Snake'

    Schwitters, R.

    1979-01-01

    As pointed out by Derbenev and Kondratenko and by the LEP Study Group, a 'Siberian Snake' may be a convenient method for providing longitudinally polarized beams at LEP. The author shows that at the highest LEP energies (approximately>60 GeV) synchrotron radiation with spin-flip may depolarize the beams. (Auth.)

  15. IMPACT OF ALL-UNION AND SIBERIAN PRESS OF 1920S ON FORMATION OF SIBERIAN WOMEN'S NEW BEHAVIORAL PATTERNS

    Мария Владимировна Васеха

    2015-12-01

    Full Text Available The article deals with specialized women's media and their role in the formation of new behavioral patterns of peasant women in the first decade of the Soviet period. The author analyzes the main behavior models, life strategies proposed for the “new” “liberated” Soviet women in media. In addition to the well-known all-Union magazines “The Communist woman” and "The Peasant Woman" in this article there were used Siberian media - the magazines “The Red Siberian Woman” and “The Siberian village”. The regional press, not so official, adapted to local realities, gives the researcher valuable representation of the Soviet propaganda influence in Siberian backwoods. The press modeled more “effective” life scenarios; women were encouraged to take up activity-position to take unconventional solutions to change theirs “hard fate”, “women's destiny”. It is important to note that the proposed patterns of behavior are not very diverse campaigning rid of “oppressive fathers, brothers and husbands”. All the scenarios again boiled down to the idea of service, but this time to the public interest. Thus, the policy of "emancipation of women" for the most part was reduced to the integration of women in the public space, without trying to understand their true needs, to take into account their aspirations and, ultimately, to protect their best interests.

  16. The Middle and Upper Eocene sections of the Omsk trough, West Siberian Platform: Palynological, stratigraphic, hydrologic, and climatic aspects

    Zaporozhets, N. I.; Akhmetiev, M. A.

    2013-01-01

    The thorough analysis and correlation of Middle-Upper Eocene sections in the Omsk trough (southern West Siberian Platform) recovered by Borehole 9 in its axial part near the Chistoozernoe Settlement (Novosibirsk region) and Borehole 8 on the southern limb near the Russkaya Polyana Settlement (southern Omsk region) revealed hiatuses at the base and top of the Russkaya Polyana Beds, a lithostratigraphic unit defined in the Lyulinvor Formation based on its substantially fine-grained composition and poor siliceous microplankton fossil remains. The overlying Tavda Formation (Middle-Upper Eocene) is traditionally accepted to consist of two subformations. The last formation was deposited in the West Siberian inner sea isolated from the Arctic basin. Particular attention is paid to eustatic sea level fluctuation especially during the period marked by accumulation of Azolla Beds under considerable desalination of surface waters in the basin. The curve of variations in the open sea factor based on the quantitative ratio between organic-walled phytoplankton fossils and higher plant palynomorphs is correlated with the modified version of the wellknown Vail curve. It is established that the West Siberian sea level experienced a brief rise in the terminal late Eocene prior to its complete desiccation at the Eocene-Oligocene transition because of global regression in response to glaciation in Antarctica.

  17. Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas.

    Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

    2017-08-15

    In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenuated combination CDV vaccine was used among almost all carnivore animals except for red pandas in which another recombinant combination CDV vaccine was used. However, about two months later, CDV re-emerged and caused the death among red pandas. Based on the vaccination records, the live combination vaccine could be considered an ideal weapon against CDV in zoo carnivore animals. Although the recombinant combination CDV vaccine was safe for red pandas, its protection effectiveness remains to be further investigated. Moreover, according to the outbreak interval time and sequence characterization, we suspected that stray cats circulating in the zoo were the intermediate host, which contributed to CDV spread from stray dogs to zoo animals. This study revealed the importance of vaccination and biosecurity for zoo animals.

  18. Genetic diversity of Siberian stone pine under introduction in the South Urals and Bashkir Cis-Urals

    Z. Kh. Shigapov

    2016-10-01

    Full Text Available Allozyme polymorphism of Siberian stone pine Pinus sibirica Du Tour has been studied in 14 artificial stands in the South Urals and Bashkir Cis-Urals on the base of 7 gene-enzyme system analysis. The following values of genetic diversity are determined: mean number of alleles per locus (A constitutes 1.69±0.08; portion of polymorphic loci (P95 – 50.0 %; the average expected heterozygosity (He – 0.121±0.015; the average observed heterozygosity (Ho – 0.127±0.017.The level of genetic variability in artificial stands of Siberian stone pine in the region is somewhat inferior to that in natural populations of the species. The highest genotype heterozygosity is determined in high-productive 110 year-old artificial stand in the South Urals (Beloretsky-2 site, and also in Ufimsky and Mishkinsky sites in Bashkir Cis-Urals. The lowest heterozygosity values are revealed in Birsky and Tuimazinsky sites characterized by the weakened vital state of individuals. In total we can speak about the maintenance of essential part of the species’ genetic polymorphism under introduction, especially in some stands. Genetic similarity of the studied stands is shown: inter-sample component of the total genetic diversity (FST constitutes 2.2 %, the average Nei’s genetic distance (D – 0.0033±0.00023, that is also typical of natural populations of Siberian stone pine in the species range. The obtained data about the genetic variability level of artificial stands in a complex with forestry characteristics give evidence of the successful species introduction in the region and the necessity of resumption of works on Siberian stone pine culture establishment in an industrial scale.

  19. Central Siberian taiga mapping using by SPOT 4 and inventory data

    Romanov, Aleksey

    2013-04-01

    training samples set has been extended manually based on the expert assessment of the first stage results. Further process was in a several iteration expanding the area for classification. The final stage classification was based on two approaches: statistical and neural network. The main problem of the first classification phase was a high degree of heterogeneity of the Reserve territory due to mixed forests; currently fuzzy neural network algorithm is under development to resolve it. The main results of the first stage of project are: percentage analysis of tree species in the Reserve (Table 1) and also geo-information analysis revealed the relationship of vegetation (tree species) distribution on the altitude. #Tree species Percentage of test forestry polygon over 70 sq km 1Pinus sibirica 24.7 2Birch (Betula) 34.3 3Siberian Spruce (Picea obovata)22.1 4Scots Pine (Pinus sylvestris) 5.3 5Larches (Larix) 7.3 6Aspen Populus tremula 3.6 7Siberian Fir 2.1 8 Other formations

  20. Complete identification of E-selectin ligand activity on neutrophils reveals a dynamic interplay and distinct functions of PSGL-1, ESL-1 and CD44

    Wild, Martin; Vestweber, Dietmar; Frenette, Paul S.

    2014-01-01

    SUMMARY The selectins and their ligands are required for leukocyte extravasation during inflammation. Several glycoproteins have been suggested to bind to E-selectin in vitro but the complete identification of its physiological ligands has remained elusive. Here, we show using gene- and RNA-targeted loss-of-function that E-selectin ligand-1 (ESL-1), PSGL-1 and CD44 encompass all endothelial selectin ligand activity on neutrophils. PSGL-1 plays a major role in the initial leukocyte capture, while ESL-1 is critical to convert initial tethers into steady slow rolling. CD44 controls rolling velocity and mediates E-selectin-dependent redistribution of PSGL-1 and L-selectin to a major pole on slowly rolling leukocytes through p38 signaling. These results suggest distinct and dynamic contributions of these three glycoproteins in selectin-mediated neutrophil adhesion and signaling. PMID:17442598

  1. An optimized histochemical method to assess skeletal muscle glycogen and lipid stores reveals two metabolically distinct populations of type I muscle fibers

    Prats Gavalda, Clara; Gomez-Cabello, Alba; Nordby, Pernille

    2013-01-01

    Skeletal muscle energy metabolism has been a research focus of physiologists for more than a century. Yet, how the use of intramuscular carbohydrate and lipid energy stores are coordinated during different types of exercise remains a subject of debate. Controversy arises from contradicting data...... preservation of muscle energy stores, air drying cryosections or cycles of freezing-thawing need to be avoided. Furthermore, optimization of the imaging settings in order to specifically image intracellular lipid droplets stained with oil red O or Bodipy-493/503 is shown. When co-staining lipid droplets...... distinct myosin heavy chain I expressing fibers: I-1 fibers have a smaller crossectional area, a higher density of lipid droplets, and a tendency to lower glycogen content compared to I-2 fibers. Type I-2 fibers have similar lipid content than IIA. Exhaustive exercise lead to glycogen depletion in type IIA...

  2. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

    Wen, Jiayu; Parker, Brian J; Jacobsen, Anders

    2011-01-01

    the predictive effect of target flanking features. We observe distinct target determinants between expression-based and CLIP-based data. Target flanking features such as flanking region conservation are an important AGO-binding determinant-we hypothesize that CLIP experiments have a preference for strongly bound......Microarray expression analyses following miRNA transfection/inhibition and, more recently, Argonaute cross-linked immunoprecipitation (CLIP)-seq assays have been used to detect miRNA target sites. CLIP and expression approaches measure differing stages of miRNA functioning-initial binding of the mi...... miRNP-target interactions involving adjacent RNA-binding proteins that increase the strength of cross-linking. In contrast, seed-related features are major determinants in expression-based studies, but less so for CLIP-seq studies, and increased miRNA concentrations typical of transfection studies...

  3. Mutant Allele-Specific Uncoupling of PENETRATION3 Functions Reveals Engagement of the ATP-Binding Cassette Transporter in Distinct Tryptophan Metabolic Pathways1[OPEN

    Lu, Xunli; Dittgen, Jan; Piślewska-Bednarek, Mariola; Molina, Antonio; Schneider, Bernd; Doubský, Jan; Schneeberger, Korbinian; Schulze-Lefert, Paul

    2015-01-01

    Arabidopsis (Arabidopsis thaliana) PENETRATION (PEN) genes quantitatively contribute to the execution of different forms of plant immunity upon challenge with diverse leaf pathogens. PEN3 encodes a plasma membrane-resident pleiotropic drug resistance-type ATP-binding cassette transporter and is thought to act in a pathogen-inducible and PEN2 myrosinase-dependent metabolic pathway in extracellular defense. This metabolic pathway directs the intracellular biosynthesis and activation of tryptophan-derived indole glucosinolates for subsequent PEN3-mediated efflux across the plasma membrane at pathogen contact sites. However, PEN3 also functions in abiotic stress responses to cadmium and indole-3-butyric acid (IBA)-mediated auxin homeostasis in roots, raising the possibility that PEN3 exports multiple functionally unrelated substrates. Here, we describe the isolation of a pen3 allele, designated pen3-5, that encodes a dysfunctional protein that accumulates in planta like wild-type PEN3. The specific mutation in pen3-5 uncouples PEN3 functions in IBA-stimulated root growth modulation, callose deposition induced with a conserved peptide epitope of bacterial flagellin (flg22), and pathogen-inducible salicylic acid accumulation from PEN3 activity in extracellular defense, indicating the engagement of multiple PEN3 substrates in different PEN3-dependent biological processes. We identified 4-O-β-d-glucosyl-indol-3-yl formamide (4OGlcI3F) as a pathogen-inducible, tryptophan-derived compound that overaccumulates in pen3 leaf tissue and has biosynthesis that is dependent on an intact PEN2 metabolic pathway. We propose that a precursor of 4OGlcI3F is the PEN3 substrate in extracellular pathogen defense. These precursors, the shared indole core present in IBA and 4OGlcI3F, and allele-specific uncoupling of a subset of PEN3 functions suggest that PEN3 transports distinct indole-type metabolites in distinct biological processes. PMID:26023163

  4. Ecology of nonnative Siberian prawn (Palaemon modestus) in the lower Snake River, Washington, USA

    Erhardt, John M.; Tiffan, Kenneth F.

    2016-01-01

    We assessed the abundance, distribution, and ecology of the nonnative Siberian prawn Palaemon modestus in the lower Snake River, Washington, USA. Analysis of prawn passage abundance at three Snake River dams showed that populations are growing at exponential rates, especially at Little Goose Dam where over 464,000 prawns were collected in 2015. Monthly beam trawling during 2011–2013 provided information on prawn abundance and distribution in Lower Granite and Little Goose Reservoirs. Zero-inflated regression predicted that the probability of prawn presence increased with decreasing water velocity and increasing depth. Negative binomial models predicted higher catch rates of prawns in deeper water and in closer proximity to dams. Temporally, prawn densities decreased slightly in the summer, likely due to the mortality of older individuals, and then increased in autumn and winter with the emergence and recruitment of young of the year. Seasonal length frequencies showed that distinct juvenile and adult size classes exist throughout the year, suggesting prawns live from 1 to 2 years and may be able to reproduce multiple times during their life. Most juvenile prawns become reproductive adults in 1 year, and peak reproduction occurs from late July through October. Mean fecundity (189 eggs) and reproductive output (11.9 %) are similar to that in their native range. The current use of deep habitats by prawns likely makes them unavailable to most predators in the reservoirs. The distribution and role of Siberian prawns in the lower Snake River food web will probably continue to change as the population grows and warrants continued monitoring and investigation.

  5. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci.

    Smeets, Daniel; Markaki, Yolanda; Schmid, Volker J; Kraus, Felix; Tattermusch, Anna; Cerase, Andrea; Sterr, Michael; Fiedler, Susanne; Demmerle, Justin; Popken, Jens; Leonhardt, Heinrich; Brockdorff, Neil; Cremer, Thomas; Schermelleh, Lothar; Cremer, Marion

    2014-01-01

    A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs). We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an 'autosomal Barr body' with less compacted chromatin and incomplete RNAP II exclusion. 3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform

  6. Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

    Gavrilov, Sergey; Podosokorskaya, Olga; Alexeev, Dmitry; Merkel, Alexander; Khomyakova, Maria; Muntyan, Maria; Altukhov, Ilya; Butenko, Ivan; Bonch-Osmolovskaya, Elizaveta; Govorun, Vadim; Kublanov, Ilya

    2017-01-01

    Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods. PMID:28713355

  7. Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

    Sergey Gavrilov

    2017-06-01

    Full Text Available Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/bo3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/bo3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.

  8. Eosinophilic granulomatous gastroenterocolitis and hepatitis in a 1-year-old male Siberian Husky.

    Brellou, G D; Kleinschmidt, S; Meneses, F; Nolte, I; Hewicker-Trautwein, M

    2006-11-01

    A case of eosinophilic granulomatous gastroenterocolitis and hepatitis in a 1-year-old male Siberian Husky is described. The dog presented with a history of diarrhea, weakness, lethargy, and anorexia of several months' duration. Hematologic and biochemical examinations, abdominal ultrasonography, computer tomography, and exploratory laparotomy were performed. Histopathologic examination of full-thickness biopsies from the gastrointestinal tract and liver revealed the presence of eosinophilic granulomatous lesions in the submucosa and tunica muscularis of stomach, jejunum, ileum, colon, and liver. Infectious agents were not detected by light microscopic and electron microscopic examination or by immunohistochemistry. On the basis of the findings, it is concluded that the disease in this dog represents an unusual manifestation of chronic idiopathic inflammatory bowel disease.

  9. Distinct abscisic acid signaling pathways for modulation of guard cell versus mesophyll cell potassium channels revealed by expression studies in Xenopus laevis oocytes

    Sutton, F.; Paul, S. S.; Wang, X. Q.; Assmann, S. M.; Evans, M. L. (Principal Investigator)

    2000-01-01

    Regulation of guard cell ion transport by abscisic acid (ABA) and in particular ABA inhibition of a guard cell inward K(+) current (I(Kin)) is well documented. However, little is known concerning ABA effects on ion transport in other plant cell types. Here we applied patch clamp techniques to mesophyll cell protoplasts of fava bean (Vicia faba cv Long Pod) plants and demonstrated ABA inhibition of an outward K(+) current (I(Kout)). When mesophyll cell protoplast mRNA (mesophyll mRNA) was expressed in Xenopus laevis oocytes, I(Kout) was generated that displayed similar properties to I(Kout) observed from direct analysis of mesophyll cell protoplasts. I(Kout) expressed by mesophyll mRNA-injected oocytes was inhibited by ABA, indicating that the ABA signal transduction pathway observed in mesophyll cells was preserved in the frog oocytes. Co-injection of oocytes with guard cell protoplast mRNA and cRNA for KAT1, an inward K(+) channel expressed in guard cells, resulted in I(Kin) that was similarly inhibited by ABA. However, oocytes co-injected with mesophyll mRNA and KAT1 cRNA produced I(Kin) that was not inhibited by ABA. These results demonstrate that the mesophyll-encoded signaling mechanism could not substitute for the guard cell pathway. These findings indicate that mesophyll cells and guard cells use distinct and different receptor types and/or signal transduction pathways in ABA regulation of K(+) channels.

  10. Serum metabolomics analysis of patients with chikungunya and dengue mono/co-infections reveals distinct metabolite signatures in the three disease conditions

    Shrinet, Jatin; Shastri, Jayanthi S.; Gaind, Rajni; Bhavesh, Neel Sarovar; Sunil, Sujatha

    2016-11-01

    Chikungunya and dengue are arboviral infections with overlapping clinical symptoms. A subset of chikungunya infection occurs also as co-infections with dengue, resulting in complications during diagnosis and patient management. The present study was undertaken to identify the global metabolome of patient sera infected with chikungunya as mono infections and with dengue as co-infections. Using nuclear magnetic resonance (NMR) spectroscopy, the metabolome of sera of three disease conditions, namely, chikungunya and dengue as mono-infections and when co-infected were ascertained and compared with healthy individuals. Further, the cohorts were analyzed on the basis of age, onset of fever and joint involvement. Here we show that many metabolites in the serum are significantly differentially regulated during chikungunya mono-infection as well as during chikungunya co-infection with dengue. We observed that glycine, serine, threonine, galactose and pyrimidine metabolisms are the most perturbed pathways in both mono and co-infection conditions. The affected pathways in our study correlate well with the clinical manifestation like fever, inflammation, energy deprivation and joint pain during the infections. These results may serve as a starting point for validations and identification of distinct biomolecules that could be exploited as biomarker candidates thereby helping in better patient management.

  11. The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination

    Ding Guohui

    2007-04-01

    Full Text Available Abstract Background Conidia are considered to be the primary cause of infections by Trichophyton rubrum. Results We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD. A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Conclusion Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.

  12. Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level.

    Andrew R Dalby

    Full Text Available Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that sub-classes were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC.

  13. Detailed LC-MS/MS analysis of ciguatoxins revealing distinct regional and species characteristics in fish and causative alga from the Pacific.

    Yogi, Kentaro; Oshiro, Naomasa; Inafuku, Yasuo; Hirama, Masahiro; Yasumoto, Takeshi

    2011-12-01

    Toxin profiles of representative ciguatera species caught at different locations of Japan were investigated in fish flesh by high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Identification and quantification of 16 toxins were facilitated by the use of 14 reference toxins prepared by either synthesis or isolation from natural sources and the previous LC-MS data thereof. Sodium adduct ions [M + Na](+) were used as parent and product ions. Distinct regional differences were unveiled: ciguatoxin-1B type toxins were found in snappers and groupers from Okinawa, ciguatoxin-3C type toxins were found in a spotted knifejaw, Oplegnathus punctatus, from Miyazaki located 730 km north of Okinawa, and both types of toxins were found in a red snapper, Lutjanus bohar, from Minamitorishima (Marcus) Island. Twelve toxins were identified in a dinoflagellate, Gambierdiscus toxicus, collected as the primary toxin source in French Polynesia. Occurrence of M-seco-toxins in fish and oxidized toxins in the dinoflagellate was confirmed for the first time. The present LC-MS/MS method is rapid, specific, and accurate. It not only outperforms the currently employed mouse bioassays but also enables the study of the toxin dynamics during the food chain transmission.

  14. Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants

    McClure Myra

    2011-07-01

    Full Text Available Abstract Background To combat the pandemic of human immunodeficiency virus 1 (HIV-1, a successful vaccine will need to cope with the variability of transmissible viruses. Human hosts infected with HIV-1 potentially harbour many viral variants but very little is known about viruses that are likely to be transmitted, or even if there are viral characteristics that predict enhanced transmission in vivo. We show for the first time that genetic divergence consistent with a single transmission event in vivo can represent several years of pre-transmission evolution. Results We describe a highly unusual case consistent with a single donor transmitting highly related but distinct HIV-1 variants to two individuals on the same evening. We confirm that the clustering of viral genetic sequences, present within each recipient, is consistent with the history of a single donor across the viral env, gag and pol genes by maximum likelihood and Bayesian Markov Chain Monte Carlo based phylogenetic analyses. Based on an uncorrelated, lognormal relaxed clock of env gene evolution calibrated with other datasets, the time since the most recent common ancestor is estimated as 2.86 years prior to transmission (95% confidence interval 1.28 to 4.54 years. Conclusion Our results show that an effective design for a preventative vaccine will need to anticipate extensive HIV-1 diversity within an individual donor as well as diversity at the population level.

  15. Distinct spatio-temporal profiles of beta-oscillations within visual and sensorimotor areas during action recognition as revealed by MEG.

    Pavlidou, Anastasia; Schnitzler, Alfons; Lange, Joachim

    2014-05-01

    The neural correlates of action recognition have been widely studied in visual and sensorimotor areas of the human brain. However, the role of neuronal oscillations involved during the process of action recognition remains unclear. Here, we were interested in how the plausibility of an action modulates neuronal oscillations in visual and sensorimotor areas. Subjects viewed point-light displays (PLDs) of biomechanically plausible and implausible versions of the same actions. Using magnetoencephalography (MEG), we examined dynamic changes of oscillatory activity during these action recognition processes. While both actions elicited oscillatory activity in visual and sensorimotor areas in several frequency bands, a significant difference was confined to the beta-band (∼20 Hz). An increase of power for plausible actions was observed in left temporal, parieto-occipital and sensorimotor areas of the brain, in the beta-band in successive order between 1650 and 2650 msec. These distinct spatio-temporal beta-band profiles suggest that the action recognition process is modulated by the degree of biomechanical plausibility of the action, and that spectral power in the beta-band may provide a functional interaction between visual and sensorimotor areas in humans. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Profiling of wheat class III peroxidase genes derived from powdery mildew-attacked epidermis reveals distinct sequence-associated expression patterns.

    Liu, Guosheng; Sheng, Xiaoyan; Greenshields, David L; Ogieglo, Adam; Kaminskyj, Susan; Selvaraj, Gopalan; Wei, Yangdou

    2005-07-01

    A cDNA library was constructed from leaf epidermis of diploid wheat (Triticum monococcum) infected with the powdery mildew fungus (Blumeria graminis f. sp. tritici) and was screened for genes encoding peroxidases. From 2,500 expressed sequence tags (ESTs), 36 cDNAs representing 10 peroxidase genes (designated TmPRX1 to TmPRX10) were isolated and further characterized. Alignment of the deduced amino acid sequences and phylogenetic clustering with peroxidases from other plant species demonstrated that these peroxidases fall into four distinct groups. Differential expression and tissue-specific localization among the members were observed during the B. graminis f. sp. tritici attack using Northern blots and reverse-transcriptase polymerase chain reaction analyses. Consistent with its abundance in the EST collection, TmPRX1 expression showed the highest induction during pathogen attack and fluctuated in response to the fungal parasitic stages. TmPRX1 to TmPRX6 were expressed predominantly in mesophyll cells, whereas TmPRX7 to TmPRX10, which feature a putative C-terminal propeptide, were detectable mainly in epidermal cells. Using TmPRX8 as a representative, we demonstrated that its C-terminal propeptide was sufficient to target a green fluorescent protein fusion protein to the vacuoles in onion cells. Finally, differential expression profiles of the TmPRXs after abiotic stresses and signal molecule treatments were used to dissect the potential role of these peroxidases in multiple stress and defense pathways.

  17. Distinguishing Clouds from Ice over the East Siberian Sea, Russia

    2002-01-01

    As a consequence of its capability to retrieve cloud-top elevations, stereoscopic observations from the Multi-angle Imaging SpectroRadiometer (MISR) can discriminate clouds from snow and ice. The central portion of Russia's East Siberian Sea, including one of the New Siberian Islands, Novaya Sibir, are portrayed in these views from data acquired on May 28, 2002.The left-hand image is a natural color view from MISR's nadir camera. On the right is a height field retrieved using automated computer processing of data from multiple MISR cameras. Although both clouds and ice appear white in the natural color view, the stereoscopic retrievals are able to identify elevated clouds based on the geometric parallax which results when they are observed from different angles. Owing to their elevation above sea level, clouds are mapped as green and yellow areas, whereas land, sea ice, and very low clouds appear blue and purple. Purple, in particular, denotes elevations very close to sea level. The island of Novaya Sibir is located in the lower left of the images. It can be identified in the natural color view as the dark area surrounded by an expanse of fast ice. In the stereo map the island appears as a blue region indicating its elevation of less than 100 meters above sea level. Areas where the automated stereo processing failed due to lack of sufficient spatial contrast are shown in dark gray. The northern edge of the Siberian mainland can be found at the very bottom of the panels, and is located a little over 250 kilometers south of Novaya Sibir. Pack ice containing numerous fragmented ice floes surrounds the fast ice, and narrow areas of open ocean are visible.The East Siberian Sea is part of the Arctic Ocean and is ice-covered most of the year. The New Siberian Islands are almost always covered by snow and ice, and tundra vegetation is very scant. Despite continuous sunlight from the end of April until the middle of August, the ice between the island and the mainland

  18. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.

    Murphy, Derek M

    2009-01-01

    BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified\\/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the

  19. Distinctive Citizenship

    Kaur, Ravinder

    2009-01-01

    The refugee, in India's Partition history, appears as an enigmatic construct - part pitiful, part heroic, though mostly shorn of agency - representing the surface of the human tragedy of Partition. Yet this archetype masks the undercurrent of social distinctions that produced hierarchies of post...

  20. Model-Based Analysis of Arabidopsis Leaf Epidermal Cells Reveals Distinct Division and Expansion Patterns for Pavement and Guard Cells1[W][OA

    Asl, Leila Kheibarshekan; Dhondt, Stijn; Boudolf, Véronique; Beemster, Gerrit T.S.; Beeckman, Tom; Inzé, Dirk; Govaerts, Willy; De Veylder, Lieven

    2011-01-01

    To efficiently capture sunlight for photosynthesis, leaves typically develop into a flat and thin structure. This development is driven by cell division and expansion, but the individual contribution of these processes is currently unknown, mainly because of the experimental difficulties to disentangle them in a developing organ, due to their tight interconnection. To circumvent this problem, we built a mathematic model that describes the possible division patterns and expansion rates for individual epidermal cells. This model was used to fit experimental data on cell numbers and sizes obtained over time intervals of 1 d throughout the development of the first leaf pair of Arabidopsis (Arabidopsis thaliana). The parameters were obtained by a derivative-free optimization method that minimizes the differences between the predicted and experimentally observed cell size distributions. The model allowed us to calculate probabilities for a cell to divide into guard or pavement cells, the maximum size at which it can divide, and its average cell division and expansion rates at each point during the leaf developmental process. Surprisingly, average cell cycle duration remained constant throughout leaf development, whereas no evidence for a maximum cell size threshold for cell division of pavement cells was found. Furthermore, the model predicted that neighboring cells of different sizes within the epidermis expand at distinctly different relative rates, which could be verified by direct observations. We conclude that cell division seems to occur independently from the status of cell expansion, whereas the cell cycle might act as a timer rather than as a size-regulated machinery. PMID:21693673

  1. A global RNA-seq-driven analysis of CHO host and production cell lines reveals distinct differential expression patterns of genes contributing to recombinant antibody glycosylation.

    Könitzer, Jennifer D; Müller, Markus M; Leparc, Germán; Pauers, Martin; Bechmann, Jan; Schulz, Patrick; Schaub, Jochen; Enenkel, Barbara; Hildebrandt, Tobias; Hampel, Martin; Tolstrup, Anne B

    2015-09-01

    Boehringer Ingelheim uses two CHO-DG44 lines for manufacturing biotherapeutics, BI-HEX-1 and BI-HEX-2, which produce distinct cell type-specific antibody glycosylation patterns. A recently established CHO-K1 descended host, BI-HEX-K1, generates antibodies with glycosylation profiles differing from CHO-DG44. Manufacturing process development is significantly influenced by these unique profiles. To investigate the underlying glycosylation related gene expression, we leveraged our CHO host and production cell RNA-seqtranscriptomics and product quality database together with the CHO-K1 genome. We observed that each BI-HEX host and antibody producing cell line has a unique gene expression fingerprint. CHO-DG44 cells only transcribe Fut10, Gfpt2 and ST8Sia6 when expressing antibodies. BI-HEX-K1 cells express ST8Sia6 at host cell level. We detected a link between BI-HEX-1/BI-HEX-2 antibody galactosylation and mannosylation and the gene expression of the B4galt gene family and genes controlling mannose processing. Furthermore, we found major differences between the CHO-DG44 and CHO-K1 lineages in the expression of sialyl transferases and enzymes synthesizing sialic acid precursors, providing a rationale for the lack of immunogenic NeuGc/NGNA synthesis in CHO. Our study highlights the value of systems biotechnology to understand glycoprotein synthesis and product glycoprofiles. Such data improve future production clone selection and process development strategies for better steering of biotherapeutic product quality. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages

    Lier, Clément; Baticle, Elodie; Horvath, Philippe; Haguenoer, Eve; Valentin, Anne-Sophie; Glaser, Philippe; Mereghetti, Laurent; Lanotte, Philippe

    2015-01-01

    CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) are found in 90% of archaea and about 40% of bacteria. In this original system, CRISPR arrays comprise short, almost unique sequences called spacers that are interspersed with conserved palindromic repeats. These systems play a role in adaptive immunity and participate to fight non-self DNA such as integrative and conjugative elements, plasmids, and phages. In Streptococcus agalactiae, a bacterium implicated in colonization and infections in humans since the 1960s, two CRISPR-Cas systems have been described. A type II-A system, characterized by proteins Cas9, Cas1, Cas2, and Csn2, is ubiquitous, and a type I–C system, with the Cas8c signature protein, is present in about 20% of the isolates. Unlike type I–C, which appears to be non-functional, type II-A appears fully functional. Here we studied type II-A CRISPR-cas loci from 126 human isolates of S. agalactiae belonging to different clonal complexes that represent the diversity of the species and that have been implicated in colonization or infection. The CRISPR-cas locus was analyzed both at spacer and repeat levels. Major distinctive features were identified according to the phylogenetic lineages previously defined by multilocus sequence typing, especially for the sequence type (ST) 17, which is considered hypervirulent. Among other idiosyncrasies, ST-17 shows a significantly lower number of spacers in comparison with other lineages. This characteristic could reflect the peculiar virulence or colonization specificities of this lineage. PMID:26124774

  3. Distinct fronto-striatal couplings reveal the double-faced nature of response-outcome relations in instruction-based learning.

    Ruge, Hannes; Wolfensteller, Uta

    2015-06-01

    Higher species commonly learn novel behaviors by evaluating retrospectively whether actions have yielded desirable outcomes. By relying on explicit behavioral instructions, only humans can use an acquisition shortcut that prospectively specifies how to yield intended outcomes under the appropriate stimulus conditions. A recent and largely unexplored hypothesis suggests that striatal areas interact with lateral prefrontal cortex (LPFC) when novel behaviors are learned via explicit instruction, and that regional subspecialization exists for the integration of differential response-outcome contingencies into the current task model. Behaviorally, outcome integration during instruction-based learning has been linked to functionally distinct performance indices. This includes (1) compatibility effects, measured in a postlearning test procedure probing the encoding strength of outcome-response (O-R) associations, and (2) increasing response slowing across learning, putatively indicating active usage of O-R associations for the online control of goal-directed action. In the present fMRI study, we examined correlations between these behavioral indices and the dynamics of fronto-striatal couplings in order to mutually constrain and refine the interpretation of neural and behavioral measures in terms of separable subprocesses during outcome integration. We found that O-R encoding strength correlated with LPFC-putamen coupling, suggesting that the putamen is relevant for the formation of both S-R habits and habit-like O-R associations. By contrast, response slowing as a putative index of active usage of O-R associations correlated with LPFC-caudate coupling. This finding highlights the relevance of the caudate for the online control of goal-directed action also under instruction-based learning conditions, and in turn clarifies the functional relevance of the behavioral slowing effect.

  4. Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires.

    Bin Jia

    Full Text Available The efficacy of protein-conjugated pneumococcal polysaccharide vaccines has been well characterized for children. The level of protection conferred by unconjugated polysaccharide vaccines remains less clear, particularly for elderly individuals who have had prior antigenic experience through immunization with unconjugated polysaccharide vaccines or natural exposure to Streptococcus pneumoniae.We compared the magnitude, diversity and genetic biases of antigen-specific memory B cells in two groups of adult cynomolgus macaques that were immunized with a 7-valent conjugated vaccine and boosted after five years with either a 13-valent pneumococcal polysaccharide conjugate vaccine (13vPnC or a 23-valent unconjugated pneumococcal polysaccharide vaccine (23vPS using microengraving (a single-cell analysis method and single-cell RT-PCR.Seven days after boosting, the mean frequency of antigen-specific memory B cells was significantly increased in macaques vaccinated with 13vPnC compared to those receiving 23vPS. The 13vPnC-vaccinated macaques also exhibited a more even distribution of antibody specificities to four polysaccharides in the vaccine (PS4, 6B, 14, 23F that were examined. However, single-cell analysis of the antibody variable region sequences from antigen-specific B cells elicited by unconjugated and conjugated vaccines indicated that both the germline gene segments forming the heavy chains and the average lengths of the Complementary Determining Region 3 (CDR3 were similar.Our results confirm that distinctive differences can manifest between antigen-specific memory B cell repertoires in nonhuman primates immunized with conjugated and unconjugated pneumococcal polysaccharide vaccines. The study also supports the notion that the conjugated vaccines have a favorable profile in terms of both the frequency and breadth of the anamnestic response among antigen-specific memory B cells.

  5. Early transcriptome analyses of Z-3-Hexenol-treated zea mays revealed distinct transcriptional networks and anti-herbivore defense potential of green leaf volatiles.

    Jurgen Engelberth

    Full Text Available Green leaf volatiles (GLV, which are rapidly emitted by plants in response to insect herbivore damage, are now established as volatile defense signals. Receiving plants utilize these molecules to prime their defenses and respond faster and stronger when actually attacked. To further characterize the biological activity of these compounds we performed a microarray analysis of global gene expression. The focus of this project was to identify early transcriptional events elicited by Z-3-hexenol (Z-3-HOL as our model GLV in maize (Zea mays seedlings. The microarray results confirmed previous studies on Z-3-HOL -induced gene expression but also provided novel information about the complexity of Z-3-HOL -induced transcriptional networks. Besides identifying a distinct set of genes involved in direct and indirect defenses we also found significant expression of genes involved in transcriptional regulation, Ca(2+-and lipid-related signaling, and cell wall reinforcement. By comparing these results with those obtained by treatment of maize seedlings with insect elicitors we found a high degree of correlation between the two expression profiles at this early time point, in particular for those genes related to defense. We further analyzed defense gene expression induced by other volatile defense signals and found Z-3-HOL to be significantly more active than methyl jasmonate, methyl salicylate, and ethylene. The data presented herein provides important information on early genetic networks that are activated by Z-3-HOL and demonstrates the effectiveness of this compound in the regulation of typical plant defenses against insect herbivores in maize.

  6. A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types

    Wagner, Emily C.; Schellenberg, John J.; Links, Matthew G.; van Schalkwyk, Julie; Reid, Gregor; Hemmingsen, Sean M.; Hill, Janet E.; Money, Deborah

    2015-01-01

    The vaginal microbiota is important in women’s reproductive and overall health. However, the relationships between the structure, function and dynamics of this complex microbial community and health outcomes remain elusive. The objective of this study was to determine the phylogenetic range and abundance of prokaryotes in the vaginal microbiota of healthy, non-pregnant, ethnically diverse, reproductive-aged Canadian women. Socio-demographic, behavioural and clinical data were collected and vaginal swabs were analyzed from 310 women. Detailed profiles of their vaginal microbiomes were generated by pyrosequencing of the chaperonin-60 universal target. Six community state types (CST) were delineated by hierarchical clustering, including three Lactobacillus-dominated CST (L. crispatus, L. iners, L. jensenii), two Gardnerella-dominated (subgroups A and C) and an “intermediate” CST which included a small number of women with microbiomes dominated by seven other species or with no dominant species but minority populations of Streptococcus, Staphylococcus, Peptoniphilus, E. coli and various Proteobacteria in co-dominant communities. The striking correspondence between Nugent score and deep sequencing CST continues to reinforce the basic premise provided by the simpler Gram stain method, while additional analyses reveal detailed cpn60-based phylogeny and estimated abundance in microbial communities from vaginal samples. Ethnicity was the only demographic or clinical characteristic predicting CST, with differences in Asian and White women (p = 0.05). In conclusion, this study confirms previous work describing four cpn60-based subgroups of Gardnerella, revealing previously undescribed CST. The data describe the range of bacterial communities seen in Canadian women presenting with no specific vaginal health concerns, and provides an important baseline for future investigations of clinically important cohorts. PMID:26266808

  7. The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells

    Andrew Parker

    2015-12-01

    Full Text Available Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182 in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss.

  8. Deglacial sea level history of the East Siberian Sea and Chukchi Sea margins

    Cronin, Thomas M.; O'Regan, Matt; Pearce, Christof; Gemery, Laura; Toomey, Michael; Semiletov, Igor

    2017-01-01

    Deglacial (12.8–10.7 ka) sea level history on the East Siberian continental shelf and upper continental slope was reconstructed using new geophysical records and sediment cores taken during Leg 2 of the 2014 SWERUS-C3 expedition. The focus of this study is two cores from Herald Canyon, piston core SWERUS-L2-4-PC1 (4-PC1) and multicore SWERUS-L2-4-MC1 (4-MC1), and a gravity core from an East Siberian Sea transect, SWERUS-L2-20-GC1 (20-GC1). Cores 4-PC1 and 20-GC were taken at 120 and 115 m of modern water depth, respectively, only a few meters above the global last glacial maximum (LGM;  ∼  24 kiloannum or ka) minimum sea level of  ∼  125–130 meters below sea level (m b.s.l.). Using calibrated radiocarbon ages mainly on molluscs for chronology and the ecology of benthic foraminifera and ostracode species to estimate paleodepths, the data reveal a dominance of river-proximal species during the early part of the Younger Dryas event (YD, Greenland Stadial GS-1) followed by a rise in river-intermediate species in the late Younger Dryas or the early Holocene (Preboreal) period. A rapid relative sea level rise beginning at roughly 11.4 to 10.8 ka ( ∼  400 cm of core depth) is indicated by a sharp faunal change and unconformity or condensed zone of sedimentation. Regional sea level at this time was about 108 m b.s.l. at the 4-PC1 site and 102 m b.s.l. at 20-GC1. Regional sea level near the end of the YD was up to 42–47 m lower than predicted by geophysical models corrected for glacio-isostatic adjustment. This discrepancy could be explained by delayed isostatic adjustment caused by a greater volume and/or geographical extent of glacial-age land ice and/or ice shelves in the western Arctic Ocean and adjacent Siberian land areas.

  9. Mg-Fe Isotope Systems of Mantle Xenoliths: Constrains on the Evolution of Siberian Craton

    An, Y.; Kiseeva, E. S.; Sobolev, N. V.; Zhang, Z.

    2017-12-01

    Mantle xenoliths bring to the surface a variety of lithologies (dunites, lherzolites, harzburgites, wehrlites, eclogites, pyroxenites, and websterites) and represent snapshots of the geochemical processes that occur deep within the Earth. Recent improvements in the precision of the MC-ICP-MS measurements have allowed us to expand the amount of data on Mg and Fe isotopes for mantle-derived samples. For instance, to constrain the isotopic composition of the Earth based on the study of spinel and garnet peridotites (An et al., 2017; Teng et al., 2010), to trace the origin and to investigate the isotopic fractionation mechanism during metamorphic process using cratonic or orogenic eclogites (Li et al., 2011; Wang et al., 2012) and to reveal the metasomatism-induced mantle heterogeneity by pyroxenites (Hu et al., 2016). Numerous multi-stage modification events and mantle layering are detected in the subcontinental lithospheric mantle under the Siberian craton (Ashchepkov et al., 2008a; Sobolev et al., 1975, etc). Combined analyses of Mg and Fe isotopic systems could provide new constraints on the formation and evolution of the ancient cratonic mantle. In order to better constrain the magnitude and mechanism of inter-mineral Mg and Fe isotopic fractionations at high temperatures, systematic studies of mantle xenoliths are needed. For example, theoretical calculations and natural samples measurements have shown that large equilibrium Mg isotope fractionations controlled by the difference in coordination number of Mg among minerals could exist (Huang et al., 2013; Li et al., 2011). Thus, the Mg isotope geothermometer could help us trace the evolution history of ancient cratons. In this study we present Mg and Fe isotopic data for whole rocks and separated minerals (clinopyroxene (cpx) and garnet (grt)) from different types of mantle xenoliths (garnet pyroxenites, eclogites, grospydites and garnet peridotites) from a number of kimberlite pipes in Siberian craton (Udachnaya

  10. Deglacial sea level history of the East Siberian Sea and Chukchi Sea margins

    T. M. Cronin

    2017-09-01

    Full Text Available Deglacial (12.8–10.7 ka sea level history on the East Siberian continental shelf and upper continental slope was reconstructed using new geophysical records and sediment cores taken during Leg 2 of the 2014 SWERUS-C3 expedition. The focus of this study is two cores from Herald Canyon, piston core SWERUS-L2-4-PC1 (4-PC1 and multicore SWERUS-L2-4-MC1 (4-MC1, and a gravity core from an East Siberian Sea transect, SWERUS-L2-20-GC1 (20-GC1. Cores 4-PC1 and 20-GC were taken at 120 and 115 m of modern water depth, respectively, only a few meters above the global last glacial maximum (LGM;  ∼  24 kiloannum or ka minimum sea level of  ∼  125–130 meters below sea level (m b.s.l.. Using calibrated radiocarbon ages mainly on molluscs for chronology and the ecology of benthic foraminifera and ostracode species to estimate paleodepths, the data reveal a dominance of river-proximal species during the early part of the Younger Dryas event (YD, Greenland Stadial GS-1 followed by a rise in river-intermediate species in the late Younger Dryas or the early Holocene (Preboreal period. A rapid relative sea level rise beginning at roughly 11.4 to 10.8 ka ( ∼  400 cm of core depth is indicated by a sharp faunal change and unconformity or condensed zone of sedimentation. Regional sea level at this time was about 108 m b.s.l. at the 4-PC1 site and 102 m b.s.l. at 20-GC1. Regional sea level near the end of the YD was up to 42–47 m lower than predicted by geophysical models corrected for glacio-isostatic adjustment. This discrepancy could be explained by delayed isostatic adjustment caused by a greater volume and/or geographical extent of glacial-age land ice and/or ice shelves in the western Arctic Ocean and adjacent Siberian land areas.

  11. Deglacial sea level history of the East Siberian Sea and Chukchi Sea margins

    Cronin, Thomas M.; O'Regan, Matt; Pearce, Christof; Gemery, Laura; Toomey, Michael; Semiletov, Igor; Jakobsson, Martin

    2017-09-01

    Deglacial (12.8-10.7 ka) sea level history on the East Siberian continental shelf and upper continental slope was reconstructed using new geophysical records and sediment cores taken during Leg 2 of the 2014 SWERUS-C3 expedition. The focus of this study is two cores from Herald Canyon, piston core SWERUS-L2-4-PC1 (4-PC1) and multicore SWERUS-L2-4-MC1 (4-MC1), and a gravity core from an East Siberian Sea transect, SWERUS-L2-20-GC1 (20-GC1). Cores 4-PC1 and 20-GC were taken at 120 and 115 m of modern water depth, respectively, only a few meters above the global last glacial maximum (LGM; ˜ 24 kiloannum or ka) minimum sea level of ˜ 125-130 meters below sea level (m b.s.l.). Using calibrated radiocarbon ages mainly on molluscs for chronology and the ecology of benthic foraminifera and ostracode species to estimate paleodepths, the data reveal a dominance of river-proximal species during the early part of the Younger Dryas event (YD, Greenland Stadial GS-1) followed by a rise in river-intermediate species in the late Younger Dryas or the early Holocene (Preboreal) period. A rapid relative sea level rise beginning at roughly 11.4 to 10.8 ka ( ˜ 400 cm of core depth) is indicated by a sharp faunal change and unconformity or condensed zone of sedimentation. Regional sea level at this time was about 108 m b.s.l. at the 4-PC1 site and 102 m b.s.l. at 20-GC1. Regional sea level near the end of the YD was up to 42-47 m lower than predicted by geophysical models corrected for glacio-isostatic adjustment. This discrepancy could be explained by delayed isostatic adjustment caused by a greater volume and/or geographical extent of glacial-age land ice and/or ice shelves in the western Arctic Ocean and adjacent Siberian land areas.

  12. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

    Laing, Chad R; Buchanan, Cody; Taboada, Eduardo N; Zhang, Yongxiang; Karmali, Mohamed A; Thomas, James E; Gannon, Victor Pj

    2009-06-29

    Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and

  13. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

    Karmali Mohamed A

    2009-06-01

    Full Text Available Abstract Background Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH. Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. Results In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. Conclusion The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping

  14. Variation in Phytochemical Composition Reveals Distinct Divergence of Aloe vera (L.) Burm.f. From Other Aloe Species: Rationale Behind Selective Preference of Aloe vera in Nutritional and Therapeutic Use

    Dey, Priyankar; Dutta, Somit; Chowdhury, Anurag; Das, Abhaya Prasad; Chaudhuri, Tapas Kumar

    2017-01-01

    In the present study, we have phytochemically characterized 5 different abundant Aloe species, including Aloe vera (L.) Burm.f., using silylation followed by Gas Chromatography-Mass Spectrometry technique and compared the data using multivariate statistical analysis. The results demonstrated clear distinction of the overall phytochemical profile of A vera, highlighted by its divergent spatial arrangement in the component plot. Lowest correlation of the phytochemical profiles were found between A vera and A aristata Haw. (−0.626), whereas highest correlation resided between A aristata and A aspera Haw. (0.899). Among the individual phytochemicals, palmitic acid was identified in highest abundance cumulatively, and carboxylic acids were the most predominant phytochemical species in all the Aloe species. Compared to A vera, linear correlation analysis revealed highest and lowest correlation with A aspera (R 2 = 0.9162) and A aristata (R 2 = 0.6745), respectively. Therefore, A vera demonstrated distinct spatial allocation, reflecting its greater phytochemical variability. PMID:29228808

  15. The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells.

    Parker, Andrew; Cross, Sally H; Jackson, Ian J; Hardisty-Hughes, Rachel; Morse, Susan; Nicholson, George; Coghill, Emma; Bowl, Michael R; Brown, Steve D M

    2015-12-01

    Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182) in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss. © 2015. Published by The Company of

  16. Factors Influencing Formation of the Siberian Stone Pine Stands Near Settlements in Northern Taiga

    V. N. Sedykh

    2014-04-01

    Full Text Available The peculiarities of formation of seed productive Siberian stone pine stands near settlements, due to the total destruction of the living ground cover and forest litter, providing heat influx in the root-inhabited zone of the Siberian stone pine trees is discussed in the paper.

  17. Nonconservative behavior of dissolved organic carbon across the Laptev and East Siberian seas

    Alling, Vanja; Sanchez-Garcia, Laura; Porcelli, Don; Pugach, Sveta; Vonk, Jorien E.; Van Dongen, Bart; Mörth, Carl Magnus; Anderson, Leif G.; Sokolov, Alexander; Andersson, Per; Humborg, Christoph; Semiletov, Igor P.; Gustafsson, Örjan

    2010-01-01

    Climate change is expected to have a strong effect on the Eastern Siberian Arctic Shelf (ESAS) region, which includes 40% of the Arctic shelves and comprises the Laptev and East Siberian seas. The largest organic carbon pool, the dissolved organic carbon (DOC), may change significantly due to

  18. Global Metabolomics of the Placenta Reveals Distinct Metabolic Profiles between Maternal and Fetal Placental Tissues Following Delivery in Non-Labored Women

    Jacquelyn M. Walejko

    2018-01-01

    Full Text Available We evaluated the metabolic alterations in maternal and fetal placental tissues from non-labored women undergoing cesarean section using samples collected from 5 min to 24 h following delivery. Using 1H-NMR, we identified 14 metabolites that significantly differed between maternal and fetal placental tissues (FDR-corrected p-value < 0.05, with 12 metabolites elevated in the maternal tissue, reflecting the flux of these metabolites from mother to fetus. In the maternal tissue, 4 metabolites were significantly altered at 15 min, 10 metabolites at 30 min, and 16 metabolites at 1 h postdelivery, while 11 metabolites remained stable over 24 h. In contrast, in the fetal placenta tissue, 1 metabolite was significantly altered at 15 min, 2 metabolites at 30 min, and 4 metabolites at 1 h postdelivery, while 22 metabolites remained stable over 24 h. Our study provides information on the metabolic profiles of maternal and fetal placental tissues delivered by cesarean section and reveals that there are different metabolic alterations in the maternal and fetal tissues of the placenta following delivery.

  19. Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome.

    Shriram N Rajpathak

    Full Text Available Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected individuals. Haploinsufficiency for a few X linked genes has been associated with some of these disease phenotypes. RNA sequencing can provide valuable insights to understand molecular mechanism of disease process. In the current study, we have analysed the transcriptome profiles of human untransformed 45,X and 46,XX fibroblast cells and identified differential expression of genes in these two karyotypes. Functional analysis revealed that these differentially expressing genes are associated with bone differentiation, glucose metabolism and gonadal development pathways. We also report differential expression of lincRNAs in X monosomic cells. Our observations provide a basis for evaluation of cellular and molecular mechanism(s in the establishment of Turner syndrome phenotypes.

  20. Loss of PTB or negative regulation of Notch mRNA reveals distinct zones of Notch and actin protein accumulation in Drosophila embryo.

    Cedric S Wesley

    Full Text Available Polypyrimidine Tract Binding (PTB protein is a regulator of mRNA processing and translation. Genetic screens and studies of wing and bristle development during the post-embryonic stages of Drosophila suggest that it is a negative regulator of the Notch pathway. How PTB regulates the Notch pathway is unknown. Our studies of Drosophila embryogenesis indicate that (1 the Notch mRNA is a potential target of PTB, (2 PTB and Notch functions in the dorso-lateral regions of the Drosophila embryo are linked to actin regulation but not their functions in the ventral region, and (3 the actin-related Notch activity in the dorso-lateral regions might require a Notch activity at or near the cell surface that is different from the nuclear Notch activity involved in cell fate specification in the ventral region. These data raise the possibility that the Drosophila embryo is divided into zones of different PTB and Notch activities based on whether or not they are linked to actin regulation. They also provide clues to the almost forgotten role of Notch in cell adhesion and reveal a role for the Notch pathway in cell fusions.

  1. Loss of PTB or Negative Regulation of Notch mRNA Reveals Distinct Zones of Notch and Actin Protein Accumulation in Drosophila Embryo

    Wesley, Cedric S.; Guo, Heng; Chaudhry, Kanita A.; Thali, Markus J.; Yin, Jerry C.; Clason, Todd; Wesley, Umadevi V.

    2011-01-01

    Polypyrimidine Tract Binding (PTB) protein is a regulator of mRNA processing and translation. Genetic screens and studies of wing and bristle development during the post-embryonic stages of Drosophila suggest that it is a negative regulator of the Notch pathway. How PTB regulates the Notch pathway is unknown. Our studies of Drosophila embryogenesis indicate that (1) the Notch mRNA is a potential target of PTB, (2) PTB and Notch functions in the dorso-lateral regions of the Drosophila embryo are linked to actin regulation but not their functions in the ventral region, and (3) the actin-related Notch activity in the dorso-lateral regions might require a Notch activity at or near the cell surface that is different from the nuclear Notch activity involved in cell fate specification in the ventral region. These data raise the possibility that the Drosophila embryo is divided into zones of different PTB and Notch activities based on whether or not they are linked to actin regulation. They also provide clues to the almost forgotten role of Notch in cell adhesion and reveal a role for the Notch pathway in cell fusions. PMID:21750738

  2. High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval.

    Shatalina, Margarita; Messmer, Monika; Feuillet, Catherine; Mascher, Fabio; Paux, Etienne; Choulet, Frédéric; Wicker, Thomas; Keller, Beat

    2014-03-01

    Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars 'Arina' and 'Forno', the physical map of chromosome 3B of cultivar 'Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs.

  3. Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas

    Grade, Marian; Hörmann, Patrick; Becker, Sandra; Hummon, Amanda B.; Wangsa, Danny; Varma, Sudhir; Simon, Richard; Liersch, Torsten; Becker, Heinz; Difilippantonio, Michael J.; Ghadimi, B. Michael; Ried, Thomas

    2016-01-01

    To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P 5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node–negative and lymph node–positive tumors (P deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/β-catenin signaling cascade, suggesting similar pathogenic pathways. PMID:17210682

  4. Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates.

    Bouts, Mark J R J; Westmoreland, Susan V; de Crespigny, Alex J; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M; Wu, Ona; D'Arceuil, Helen E

    2015-12-15

    Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by combining quantitative T2 and diffusion MRI indices into MRI 'tissue signatures', (2) to evaluate temporal differences in these signatures between transient (n = 2) and permanent (n = 2) middle cerebral artery occlusion, and (3) to correlate histopathology findings in the chronic stroke period to the acute and subacute MRI derived tissue signatures. An improved iterative self-organizing data analysis algorithm was used to combine T2, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) maps across seven successive timepoints (1, 2, 3, 24, 72, 144, 240 h) which revealed five temporal MRI signatures, that were different from the normal tissue pattern (P MRI signatures associated with specific tissue fates may further aid in assessing and monitoring the efficacy of novel pharmaceutical treatments for stroke in a pre-clinical and clinical setting.

  5. Effects of poly-β-hydroxybutyrate (PHB) on Siberian sturgeon (Acipenser baerii) fingerlings performance and its gastrointestinal tract microbial community.

    Najdegerami, Ebrahim H; Tran, Tiet Ngoc; Defoirdt, Tom; Marzorati, Massimo; Sorgeloos, Patrick; Boon, Nico; Bossier, Peter

    2012-01-01

    Poly-β-hydroxybutyrate (PHB) is a natural polymer that can be depolymerized into water-soluble short-chain fatty acid monomers. These monomers can act as microbial control agents. In this study, the effects of partially replacing the diet of Siberian sturgeon fingerlings with 2% and 5% PHB were investigated. Replacing 2% of the diet with PHB improved weight gain, specific growth rate (SGR) and survival in the sturgeon fingerlings during the 10-week experimental period. Community-level physiological profiling and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) were used to analyze the microbial community diversity and community organization in the sturgeon gastrointestinal tract. DGGE analysis revealed that PHB affected the intestinal microbial species richness and diversity. The highest species richness was observed with 2% PHB. DNA sequencing of the dominant bands in 2% and 5% PHB treatments revealed that PHB stimulated bacteria belonging to the genera Bacillus and Ruminococcaceae. Principal component analysis, Lorenz curves and the Shannon index of Biolog Ecoplate data revealed that aerobic metabolic potential of the bacterial community was different in the PHB-treated fishes as compared with the control situation. Overall, our results indicate that PHB act as microbial control agents and replacement of 2% of Siberian sturgeon fingerling diet with PHB has beneficial effects.

  6. Sequencing of emerging canine distemper virus strain reveals new distinct genetic lineage in the United States associated with disease in wildlife and domestic canine populations.

    Riley, Matthew C; Wilkes, Rebecca P

    2015-12-18

    Recent outbreaks of canine distemper have prompted examination of strains from clinical samples submitted to the University of Tennessee College of Veterinary Medicine (UTCVM) Clinical Virology Lab. We previously described a new strain of CDV that significantly diverged from all genotypes reported to date including America 2, the genotype proposed to be the main lineage currently circulating in the US. The aim of this study was to determine when this new strain appeared and how widespread it is in animal populations, given that it has also been detected in fully vaccinated adult dogs. Additionally, we sequenced complete viral genomes to characterize the strain and determine if variation is confined to known variable regions of the genome or if the changes are also present in more conserved regions. Archived clinical samples were genotyped using real-time RT-PCR amplification and sequencing. The genomes of two unrelated viruses from a dog and fox each from a different state were sequenced and aligned with previously published genomes. Phylogenetic analysis was performed using coding, non-coding and genome-length sequences. Virus neutralization assays were used to evaluate potential antigenic differences between this strain and a vaccine strain and mixed ANOVA test was used to compare the titers. Genotyping revealed this strain first appeared in 2011 and was detected in dogs from multiple states in the Southeast region of the United States. It was the main strain detected among the clinical samples that were typed from 2011-2013, including wildlife submissions. Genome sequencing demonstrated that it is highly conserved within a new lineage and preliminary serologic testing showed significant differences in neutralizing antibody titers between this strain and the strain commonly used in vaccines. This new strain represents an emerging CDV in domestic dogs in the US, may be associated with a stable reservoir in the wildlife population, and could facilitate vaccine

  7. Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects.

    Foyer, Christine H; Verrall, Susan R; Hancock, Robert D

    2015-02-01

    Phloem-feeding insects (PFIs), of which aphids are the largest group, are major agricultural pests causing extensive damage to crop plants. In contrast to chewing insects, the nature of the plant response to PFIs remains poorly characterized. Scrutiny of the literature concerning transcriptional responses of model and crop plant species to PFIs reveals surprisingly little consensus with respect to the transcripts showing altered abundance following infestation. Nevertheless, core features of the transcriptional response to PFIs can be defined in Arabidopsis thaliana. This comparison of the PFI-associated transcriptional response observed in A. thaliana infested by the generalists Myzus persicae and Bemisia tabaci with the specialist Brevicoryne brassicae highlights the importance of calcium-dependent and receptor kinase-associated signalling. We discuss these findings within the context of the complex cross-talk between the different hormones regulating basal immune response mechanisms in plants. We identify PFI-responsive genes, highlighting the importance of cell wall-associated kinases in plant-PFI interactions, as well as the significant role of kinases containing the domain of unknown function 26. A common feature of plant-PFI interaction is enhanced abundance of transcripts encoding WRKY transcription factors. However, significant divergence was observed with respect to secondary metabolism dependent upon the insect attacker. Transcripts encoding enzymes and proteins associated with glucosinolate metabolism were decreased following attack by the generalist M. persicae but not by the specialist B. brassicae. This analysis provides a comprehensive overview of the molecular patterns associated with the plant response to PFIs and suggests that plants recognize and respond to perturbations in the cell wall occurring during PFI infestation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  8. Sequence-based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families.

    Janine Maimanakos

    2016-08-01

    Full Text Available Arylmalonate-Decarboxylases (AMDases, EC 4.1.1.76 are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta- and Gammaproteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the TTT family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99% of the (R-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes.

  9. A novel whole-bacterial enzyme linked-immunosorbant assay to quantify Chlamydia trachomatis specific antibodies reveals distinct differences between systemic and genital compartments.

    Hannah L Albritton

    Full Text Available Chlamydia trachomatis (CT is the leading sexually transmitted bacterial infection. The continued global burden of CT infection strongly predicates the need for a vaccine to supplement current chlamydial control programs. The correlates of protection against CT are currently unknown, but they must be carefully defined to guide vaccine design. The localized nature of chlamydial infection in columnar epithelial cells of the genital tract necessitates investigation of immunity at the site of infection. The purpose of this study was to develop a sensitive whole bacterial enzyme-linked immunosorbent assay (ELISA to quantify and compare CT-specific IgG and IgA in sera and genital secretions from CT-infected women. To achieve this, elementary bodies (EBs from two of the most common genital serovars (D and E were attached to poly-L-lysine-coated microtiter plates with glutaraldehyde. EB attachment and integrity were verified by the presence of outer membrane antigens and the absence of bacterial cytoplasmic antigens. EB-specific IgG and IgA standards were developed by pooling sera with high titers of CT-specific antibodies from infected women. Serum, endocervical and vaginal secretions, and endocervical cytobrush specimens from CT-infected women were used to quantify CT-specific IgG and IgA which were then normalized to total IgG and IgA, respectively. Analyses of paired serum and genital samples revealed significantly higher proportions of EB-specific antibodies in genital secretions compared to sera. Cervical and vaginal secretions and cytobrush specimens had similar proportions of EB-specific antibodies, suggesting any one of these genital sampling techniques could be used to quantify CT-specific antibodies when appropriate normalization methodologies are implemented. Overall, these results illustrate the need to investigate genital tract CT antibody responses, and our assay provides a useful quantitative tool to assess natural immunity in defined

  10. Multi-gene phylogenetic analysis reveals that shochu-fermenting Saccharomyces cerevisiae strains form a distinct sub-clade of the Japanese sake cluster.

    Futagami, Taiki; Kadooka, Chihiro; Ando, Yoshinori; Okutsu, Kayu; Yoshizaki, Yumiko; Setoguchi, Shinji; Takamine, Kazunori; Kawai, Mikihiko; Tamaki, Hisanori

    2017-10-01

    Shochu is a traditional Japanese distilled spirit. The formation of the distinguishing flavour of shochu produced in individual distilleries is attributed to putative indigenous yeast strains. In this study, we performed the first (to our knowledge) phylogenetic classification of shochu strains based on nucleotide gene sequences. We performed phylogenetic classification of 21 putative indigenous shochu yeast strains isolated from 11 distilleries. All of these strains were shown or confirmed to be Saccharomyces cerevisiae, sharing species identification with 34 known S. cerevisiae strains (including commonly used shochu, sake, ale, whisky, bakery, bioethanol and laboratory yeast strains and clinical isolate) that were tested in parallel. Our analysis used five genes that reflect genome-level phylogeny for the strain-level classification. In a first step, we demonstrated that partial regions of the ZAP1, THI7, PXL1, YRR1 and GLG1 genes were sufficient to reproduce previous sub-species classifications. In a second step, these five analysed regions from each of 25 strains (four commonly used shochu strains and the 21 putative indigenous shochu strains) were concatenated and used to generate a phylogenetic tree. Further analysis revealed that the putative indigenous shochu yeast strains form a monophyletic group that includes both the shochu yeasts and a subset of the sake group strains; this cluster is a sister group to other sake yeast strains, together comprising a sake-shochu group. Differences among shochu strains were small, suggesting that it may be possible to correlate subtle phenotypic differences among shochu flavours with specific differences in genome sequences. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  11. Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections.

    Chalmet, Kristen; Staelens, Delfien; Blot, Stijn; Dinakis, Sylvie; Pelgrom, Jolanda; Plum, Jean; Vogelaers, Dirk; Vandekerckhove, Linos; Verhofstede, Chris

    2010-09-07

    The number of HIV-1 infected individuals in the Western world continues to rise. More in-depth understanding of regional HIV-1 epidemics is necessary for the optimal design and adequate use of future prevention strategies. The use of a combination of phylogenetic analysis of HIV sequences, with data on patients' demographics, infection route, clinical information and laboratory results, will allow a better characterization of individuals responsible for local transmission. Baseline HIV-1 pol sequences, obtained through routine drug-resistance testing, from 506 patients, newly diagnosed between 2001 and 2009, were used to construct phylogenetic trees and identify transmission-clusters. Patients' demographics, laboratory and clinical data, were retrieved anonymously. Statistical analysis was performed to identify subtype-specific and transmission-cluster-specific characteristics. Multivariate analysis showed significant differences between the 59.7% of individuals with subtype B infection and the 40.3% non-B infected individuals, with regard to route of transmission, origin, infection with Chlamydia (p = 0.01) and infection with Hepatitis C virus (p = 0.017). More and larger transmission-clusters were identified among the subtype B infections (p HIV (p = 0.017). Combination of phylogenetics with demographic information, laboratory and clinical data, revealed that HIV-1 subtype B infected Caucasian men-who-have-sex-with-men with high prevalence of sexually transmitted diseases, account for the majority of local HIV-transmissions. This finding elucidates observed epidemiological trends through molecular analysis, and justifies sustained focus in prevention on this high risk group.

  12. [Genetic passportization and identification of Siberian cranes (Grus leucogeranus Pallas) in captivity].

    Mudrik, E A; Kashentseva, T A; Gamburg, E A; Politov, D V

    2014-01-01

    The genetic diversity of the founders of an artificial population of the Siberian crane Grus leucogeranus Pallas (rare species of cranes) was characterized using 10 microsatellite loci. It was established that the allelic diversity (on average, 5.9 alleles per locus) and genic (H(o) = 0.739) diversity of the Siberian crane is rather high and comparable with the estimations for natural populations of different crane species. Genetic passportization of the birds (119 individuals) from the register of the Siberian crane International Studbook was carried out at the initial stage. The efficiency of genetic passportization for individual identification, identification of the origin, paternity analysis, and exclusion of inbreeding was demonstrated in Siberian cranes under natural mating and artificial insemination. Cases of natural reproduction in pairs of Siberian cranes imprinted to the human and continuous storage of spermatozoa in the female reproductive ducts were registered.

  13. WARMER URBAN CLIMATES FOR DEVELOPMENT OF GREEN SPACES IN NORTHERN SIBERIAN CITIES

    Igor Esau

    2016-01-01

    Full Text Available Modern human societies have accumulated considerable power to modify their environment and the earth’s system climate as the whole. The most significant environmental changes are found in the urbanized areas. This study considers coherent changes in vegetation productivity and land surface temperature (LST around four northern West Siberian cities, namely, Tazovsky, Nadym, Noyabrsk and Megion. These cities are located in tundra, forest-tundra, northern taiga and middle taiga bioclimatic zones correspondingly. Our analysis of 15 years (2000–2014 Moderate Resolution Imaging Spectroradiometer (MODIS data revealed significantly (1.3 °C to 5.2 °C warmer seasonally averaged LST within the urbanized territories than those of the surrounding landscapes. The magnitude of the urban LST anomaly corresponds to climates found 300–600 km to the South. In the climate change perspective, this magnitude corresponds to the expected regional warming by the middle or the end of the 21st century. Warmer urban climates, and specifically warmer upper soil layers, can support re-vegetation of the disturbed urban landscapes with more productive trees and tall shrubs. This afforestation is welcome by the migrant city population as it is more consistent with their traditional ecological knowledge. Survival of atypical, southern plant species encourages a number of initiatives and investment to introduce even broader spectrum of temperate blossoming trees and shrubs in urban landscapes. The unintended changes of the urban micro-climates in combination with knowledgeable urban planning could transform the Siberian pioneer settlements into places of belonging.

  14. VGF-derived peptide, TLQP-21, regulates food intake and body weight in Siberian hamsters.

    Jethwa, Preeti H; Warner, Amy; Nilaweera, Kanishka N; Brameld, John M; Keyte, John W; Carter, Wayne G; Bolton, Neil; Bruggraber, Michael; Morgan, Peter J; Barrett, Perry; Ebling, Francis J P

    2007-08-01

    The Siberian hamster survives winter by decreasing food intake and catabolizing abdominal fat reserves, resulting in a sustained, profound loss of body weight. VGF gene expression is photoperiodically regulated in the hypothalamus with significantly higher expression in lean Siberian hamsters. The aim of this study was to investigate the role of VGF in regulating these seasonal cycles by determining the effects of a VGF-derived peptide (TLQP-21) on food intake and body weight. Acute intracerebroventricular administration of TLQP-21 decreased food intake, and chronic treatment caused a sustained reduction in food intake and body weight and decreased abdominal fat depots. Behavioral analysis revealed that TLQP-21 reduced meal size but not the frequency of feeding bouts, suggesting a primary action on satiety. Hamsters treated with TLQP-21 lost a similar amount of weight as a pair-fed group in which food intake was matched to that of the TLQP-21-treated group. Central or peripheral treatment with TLQP-21 did not produce a significant effect on resting metabolic rate. We conclude that the primary action of TLQP-21 is to decrease food intake rather than increase energy expenditure. TLQP-21 treatment caused a decrease in UCP-1 mRNA in brown adipose tissue, but hypothalamic expression of orexigenic and anorexigenic neuropeptide genes remained unchanged after TLQP-21 treatment, although compensatory increases in NPY and AgRP mRNA were observed in the pair-fed hamsters. The effects of TLQP-21 administration are similar to those in hamsters in short days, suggesting that increased VGF activity may contribute to the hypophagia that underlies the seasonal catabolic state.

  15. A novel method for measuring cellular antibody uptake using imaging flow cytometry reveals distinct uptake rates for two different monoclonal antibodies targeting L1.

    Hazin, John; Moldenhauer, Gerhard; Altevogt, Peter; Brady, Nathan R

    2015-08-01

    Monoclonal antibodies (mAbs) have emerged as a promising tool for cancer therapy. Differing approaches utilize mAbs to either deliver a drug to the tumor cells or to modulate the host's immune system to mediate tumor kill. The rate by which a therapeutic antibody is being internalized by tumor cells is a decisive feature for choosing the appropriate treatment strategy. We herein present a novel method to effectively quantitate antibody uptake of tumor cells by using image-based flow cytometry, which combines image analysis with high throughput of sample numbers and sample size. The use of this method is established by determining uptake rate of an anti-EpCAM antibody (HEA125), from single cell measurements of plasma membrane versus internalized antibody, in conjunction with inhibitors of endocytosis. The method is then applied to two mAbs (L1-9.3, L1-OV52.24) targeting the neural cell adhesion molecule L1 (L1CAM) at two different epitopes. Based on median cell population responses, we find that mAb L1-OV52.24 is rapidly internalized by the ovarian carcinoma cell line SKOV3ip while L1 mAb 9.3 is mainly retained at the cell surface. These findings suggest the L1 mAb OV52.24 as a candidate to be further developed for drug-delivery to cancer cells, while L1-9.3 may be optimized to tag the tumor cells and stimulate immunogenic cancer cell killing. Furthermore, when analyzing cell-to-cell variability, we observed L1 mAb OV52.24 rapidly transition into a subpopulation with high-internalization capacity. In summary, this novel high-content method for measuring antibody internalization rate provides a high level of accuracy and sensitivity for cell population measurements and reveals further biologically relevant information when taking into account cellular heterogeneity. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Distinct BOLD fMRI Responses of Capsaicin-Induced Thermal Sensation Reveal Pain-Related Brain Activation in Nonhuman Primates.

    Abu Bakar Ali Asad

    Full Text Available Approximately 20% of the adult population suffer from chronic pain that is not adequately treated by current therapies, highlighting a great need for improved treatment options. To develop effective analgesics, experimental human and animal models of pain are critical. Topically/intra-dermally applied capsaicin induces hyperalgesia and allodynia to thermal and tactile stimuli that mimics chronic pain and is a useful translation from preclinical research to clinical investigation. Many behavioral and self-report studies of pain have exploited the use of the capsaicin pain model, but objective biomarker correlates of the capsaicin augmented nociceptive response in nonhuman primates remains to be explored.Here we establish an aversive capsaicin-induced fMRI model using non-noxious heat stimuli in Cynomolgus monkeys (n = 8. BOLD fMRI data were collected during thermal challenge (ON:20 s/42°C; OFF:40 s/35°C, 4-cycle at baseline and 30 min post-capsaicin (0.1 mg, topical, forearm application. Tail withdrawal behavioral studies were also conducted in the same animals using 42°C or 48°C water bath pre- and post- capsaicin application (0.1 mg, subcutaneous, tail.Group comparisons between pre- and post-capsaicin application revealed significant BOLD signal increases in brain regions associated with the 'pain matrix', including somatosensory, frontal, and cingulate cortices, as well as the cerebellum (paired t-test, p<0.02, n = 8, while no significant change was found after the vehicle application. The tail withdrawal behavioral study demonstrated a significant main effect of temperature and a trend towards capsaicin induced reduction of latency at both temperatures.These findings provide insights into the specific brain regions involved with aversive, 'pain-like', responses in a nonhuman primate model. Future studies may employ both behavioral and fMRI measures as translational biomarkers to gain deeper understanding of pain processing and evaluate

  17. Airway epithelial cell exposure to distinct e-cigarette liquid flavorings reveals toxicity thresholds and activation of CFTR by the chocolate flavoring 2,5-dimethypyrazine.

    Sherwood, Cara L; Boitano, Scott

    2016-05-17

    The potential for adverse respiratory effects following exposure to electronic (e-) cigarette liquid (e-liquid) flavorings remains largely unexplored. Given the multitude of flavor permutations on the market, identification of those flavor constituents that negatively impact the respiratory tract is a daunting task. In this study we examined the impact of common e-liquid flavoring chemicals on the airway epithelium, the cellular monolayer that provides the first line of defense against inhaled particulates, pathogens, and toxicants. We used the xCELLigence real-time cell analyzer (RTCA) as a primary high-capacity screening tool to assess cytotoxicity thresholds and physiological effects of common e-liquid flavoring chemicals on immortalized human bronchial epithelial cells (16HBE14o-). The RTCA was used secondarily to assess the capability of 16HBE14o- cells to respond to cellular signaling agonists following a 24 h exposure to select flavoring chemicals. Finally, we conducted biophysical measurements of well-differentiated primary mouse tracheal epithelial (MTE) cells with an Ussing chamber to measure the effects of e-cigarette flavoring constituents on barrier function and ion conductance. In our high-capacity screens five of the seven flavoring chemicals displayed changes in cellular impedance consistent with cell death at concentrations found in e-liquid. Vanillin and the chocolate flavoring 2,5-dimethylpyrazine caused alterations in cellular physiology indicative of a cellular signaling event. At subcytotoxic levels, 24 h exposure to 2,5-dimethylpyrazine compromised the ability of airway epithelial cells to respond to signaling agonists important in salt and water balance at the airway surface. Biophysical measurements of 2,5-dimethylpyrazine on primary MTE cells revealed alterations in ion conductance consistent with an efflux at the apical airway surface that was accompanied by a transient loss in transepithelial resistance. Mechanistic studies confirmed

  18. Deep sequencing of small RNA libraries from human prostate epithelial and stromal cells reveal distinct pattern of microRNAs primarily predicted to target growth factors.

    Singh, Savita; Zheng, Yun; Jagadeeswaran, Guru; Ebron, Jey Sabith; Sikand, Kavleen; Gupta, Sanjay; Sunker, Ramanjulu; Shukla, Girish C

    2016-02-28

    Complex epithelial and stromal cell interactions are required during the development and progression of prostate cancer. Regulatory small non-coding microRNAs (miRNAs) participate in the spatiotemporal regulation of messenger RNA (mRNA) and regulation of translation affecting a large number of genes involved in prostate carcinogenesis. In this study, through deep-sequencing of size fractionated small RNA libraries we profiled the miRNAs of prostate epithelial (PrEC) and stromal (PrSC) cells. Over 50 million reads were obtained for PrEC in which 860,468 were unique sequences. Similarly, nearly 76 million reads for PrSC were obtained in which over 1 million were unique reads. Expression of many miRNAs of broadly conserved and poorly conserved miRNA families were identified. Sixteen highly expressed miRNAs with significant change in expression in PrSC than PrEC were further analyzed in silico. ConsensusPathDB showed the target genes of these miRNAs were significantly involved in adherence junction, cell adhesion, EGRF, TGF-β and androgen signaling. Let-7 family of tumor-suppressor miRNAs expression was highly pervasive in both, PrEC and PrSC cells. In addition, we have also identified several miRNAs that are unique to PrEC or PrSC cells and their predicted putative targets are a group of transcription factors. This study provides perspective on the miRNA expression in PrEC and PrSC, and reveals a global trend in miRNA interactome. We conclude that the most abundant miRNAs are potential regulators of development and differentiation of the prostate gland by targeting a set of growth factors. Additionally, high level expression of the most members of let-7 family miRNAs suggests their role in the fine tuning of the growth and proliferation of prostate epithelial and stromal cells. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Fir Decline and Mortality in the Southern Siberian Mountains

    Kharuk, Viacheslav I.; Im, Sergei T.; Petrov, Ilya A.; Dvinskaya, Mariya, L.; Fedotova, Elena V.; Ranson, Kenneth J.

    2016-01-01

    Increased dieback and mortality of dark needle conifer (DNC) stands (composed of fir (Abies sibirica),Siberian pine (Pinus sibirica) and spruce (Picea obovata))were documented in Russia during recent decades. Here we analyzed spatial and temporal patterns of fir decline and mortality in the southern Siberian Mountains based on satellite, in situ and dendrochronological data. The studied stands are located within the boundary between DNC taiga to the north and forest-steppe to the south. Fir decline and mortality were observed to originate where topographic features contributed to maximal water-stress risk, i.e., steep (1825),convex, south-facing slopes with a shallow well-drained root zone. Fir regeneration survived droughts and increased stem radial growth, while upper canopy trees died. Tree ring width(TRW) growth negatively correlated with vapor pressure deficit (VPD), drought index and occurrence of late frosts, and positively with soil water content. Previous year growth conditions (i.e., drought index, VPD, soil water anomalies)have a high impact on current TRW (r 0.600.74). Fir mortality was induced by increased water stress and severe droughts (as a primary factor) in synergy with bark-beetles and fungi attacks (as secondary factors). Dendrochronology data indicated that fir mortality is a periodic process. In a future climate with increased aridity and drought frequency, fir (and Siberian pine) may disappear from portions of its current range (primarily within the boundary with the forest steppe)and is likely to be replaced by drought-tolerant species such as Pinus sylvestris and Larix sibirica.

  20. Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei

    Keith M. Bayha

    2017-10-01

    Full Text Available Background Species of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts. Methods We collected nuclear (28S rDNA and mitochondrial (cytochrome c oxidase I and 16S rDNA sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species of Chrysaora. To examine species boundaries in the U.S. Atlantic sea nettle Chrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome. Results Phylogenetic analyses show that the genus Chrysaora is paraphyletic with respect to other pelagiid genera. In combined analyses, Mawia, sampled from the coast of Senegal, is most closely related to Sanderia malayensis, and Pelagia forms a close relationship to a clade of Pacific Chrysaora species (Chrysaora achlyos, Chrysaora colorata, Chrysaora fuscescens, and Chrysaora melanaster. Chrysaora quinquecirrha is polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade of Chrysaora quinquecirrha. Discussion Our phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and

  1. Blueschist facies fault tectonites from the western margin of the Siberian Craton: Implications for subduction and exhumation associated with early stages of the Paleo-Asian Ocean

    Likhanov, Igor I.; Régnier, Jean-Luc; Santosh, M.

    2018-04-01

    The tectonic evolution of the Siberian Cratonic margins offers important clues for global paleogeographic reconstructions, particularly with regard to the complex geological history of Central Asia. The Yenisey Ridge fold-and-thrust belt at the western margin of the Siberian Craton forms part of the Central Asian Orogenic Belt (CAOB) and is a key to understand the Precambrian tectonic evolution of the Siberian Craton and crustal growth in the CAOB, the world's largest Phanerozoic accretionary orogenic belt. Here we report for the first time, the occurrence of glaucophane schist relics in tectonites within the Yenisey shear zone which provides insights on Chilean-type convergent boundary. We present results from isotope geochronology (SHRIMP zircon analysis and mica 40Ar/39Ar dating), coupled with P-T calculations derived from conventional geothermobarometry and pseudosections in the system NCKFMASH that suggest two superimposed metamorphic events. During the first stage, glaucophane schists formed at around 640-620 Ma at P-T conditions of 8-10 kbar and 400-450 °C. In the second stage, the rocks experienced dynamic metamorphism (c. 600 Ma) at 11-15 kbar/550-640 °C. The differences in P-T parameters between weakly deformed rocks and intensely deformed tectonites and P-T paths suggest distinct tectonic processes. Geochemical features of the mafic tectonites suggest N-MORB and E-MORB affinity, and the zircon U-Pb ages suggest formation of the protoliths at 701.6 ± 8.4. The sequence of spreading, subduction and shear deformation identified in our study correlate with the early stages of development of the Paleo-Asian Ocean at the western margin of the Siberian Craton and supports the spatial proximity of Siberia and Laurentia at 700-600 Ma, as proposed for the Late Neoproterozoic paleogeographic reconstructions and as robustly constrained from large igneous province (LIP) record.

  2. The new petrographic data about the Maymecha-Kotuy area of the Siberian flood-basalt province

    Latyshev, Anton; Veselovskiy, Roman

    2010-05-01

    The Maymecha-Kotuy area of the Siberian flood-basalt province is of great interest because of its exceptional composition of igneous rocks. Alkaline-ultramafic rocks prevail there over basalts. It seems to be the only such trap province in the world. Investigation of the magma evolution and revealing of sources of magma is the task of an immense importance. Now there is a discussion about possible connections between the mass extinction on the boundary between Paleozoic and Mesozoic and magmatic activity expressed in formation of the largest Siberian flood-basalt province. Absence of the precise correlation of Maymecha-Kotuy area with other areas of the Siberian province does not allow estimating duration and volumes of the eruption of traps. Another question is if eruption of traps was uninterrupted or it had several pulses of magmatic activity. The solution of this problem will let estimate the degree of possible influence of the flood-basalt eruption to the environment. The represented results of investigations comprise all five igneous suites of Maymecha-Kotuy area. Petrographic investigation included research of thin sections and microprobe analyzes. The most entire sequences of Arydzhangsky and Kogotoksky suites and partly sequences of Pravoboyarsky, Delkansky and Maymechinsky suites were studied. This research allowed to reveal that the section of "Truba" on the Kotuy River belongs to Onkuchaksky suite (former lower Kogotoksky subsuite) and to reconsider the petrography of Arydzhangsky suite. Also, the research of geochemistry based on data of Fedorenko et al. (1997, 2000) lets suggest the sources of magma and its evolution. According to the new paleomagnetic data (Pavlov, Veselovskiy, Fetisova, EGU-2010), the new scheme of correlation of Maymecha-Kotuy trap section with Norilsk trap section was worked out and it became possible to estimate character of the magmatic activity in this region. In addition, it makes the contribution into the working out the

  3. Biologic rhythms derived from Siberian mammoths' hairs.

    Mike Spilde

    Full Text Available Hair is preserved for millennia in permafrost; it enshrines a record of biologic rhythms and offers a glimpse at chronobiology as it was in extinct animals. Here we compare biologic rhythms gleaned from mammoth's hairs with those of modern human hair. Four mammoths' hairs came from varying locations in Siberia 4600 km, four time zones, apart ranging in age between 18,000 and 20,000 years before present. We used two contemporaneous human hairs for comparison. Power spectra derived from hydrogen isotope ratios along the length of the hairs gave insight into biologic rhythms, which were different in the mammoths depending on location and differed from humans. Hair growth for mammoths was ∼31 cms/year and ∼16 cms/year for humans. Recurrent annual rhythms of slow and fast growth varying from 3.4 weeks/cycles to 8.7 weeks/cycles for slow periods and 1.2 weeks/cycles to 2.2 weeks/cycles for fast periods were identified in mammoth's hairs. The mineral content of mammoth's hairs was measured by electron microprobe analysis (k-ratios, which showed no differences in sulfur amongst the mammoth hairs but significantly more iron then in human hair. The fractal nature of the data derived from the hairs became evident in Mandelbrot sets derived from hydrogen isotope ratios, mineral content and geographic location. Confocal microscopy and scanning electron microscopy showed varied degrees of preservation of the cuticle largely independent of age but not location of the specimens. X-ray fluorescence microprobe and fluorescence computed micro-tomography analyses allowed evaluation of metal distribution and visualization of hollow tubes in the mammoth's hairs. Seasonal variations in iron and copper content combined with spectral analyses gave insights into variation in food intake of the animals. Biologic rhythms gleaned from power spectral plots obtained by modern methods revealed life style and behavior of extinct mega-fauna.

  4. Siberian Chemical Combine laboratory project work plan, fiscal year 1999

    Morgado, R.E.; Acobyan, R.; Shropsire, R.

    1998-01-01

    The Siberian Chemical Combine (SKhK), Laboratory Project Work Plan (Plan) is intended to assist the US Laboratory Project Team, and Department of Energy (DOE) staff with the management of the FY99 joint material protection control and accounting program (MPC and A) for enhancing nuclear material safeguards within the Siberian Chemical Combine. The DOE/Russian/Newly Independent States, Nuclear Material Task Force, uses a project work plan document for higher-level program management. The SKhK Plan is a component of the Russian Defense related Sites' input to that document. In addition, it contains task descriptions and a Gantt Chart covering the FY99 time-period. This FY99 window is part of a comprehensive, Project Status Gantt Chart for tasking and goal setting that extends to the year 2003. Secondary and tertiary levels of detail are incorporated therein and are for the use of laboratory project management. The SKhK Plan is a working document, and additions and modifications will be incorporated as the MPC and A project for SKhK evolves

  5. Biologic Rhythms Derived from Siberian Mammoths Hairs

    M Spilde; A Lanzirotti; C Qualls; G Phillips; A Ali; L Agenbroad; O Appenzeller

    2011-12-31

    Hair is preserved for millennia in permafrost; it enshrines a record of biologic rhythms and offers a glimpse at chronobiology as it was in extinct animals. Here we compare biologic rhythms gleaned from mammoth's hairs with those of modern human hair. Four mammoths' hairs came from varying locations in Siberia 4600 km, four time zones, apart ranging in age between 18,000 and 20,000 years before present. We used two contemporaneous human hairs for comparison. Power spectra derived from hydrogen isotope ratios along the length of the hairs gave insight into biologic rhythms, which were different in the mammoths depending on location and differed from humans. Hair growth for mammoths was {approx}31 cms/year and {approx}16 cms/year for humans. Recurrent annual rhythms of slow and fast growth varying from 3.4 weeks/cycles to 8.7 weeks/cycles for slow periods and 1.2 weeks/cycles to 2.2 weeks/cycles for fast periods were identified in mammoth's hairs. The mineral content of mammoth's hairs was measured by electron microprobe analysis (k-ratios), which showed no differences in sulfur amongst the mammoth hairs but significantly more iron then in human hair. The fractal nature of the data derived from the hairs became evident in Mandelbrot sets derived from hydrogen isotope ratios, mineral content and geographic location. Confocal microscopy and scanning electron microscopy showed varied degrees of preservation of the cuticle largely independent of age but not location of the specimens. X-ray fluorescence microprobe and fluorescence computed micro-tomography analyses allowed evaluation of metal distribution and visualization of hollow tubes in the mammoth's hairs. Seasonal variations in iron and copper content combined with spectral analyses gave insights into variation in food intake of the animals. Biologic rhythms gleaned from power spectral plots obtained by modern methods revealed life style and behavior of extinct mega-fauna.

  6. Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations.

    Nadezhda V Vorobieva

    Full Text Available BACKGROUND: The extant roe deer (Capreolus Gray, 1821 includes two species: the European roe deer (C. capreolus and the Siberian roe deer (C. pygargus that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia, where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan, Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. CONCLUSION/SIGNIFICANCE: Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian

  7. Isolation and characterization of an atypical Siberian sturgeon herpesvirus strain in Russia: novel North American Acipenserid herpesvirus 2 strain in Europe?

    Doszpoly, A; Kalabekov, I M; Breyta, R; Shchelkunov, I S

    2017-10-01

    Siberian sturgeon herpesvirus (SbSHV) was isolated in Russia for the first time in 2006. Nine SbSHV isolates were recovered from different fish hatcheries producing the same cytopathic effect in cell cultures, the same clinical signs and mortality kinetics in virus-infected fish and the same virus neutralization pattern and shared identical nucleotide sequences. In 2011, a new isolate was recovered from juvenile sturgeon, which caused completely different cytopathic effect. That isolate was not readily neutralized by Siberian sturgeon hyperimmune antisera, and its DNA was not recognized by the routine PCR developed for SbSHV detection. Molecular study of the novel isolate revealed that it was more closely related to North American Acipenserid herpesvirus 2 (AciHV-2) isolates from white sturgeon, while the genome sequences of the former SbSHV isolates showed high similarity to the AciHV-2 isolated from shortnose sturgeon. While clinical signs and mortality caused by the novel isolate in infected Siberian sturgeon were similar to those of the formerly described SbSHV isolates, the incubation period and mean time to death produced by the novel isolate were twice as long. The differences between the former isolates and the recent one suggest that a novel SbSHV strain emerged in Europe and the molecular findings imply its North American origin. © 2017 John Wiley & Sons Ltd.

  8. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2014-01-01

    Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger. PMID:24608928

  9. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    Changqing Liu

    2014-03-01

    Full Text Available Bacterial artificial chromosome (BAC libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12, consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.

  10. Age and Heat Stress as Determinants of Telomere Length in a Long-Lived Fish, the Siberian Sturgeon.

    Simide, Rémy; Angelier, Frédéric; Gaillard, Sandrine; Stier, Antoine

    2016-01-01

    Telomeres shorten at each cell division due to the end-replication problem but also in response to oxidative stress. Consequently, telomeres shorten with age in many endotherms, and this shortening is accelerated under stressful environmental conditions. Data in ectotherm vertebrates remain scarce so far, so our goal was to review existing data for fish and to test the influence of age and stress on telomere length in a very long-lived fish, the Siberian sturgeon (Acipenser baerii). Our review of the literature revealed age-related telomere shortening in approximately half of the published studies. In the Siberian sturgeon, we found a significant telomere shortening with age, both at the intraindividual level using red blood cells (-12.5% in 16 mo) and at the interindividual level using cross-sectional samples of fin over an age range of 8 yr. We also found that heat stress (30°C) significantly reduced telomere length by 15.0% after only 1 mo of exposure. Our results highlight that both age and stressful environmental conditions might be important determinants of telomere length in fish.

  11. Spin Flipping in the Presence of a Full Siberian Snake

    Blinov, B.B.; Anferov, V.A.; Derbenev, Y.S.; Kageya, T.; Krisch, A.D.; Lorenzon, W.; Ratner, L.G.; Sivers, D.W.; Sourkont, K.V.; Wong, V.K.; Chu, C.M.; Lee, S.Y.; Rinckel, T.; Schwandt, P.; Sperisen, F.; Przewoski, B. von; Sato, H.

    1998-01-01

    We have demonstrated for the first time spin flipping of a polarized proton beam stored in a ring containing a nearly 100% Siberian snake; we did this using a 'snake' depolarizing resonance induced by an rf solenoid magnet. By varying the rf solenoid close-quote s ramp time, frequency range, and voltage, we reached a spin-flip efficiency of about 91% . This spin-flip efficiency was probably reduced because the horizontal stable spin direction was not perpendicular to the longitudinal field of the rf solenoid, and was possibly reduced by nearby synchrotron sideband resonances. The planned use of a vertical rf dipole may improve the spin-flip efficiency. copyright 1998 The American Physical Society

  12. Differentiation of Siberian Miners’ Salaries in Late XIX – Early XX Centuries

    Vasiliy P. Zinovyev

    2014-06-01

    Full Text Available The work considers seasonal variations and differentiation of Siberian miners’ salaries in late XIX – early XX centuries, proves that seasonal variations of salaries depended on the excess demand on labor in summer and the contraction of demand in winter, detects that salary differentiated, depending on workers’ qualification, sex, age, nationality, industry, location of an enterprise. Such differences in Siberian miners’ salaries were typical for early industrial period of the development of the society.

  13. Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas

    Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

    2017-01-01

    In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenu...

  14. Memoranda by A.P. Uspensky to the Council of Ministers of the Provisional Siberian government

    Sukhanov Aleksandr

    2015-01-01

    This publication offers a previously unknown memoranda by representative of the diocesan assembly of deputies of the clergy and laity of the Tomsk diocese A. P. Uspensky, addressed to the Council of Ministers of the Provisional Siberian government in July 1918. A.P. Uspensky solicited for formation of the Ministry of confessions in the Provisional Siberian government. Memoranda are initiative documents to the Statute on the Chief Administration of religious denominations adopted by the Council...

  15. DEEP STRUCTURE OF THE SIBERIAN PLATFORM – CENTRAL ASIAN MOBILE BELT TRANSITION ZONE FROM TELESEISMIC DATA

    V. V. Mordvinova

    2016-01-01

    Full Text Available Deep velocity sections of the transition zone from the Siberian platform to the Central Asian mobile belt are constructed by teleseismic tomography and P-receiver function techniques. An array of the dense ancient Siberian craton is identified in the velocity sections with areas of high seismic velocity. In the SSW section MOBAL_2003, the surface boundary of the craton corresponds to the southern margin of the Siberian platform and is nearly vertical to a depth of 120 km. At larger depths, the craton slides almost horizontally underneath the Tunka rift area. At depths from 150 to 250 km, it is in contact with the area under the Khamar-Daban mountain range. In the southeast, according to the SE velocity section PASSCAL_1992 across the South Baikal basin and the Khamar-Daban mountain range, the Siberian craton thickness is reduced from 270 to 150 km at the contact of the Siberian platform with the Baikal folded area. In this contact zone, the upper part of the craton is wedge-shaped and has an angle of about 45° with the ground surface; it completely tapers off at a depth of 150 km to the east of Lake Baikal. The vertical configuration of the southern segment of the Siberian craton, which evolved with time, may determine the nature of the Baikal rifting in the Cenozoic. 

  16. Spatio-temporal analysis of agricultural land-use intensity across the Western Siberian grain belt.

    Kühling, Insa; Broll, Gabriele; Trautz, Dieter

    2016-02-15

    The Western Siberian grain belt covers 1millionkm² in Asiatic Russia and is of global importance for agriculture. Massive land-use changes took place in that region after the dissolution of the Soviet Union and the collapse of the state farm system. Decreasing land-use intensity (LUI) in post-Soviet Western Siberia was observed on grassland due to declining livestock whilst on cropland trends of land abandonment reversed in the early 2000s. Recultivation of abandoned cropland as well as increasing fertilizer inputs and narrowing crop rotations led to increasing LUI on cropland during the last two decades. Beyond that general trend, no information is available about spatial distribution and magnitude but a crucial precondition for the development of strategies for sustainable land management. To quantify changes and patterns in LUI, we developed an intensity index that reflects the impacts of land-based agricultural production. Based on subnational yearly statistical data, we calculated two separate input-orientated indices for cropland and grassland, respectively. The indices were applied on two spatial scale: at seven provinces covering the Western Siberian grain belt (Altay Kray, Chelyabinsk, Kurgan, Novosibirsk, Omsk, Sverdlovsk and Tyumen) and at all districts of the central province Tyumen. The spatio-temporal analysis clearly showed opposite trends for the two land-use types: decreasing intensity on grassland (-0.015 LUI units per year) and intensification on cropland (+0.014 LUI units per year). Furthermore, a spatial concentration towards intensity centres occurred during transition from a planned to a market economy. A principal component analysis enabled the individual calculations of both land-use types to be combined and revealed a strong link between biophysical conditions and LUI. The findings clearly showed the need for having a different strategy for future sustainable land management for grassland (predominantly used by livestock of households

  17. Reserve Growth in Oil Fields of West Siberian Basin, Russia

    Verma, Mahendra K.; Ulmishek, Gregory F.

    2006-01-01

    Although reserve (or field) growth has proven to be an important factor contributing to new reserves in mature petroleum basins, it is still a poorly understood phenomenon. Limited studies show that the magnitude of reserve growth is controlled by several major factors, including (1) the reserve booking and reporting requirements in each country, (2) improvements in reservoir characterization and simulation, (3) application of enhanced oil recovery techniques, and (4) the discovery of new and extensions of known pools in discovered fields. Various combinations of these factors can affect the estimates of proven reserves in particular fields and may dictate repeated estimations of reserves during a field's life. This study explores the reserve growth in the 42 largest oil fields in the West Siberian Basin, which contain about 55 percent of the basin's total oil reserves. The West Siberian Basin occupies a vast swampy plain between the Ural Mountains and the Yenisey River, and extends offshore into the Kara Sea; it is the richest petroleum province in Russia. About 600 oil and gas fields with original reserves of 144 billion barrels of oil (BBO) and more than 1,200 trillion cubic feet of gas (TCFG) have been discovered. The principal oil reserves and most of the oil fields are in the southern half of the basin, whereas the northern half contains mainly gas reserves. Sedimentary strata in the basin consist of Upper Triassic through Tertiary clastic rocks. Most oil is produced from Neocomian (Lower Cretaceous) marine to deltaic sandstone reservoirs, although substantial oil reserves are also in the marine Upper Jurassic and continental to paralic Lower to Middle Jurassic sequences. The majority of oil fields are in structural traps, which are gentle, platform-type anticlines with closures ranging from several tens of meters to as much as 150 meters (490 feet). Fields producing from stratigraphic traps are generally smaller except for the giant Talin field which

  18. Canine distemper in Siberian tiger cubs from Zagreb ZOO: case report

    Dean Konjević

    2011-01-01

    Full Text Available Canine distemper is a contagious, potentially lethal disease of mainly domestic and wild canids, but also of many other mammalian species including large felids. In February 2004, two Siberian tiger (Panthera tigris altaica cubs at the age of six months died at the Zagreb ZOO. The animals were presented for necropsy with two days history of severe digestive disorders, characterized mainly by haemathemesis. Dissections revealed catarrhal to pseudomembranous gastroenteritis (depending on the animal accompanied with haemorrhagic oedema of the lungs. Necrotic tonsillitis and disseminated depletion of the lymphocytes were the most prominent histological findings in both examined animals, while intranuclear and intracytoplasmatic inclusion bodies were found in the samples of the tongues and intestines. Representative portions of the livers, intestines, tonsils and lymph nodes were submitted for bacteriological and mycological analysis. The presence of Clostridium spp., Campylobacter coli and Escherichia coli was detected in gut samples, coli-like bacteria were found in samples of liver, tonsils and lymph nodes, while Candida sp. was found in the gut and pharynx samples. Toxicological analysis excluded anticoagulant and organophosphorous intoxication as the cause of death. Immunohistochemical analysis was positive for canine distemper virus. Based on all this, epizootiological, clinical and additional findings, canine distemper was recognized as the cause of the observed condition in these animals.

  19. Simultaneous Occurrence of Pancreatic Adenocarcinoma and Brunner's Gland Adenoma in a Siberian Tiger (Panthera tigris altaica).

    Gombač, M; Dolenšek, T; Jaušovec, D; Kvapil, P; Švara, T; Pogačnik, M

    2015-11-01

    We describe a case of pancreatic adenocarcinoma and Brunner's gland adenoma in an 18-year-old male Siberian tiger (Panthera tigris altaica) from the Ljubljana Zoo. The tiger was humanely destroyed due to weakness and progressive weight loss. Necropsy examination revealed a large, grey, predominantly necrotic mass replacing the major part of the pancreatic body. Microscopically, the mass was unencapsulated, poorly demarcated, highly cellular and composed of highly pleomorphic, cuboidal to tall columnar cells with basal, round or oval, moderately anisokaryotic nuclei with prominent nucleoli and moderate to large amounts of eosinophilic cytoplasm. The tumour was diagnosed as pancreatic tubular adenocarcinoma with infiltration into the duodenum and mesentery. There were tumour emboli in mesenteric blood vessels and hepatic metastases. The non-affected part of the pancreas exhibited severe chronic pancreatitis. In addition, one firm white neoplastic nodule was observed in the duodenal wall. The nodule was set in the tunica muscularis and was unencapsulated, well demarcated and highly cellular, and consisted of a closely packed layer of normal Brunner's glands and a centrally positioned group of irregularly branched tubules with small amounts of debris in the lumen. The neoplastic nodule was diagnosed as Brunner's gland adenoma. The present case is, to the best of our knowledge, the first report of concurrent pancreatic adenocarcinoma and Brunner's gland adenoma, most probably induced by chronic pancreatitis, either in man or animals. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. An odorant-binding protein as a new allergen from Siberian hamster (Phodopus sungorus).

    Torres, J A; Pastor-Vargas, C; de las Heras, M; Vivanco, F; Cuesta, Javier; Sastre, J

    2012-01-01

    A case of anaphylaxis following a bite from a Siberian hamster (SH; Phodopus sungorus) is described. Skin prick tests with hair, urine and salivary gland extracts from SH were positive, while the tests were negative for hair extracts from other rodents. IgE immunoblotting with the patient serum revealed 3 IgE-binding bands of about 18, 21 and 23 kDa. When the patient's serum was preincubated with rabbit, mouse and gerbil hair extracts, no inhibition of the 3 SH IgE-binding bands was demonstrated. Proteins extracted from the 3 bands were analyzed by N-terminal sequencing and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry, and peptides were sequenced. IgE-binding bands were identified as being an odorant-binding protein belonging to the lipocalin family. Analysis of the 3 IgE-binding bands found in the hair, urine and salivary glands of SH showed a new allergenic protein lacking cross-reactivity with allergens from other rodents. The 3 bands likely correspond to isoforms of a single allergen. Copyright © 2011 S. Karger AG, Basel.

  1. Reactivity of Pleistocene aged organic matter in the Siberian Arctic

    Davydov, S.; Vonk, J. E.; Mann, P. J.; Davydova, A.; Sobczak, W. V.; Schade, J. D.; Bulygina, E. B.; Zimov, S. A.; Holmes, R. M.

    2011-12-01

    Half of the global stock of soil organic carbon (OC) is stored in Arctic permafrost. About one third of this pool consists of so-called yedoma, organic-rich deposits that were formed during the Pleistocene. Previous studies show rapid respiration of yedoma upon thawing, with the potential release of large quantities of relict OC into the contemporary C cycle. The fluvial and coastal reactivity of this OC, however, and its fate remain unclear. Duvannyi Yar is a well-studied yedoma exposure on the banks of Kolyma River in Northeastern Siberia. It can serve as a model for the >7000 km long East Siberian Arctic coastline that is dominated by similarly exposed yedoma cliffs, and is increasingly vulnerable to erosion with climate warming-induced decreases in sea-ice, and increases in storms and wave-fetch. Permafrost thaw causes the slopes of Duvannyi Yar to retreat 3-5 m/y, producing mudstreams that drain into the Kolyma River. These streams are heavily loaded with freshly thawed yedoma sediments (ca. 650 g/L; POC ca. 10 g/L; DOC ca. 150 mg/L). Partial CO2 pressure in these streams was on average 8400 ppm (stdev 2100; n=4) whereas the Kolyma River at the stream mouth contained CO2 concentrations of ca. 900 ppm (stdev 90; n=4), suggesting substantial outgassing during transport. We performed biological oxygen demand assays in combination with a set of incubations to estimate OC lability in a range of dilutions of Duvannyi Yar water with Kolyma River and East Siberian Sea water, in combination with nutrient and enzymatic activity rate analysis to identify potential limitation processes. Our goal was to assess carbon consumption rates and the effect of different microbial communities along its transport towards the ocean. O2 loss (% after 24h) increased significantly from undiluted Kolyma water to increasingly spiked dilutions with filtered Duvannyi Yar filtered water; 0%/0.5%/1%/10%/100% dilutions showed O2 losses of 1.6%, 3.5%, 5.1%, 13% and 35%, respectively. However, C

  2. Statistical modeling of temperature, humidity and wind fields in the atmospheric boundary layer over the Siberian region

    Lomakina, N. Ya.

    2017-11-01

    The work presents the results of the applied climatic division of the Siberian region into districts based on the methodology of objective classification of the atmospheric boundary layer climates by the "temperature-moisture-wind" complex realized with using the method of principal components and the special similarity criteria of average profiles and the eigen values of correlation matrices. On the territory of Siberia, it was identified 14 homogeneous regions for winter season and 10 regions were revealed for summer. The local statistical models were constructed for each region. These include vertical profiles of mean values, mean square deviations, and matrices of interlevel correlation of temperature, specific humidity, zonal and meridional wind velocity. The advantage of the obtained local statistical models over the regional models is shown.

  3. Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36

    Jung, Hye Ryung; Pasini, Diego; Helin, Kristian

    2010-01-01

    distinct coexisting modifications. In certain cases, high mass accuracy LTQ-Orbitrap MS/MS allowed precise localization of near isobaric coexisting PTMs such as trimethylation and acetylation within individual peptides. ETD MS/MS facilitated sequencing and annotation of phosphorylated histone peptides....... The combined use of ETD and CID MS/MS increased the total number of identified modified peptides. Comparative quantitative analysis of histones from wild type and Suz12-deficient ESCs using stable isotope labeling with amino acids in cell culture and LC-MS/MS revealed a dramatic reduction of H3K27me2 and H3K27......me3 and an increase of H3K27ac, thereby uncovering an antagonistic methyl/acetyl switch at H3K27. The reduction in H3K27 methylation and increase in H3K27 acetylation was accompanied by H3K36 acetylation and methylation. Estimation of the global isoform percentage of unmodified and modified histone...

  4. Amino acid production exceeds plant nitrogen demand in Siberian tundra

    Wild, Birgit; Eloy Alves, Ricardo J.; Bárta, Jiři; Čapek, Petr; Gentsch, Norman; Guggenberger, Georg; Hugelius, Gustaf; Knoltsch, Anna; Kuhry, Peter; Lashchinskiy, Nikolay; Mikutta, Robert; Palmtag, Juri; Prommer, Judith; Schnecker, Jörg; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Richter, Andreas

    2018-03-01

    Arctic plant productivity is often limited by low soil N availability. This has been attributed to slow breakdown of N-containing polymers in litter and soil organic matter (SOM) into smaller, available units, and to shallow plant rooting constrained by permafrost and high soil moisture. Using 15N pool dilution assays, we here quantified gross amino acid and ammonium production rates in 97 active layer samples from four sites across the Siberian Arctic. We found that amino acid production in organic layers alone exceeded literature-based estimates of maximum plant N uptake 17-fold and therefore reject the hypothesis that arctic plant N limitation results from slow SOM breakdown. High microbial N use efficiency in organic layers rather suggests strong competition of microorganisms and plants in the dominant rooting zone. Deeper horizons showed lower amino acid production rates per volume, but also lower microbial N use efficiency. Permafrost thaw together with soil drainage might facilitate deeper plant rooting and uptake of previously inaccessible subsoil N, and thereby promote plant productivity in arctic ecosystems. We conclude that changes in microbial decomposer activity, microbial N utilization and plant root density with soil depth interactively control N availability for plants in the Arctic.

  5. Being at the right time at the right place: interpreting the annual life cycle of Afro-Siberian red knots

    Leyrer, J.

    2011-01-01

    This thesis describes the possible selection pressures acting on survival and, indirectly, on reproduction of Afro-Siberian red knots Calidris canutus canutus while wintering and migrating. Afro-Siberian red knots are long-distance migrants. They travel between the West African wintering areas and

  6. Water track distribution and effects on carbon dioxide flux in an eastern Siberian upland tundra landscape

    Curasi, Salvatore R; Loranty, Michael M; Natali, Susan M

    2016-01-01

    Shrub expansion in tundra ecosystems may act as a positive feedback to climate warming, the strength of which depends on its spatial extent. Recent studies have shown that shrub expansion is more likely to occur in areas with high soil moisture and nutrient availability, conditions typically found in sub-surface water channels known as water tracks. Water tracks are 5–15 m wide channels of subsurface water drainage in permafrost landscapes and are characterized by deeper seasonal thaw depth, warmer soil temperatures, and higher soil moisture and nutrient content relative to adjacent tundra. Consequently, enhanced vegetation productivity, and dominance by tall deciduous shrubs, are typical in water tracks. Quantifying the distribution of water tracks may inform investigations of the extent of shrub expansion and associated impacts on tundra ecosystem carbon cycling. Here, we quantify the distribution of water tracks and their contribution to growing season CO 2 dynamics for a Siberian tundra landscape using satellite observations, meteorological data, and field measurements. We find that water tracks occupy 7.4% of the 448 km 2 study area, and account for a slightly larger proportion of growing season carbon uptake relative to surrounding tundra. For areas inside water tracks dominated by shrubs, field observations revealed higher shrub biomass and higher ecosystem respiration and gross primary productivity relative to adjacent upland tundra. Conversely, a comparison of graminoid-dominated areas in water tracks and inter-track tundra revealed that water track locations dominated by graminoids had lower shrub biomass yet increased net uptake of CO 2 . Our results show water tracks are an important component of this landscape. Their distribution will influence ecosystem structural and functional responses to climate, and is therefore of importance for modeling. (letter)

  7. Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region.

    Hernández, Candela L; Reales, Guillermo; Dugoujon, Jean-Michel; Novelletto, Andrea; Rodríguez, Juan Nicolás; Cuesta, Pedro; Calderón, Rosario

    2014-01-24

    The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region. The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population. The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements

  8. Review of the Book: Trepavlov V.V., Belyakov A.V. Sibirskie tsarevichi v istorii Rossii [The Siberian Princes in the History of Russia

    D.N. Maslyuzhenko

    2018-03-01

    Full Text Available This article analyzes the new book by Russian historians V.V. Trepavlov and A.V. Be­lyakov dedicated to the Siberian princes and their role in national history. The first part of the book is dedicated to the struggle of Kuchum Khan and his descendants for revenge in Siberia and the restoration of the Siberian Khanate, and the second one – to the conditions of the Kuchumovichi’s appearances in the Moscow state, their inhabitancy, the role in political processes and the further disappearance of the dynasty. The book is written on the basis of a large number of archival documents, mainly from the Russian State Archives of Ancient Acts (RGADA. It allowed reconstructing the rich tapestry of the Kuchumovichi’s life in Siberia and the Moscow state based on the methods and traditions of political history, studies of everyday life, prosopography, microhistory and genealogy. On the one hand, the book will be important for studies of Siberia, because the Siberian kings and princes in the Moscow state tried, if possible, to keep their familiar surroundings for a long time that preserved some distinctive features of their prior life’s period, which cannot be directly reconstructed with local materials. On the other hand, many nuances of the everyday life of these dynasts and their entourage can characterize not only the Siberian aristocracy but also the relevant layers of Moscow society as a whole, for which the Eastern traditions were also not immune to. Therein, we get an interesting slice of the Moscow society of the 16th–17th centuries: notably, the gradual forfeiture of the princes directly coincided with the exhaustion of the post-Horde and Eastern traditions in Russia as a whole. Despite some minor shortcomings, the materials of the monograph are so manifold so each reader will find in it some of his or her own interesting aspects, and will get an idea of an interesting slice of the Russian history of the 16th–17th centuries.

  9. Changes in the contents of nitrogen fractions with loosing vital capacity of the Siberian fir Abies sibirica Ledeb. seeds

    S. G. Prokushkin

    2017-02-01

    Full Text Available Siberian fir seeds often lose their germinating capacity during storage. This results from, among other factors, changing contents of nitrogen compounds in the seeds, especially those of protein fractions. This paper focuses on analyzing changes of these compounds in nonviable seeds of the species depending on ecological and conditions and stand location, as well as on tree growth class (Kraft growth classes I and IV. The contents of the total and protein nitrogen in the nonviable seeds of the trees of growth classes I and IV appeared to vary widely and to depend on stand location and seed location in the tree crown. The maximum contents were in the seeds located in the upper part of the crown. The seeds from the middle and lower crown parts contained much less total and protein nitrogen. The hard-to-solve protein fraction dominated over other protein fraction in the seeds from the upper part of the crowns of the trees of growth classes I and IV. However, this fraction, like prolamines, changed uniformly throughout the crowns, whereas seed glutelin content varied insignificantly among the crown parts. Albumins and globulins showed a uniform crown top-to-bottom decrease. A comparison of viable seed with unviable seeds for contents of the nitrogen forms revealed a marked decrease in the total and protein nitrogen in the latter, especially for the trees of growth class IV. The seeds that lost their germinating capacity exhibited increasingly hard-to-solve protein fraction and drastically decreasing albumins and globulins wherever the seeds were in the crown. Their glutelin and prolamine contents changed inconsiderably.The changes of the quantitative ratio between the protein fractions found by the study cause, along with other physiological and biochemical factors, the loss of viability of Siberian fir seeds during storage.

  10. Mitochondrial cytochrome b sequence variations and population structure of Siberian chipmunk (Tamias sibiricus) in Northeastern Asia and population substructure in South Korea.

    Lee, Mu-Yeong; Lissovsky, Andrey A; Park, Sun-Kyung; Obolenskaya, Ekaterina V; Dokuchaev, Nikolay E; Zhang, Ya-Ping; Yu, Li; Kim, Young-Jun; Voloshina, Inna; Myslenkov, Alexander; Choi, Tae-Young; Min, Mi-Sook; Lee, Hang

    2008-12-31

    Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia--northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia--northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

  11. Histaminergic regulation of seasonal metabolic rhythms in Siberian hamsters.

    I'anson, Helen; Jethwa, Preeti H; Warner, Amy; Ebling, Francis J P

    2011-06-01

    We investigated whether histaminergic tone contributes to the seasonal catabolic state in Siberian hamsters by determining the effect of ablation of histaminergic neurons on food intake, metabolic rate and body weight. A ribosomal toxin (saporin) conjugated to orexin-B was infused into the ventral tuberomammillary region of the hypothalamus, since most histaminergic neurons express orexin receptors. This caused not only 75-80% loss of histaminergic neurons in the posterior hypothalamus, but also some loss of other orexin-receptor expressing cells e.g. MCH neurons. In the long-day anabolic state, lesions produced a transient post-surgical decrease in body weight, but the hamsters recovered and maintained constant body weight, whereas weight gradually increased in sham-lesioned hamsters. VO(2) in the dark phase was significantly higher in the lesioned hamsters compared to shams, and locomotor activity also tended to be higher. In a second study in short days, sham-treated hamsters showed the expected seasonal decrease in body weight, but weight remained constant in the lesioned hamsters, as in the long-day study. Lesioned hamsters consumed more during the early dark phase and less during the light phase due to an increase in the frequency of meals during the dark and decreased meal size during the light, and their cumulative food intake in their home cages was greater than in the control hamsters. In summary, ablation of orexin-responsive cells in the posterior hypothalamus blocks the short-day induced decline in body weight by preventing seasonal hypophagia, evidence consistent with the hypothesis that central histaminergic mechanisms contribute to long-term regulation of body weight. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. POLARIZED BEAMS: 2 - Partial Siberian Snake rescues polarized protons at Brookhaven

    Huang, Haixin

    1994-01-01

    To boost the level of beam polarization (spin orientation), a partial 'Siberian Snake' was recently used to overcome imperfection depolarizing resonances in the Brookhaven Alternating Gradient Synchrotron (AGS). This 9-degree spin rotator recently permitted acceleration with no noticeable polarization loss. The intrinsic AGS depolarizing resonances (which degrade the polarization content) had been eliminated by betatron tune jumps, but the imperfection resonances were compensated by means of harmonic orbit corrections. However, at high energies these orbit corrections are difficult and tedious and a Siberian Snake became an attractive alternative

  13. Memoranda by A.P. Uspensky to the Council of Ministers of the Provisional Siberian government

    Sukhanov Aleksandr

    2015-06-01

    Full Text Available This publication offers a previously unknown memoranda by representative of the diocesan assembly of deputies of the clergy and laity of the Tomsk diocese A. P. Uspensky, addressed to the Council of Ministers of the Provisional Siberian government in July 1918. A.P. Uspensky solicited for formation of the Ministry of confessions in the Provisional Siberian government. Memoranda are initiative documents to the Statute on the Chief Administration of religious denominations adopted by the Council of Ministers of the Russian government on December 27, 1918.

  14. Co-Opetition (Coexisting Competition and Competitive Coexistaence in the Tourism Field in Siberian Regions

    Olga Pavlovna Kuznetsova

    2017-03-01

    Full Text Available The relevance of the topic is due to the need to use of such category as “co-opetition” by public and local government authorities when implementing their powers in the tourism sphere. We divide the term “co-opetition” into two categories: “coexisting competition” and “competitive coexistence”. The problem field of the study is that in the conditions of crisis development, it is difficult to choose and implement new measures and approaches aimed at improving the economic situation in Russia and its regions, diversify the economy. In modern conditions, it is important and effective to develop domestic tourism and incoming tourism in Russia as well as its effective functioning. Russia has considerable natural and ecological, cultural and historical resources. However, the imperfection of the authorities operation and a mechanism of combined implementation of projects by different territories prevent the transformation of tourism industry into the economic powerhouse. In this regard, on the example of Siberian regions, we offer to the authorities to use co-opetition (in both of its meanings in the combined development of tourism and to establish on this basis the tourist mega-cluster “Fairy Siberia”. The study of foreign experience has allowed revealing the positions, in which Russia falls behind other countries-leaders in the tourism industry. The proposed approach is promising, and it is based on joint efforts of regions and saving money due to the economies of scale. At the same time, it allows the regions to develop their competitive advantages. The practical significance of the received results consists in the possibility of their use by the public and local authorities in the implementation of effective policy for the development of tourism industry.

  15. Seasonal dynamics of structure and functional activity of ectomycorrhizal roots of the Siberian fir

    T. A. Sizonenko

    2017-12-01

    Full Text Available The aim of our work was to study seasonal dynamics of the Siberian fir Abies sibirica Ledeb. ectomycorrhizal morpho-anatomical structure, respiration rate and fluorescence. The study was carried out in the bilberry-sphagnum spruce forest in the middle taiga of the Komi Republic, Russia. The morpho-anatomical structure and fluorescence parameters were studied by light and luminescence microscopy. Thin root respiration was studied in intact fine roots in the field using an infrared gas analyzer. 12 subtypes of fungal mantels were revealed in ectomycorrhizal fir roots; their amount and composition demonstrated seasonal dynamic changes. At the beginning vegetation stage, the diversity and proportion of pseudoparenchymatous and double covers were maximal. Plant component of ectomycorrhizae that includes cortical parenchyma and stele had high activity of fluorescence during the entire vegetation period. The dynamics of staining of fungal component (fungal mantel and Hartig net was more contrasting. The highest fluorescence intensity of cortical parenchyma was found in ectomycorrhizae with maximal fungal mantel thickness. High proportion of tannin cells in cortical parenchyma was related with low intensity of fungal mantel and Hartig net fluorescence. During vegetation season, maximal amount of intensively strained ectomycorrhizal elements occurred in July and unstrained – in June and August. Relation between fine roots respiration and an increase of brightly strained ectomycorrhizal structural elements in fir roots was not statistically significant. Root CO2-emission was lower in May and September in comparison with summer months. For respiration rate of fir fine roots we found its strong positive correlation with the litter temperature.

  16. Widespread release of old carbon across the Siberian Arctic echoed by its large rivers

    Ö. Gustafsson

    2011-06-01

    Full Text Available Over decadal-centennial timescales, only a few mechanisms in the carbon-climate system could cause a massive net redistribution of carbon from land and ocean systems to the atmosphere in response to climate warming. The largest such climate-vulnerable carbon pool is the old organic carbon (OC stored in Arctic permafrost (perennially frozen soils. Climate warming, both predicted and now observed to be the strongest globally in the Eurasian Arctic and Alaska, causes thaw-release of old permafrost carbon from local tundra sites. However, a central challenge for the assessment of the general vulnerability of this old OC pool is to deduce any signal integrating its release over larger scales. Here we examine radiocarbon measurements of molecular soil markers exported by the five Great Russian-Arctic Rivers (Ob, Yenisey, Lena, Indigirka and Kolyma, employed as natural integrators of carbon release processes in their watersheds. The signals held in estuarine surface sediments revealed that average radiocarbon ages of n-alkanes increased east-to-west from 6400 yr BP in Kolyma to 11 400 yr BP in Ob. This is consistent with westwards trends of both warmer climate and more degraded organic matter as indicated by the ratio of high molecular weight (HMW n-alkanoic acids to HMW n-alkanes. The dynamics of Siberian permafrost can thus be probed via the molecular-radiocarbon signal as carried by Arctic rivers. Old permafrost carbon is at present vulnerable to mobilization over continental scales. Climate-induced changes in the radiocarbon fingerprint of released permafrost carbon will likely depend on changes in both permafrost coverage and Arctic soil hydraulics.

  17. Independence of circadian entrainment state and responses to melatonin in male Siberian hamsters

    Gorman Michael R

    2003-10-01

    Full Text Available Abstract Background Seasonal fluctuations in physiology and behavior depend on the duration of nocturnal melatonin secretion programmed by the circadian system. A melatonin signal of a given duration, however, can elicit different responses depending on whether an animal was previously exposed to longer or shorter photoperiod signals (i.e., its photoperiodic history. This report examined in male Siberian hamsters which of two aspects of photoperiod history – prior melatonin exposure or entrainment state of the circadian system – is critical for generating contingent responses to a common photoperiodic signal. Results In Experiment #1, daily melatonin infusions of 5 or 10 h duration stimulated or inhibited gonadal growth, respectively, but had no effect on entrainment of the locomotor activity rhythm to long or short daylengths, thereby demonstrating that melatonin history and entrainment status could be experimentally dissociated. These manipulations were repeated in Experiment #2, and animals were subsequently exposed to a 12 week regimen of naturalistic melatonin signals shown in previous experiments to reveal photoperiodic history effects. Gonadal responses differed as a function of prior melatonin exposure but were unaffected by the circadian entrainment state. Experiment #3 demonstrated that a new photoperiodic history could be imparted during four weeks of exposure to long photoperiods. This effect, moreover, was blocked in animals treated concurrently with constant release melatonin capsules that obscured the endogenous melatonin signal: Following removal of the implants, the gonadal response depended not on the immediately antecedent circadian entrainment state, but on the more remote photoperiodic conditions prior to the melatonin implant. Conclusions The interpretation of photoperiodic signals as a function of prior conditions depends specifically on the history of melatonin exposure. The photoperiodic regulation of circadian

  18. Glacial-interglacial variations of microbial communities in permafrost and lake deposits in the Siberian Arctic

    Mangelsdorf, Kai; Bischoff, Juliane; Gattinger, Andreas; Wagner, Dirk

    2013-04-01

    The Artic regions are expected to be very sensitive to the currently observed climate change. When permafrost is thawing, the stored carbon becomes available again for microbial degradation, forming a potential source for the generation of carbon dioxide and methane with their positive feedback effect on the climate warming. For the prediction of future climate evolution it is, therefore, important to improve our knowledge about the microbial-driven greenhouse gas dynamics in the Siberian Arctic and their response to glacial-interglacial changes in the past. Sample material was drilled on Kurungnahk Island (Russian-German LENA expedition) located in the southern part of the Lena delta and in lake El'gygytgyn (ICDP-project) in the eastern part of Siberia. The Kurungnahk samples comprise Late Pleistocene to Holocene deposits, whereas the lake El'gygytgyn samples cover Middle to Late Pleistocene sediments. Samples were investigated applying a combined biogeochemical and microbiological approach. The methane profile of the Kurungnahk core reveals highest methane contents in the warm and wet Holocene and Late Pleistocene (LP) deposits and correlates largly to the organic carbon (TOC) contents. Archaeol concentrations, being a biomarker for past methanogenic archaea, are also high during the warm and wet Holocene and LP intervals and low during the cold and dry LP periods. This indicates that part of the methane might be produced and trapped in the past. However, biomarkers for living microorganisms (bacteria and archaea) and microbial activity measurements of methanogens point, especially, for the Holocene to a viable archaeal community, indicating a possible in-situ methane production. Furthermore, warm/wet-cold/dry climate cycles are recorded in the archaeal diversity as revealed by genetic fingerprint analysis. Although the overlying lake water buffers the temperature effect on the lake sediments, which never became permafrost, the bacterial and archaeal biomarker

  19. Terpenoid emissions from fully grown east Siberian Larix cajanderi trees

    M. K. Kajos

    2013-07-01

    Full Text Available While emissions of many biogenic volatile organic compounds (BVOCs, such as terpenoids, have been studied quite intensively in North American and Scandinavian boreal forests, the vast Siberian boreal forests have remained largely unexplored by experimental emission studies. In this study the shoot-scale terpenoid emission rates from two mature Larix cajanderi trees growing in their natural habitat in eastern Siberia were measured at the Spasskaya Pad flux measurement site (62°15´18.4" N, 129°37´07.9" E located on the western bank of the Lena river. The measurements were conducted during three campaigns: 3–24 June, 8–26 July, and 14–30 August, in the summer of 2009. A dynamic flow-through enclosure technique was applied for adsorbent sampling, and the samples were analysed offline with a gas chromatograph. Between 29 and 45 samples were taken from each shoot during all three campaigns. Seven different monoterpenes, six different sesquiterpenes, linalool isoprene, and 2-methyl-3-buten-2-ol (MBO were identified. The monthly median value of the total terpenoid emissions varied between 0.006 and 10.6 μg gdw−1 h−1. The emissions were dominated by monoterpenes, which constituted between 61 and 92% of the total emissions. About half of the monoterpene emissions were comprised of Δ 3-carene; α- and β-pinene had significant emissions as well. Linalool emissions were also substantial, comprising 3–37% of the total emissions, especially in June. Sesquiterpenes accounted for less than 3% and isoprene less than 1% of the total emissions. Based on the measured emission rates, the relative atmospheric concentration of each compound was estimated. Monoterpenes were the species with the highest relative concentration, while linalool and sesquiterpenes had a notably smaller contribution to the estimated atmospheric concentration than to the emission rates. A temperature-dependent pool algorithm with a constant β (0.09 °C−1 for monoterpenes

  20. 'Abd al-Rashid Ibrahim's Biographical Dictionary on Siberian Islamic Scholars

    Bustanov, A.K.

    2014-01-01

    This article is a publication of facsimiles and annotated English translations of two versions of a biographical dictionary of Siberian Islamic scholars. The work written by ‘Abd al-Rashīd Ibrāhīm deserves serious attention from scholars because it opens up a world of intellectual life among the

  1. The Central European, Tarim and Siberian Large Igneous Provinces, Late Palaeozoic orogeny and coeval metallogeny

    de Boorder, H.|info:eu-repo/dai/nl/098199056

    2014-01-01

    The formation of the Central European and Tarim Large Igneous Provinces (LIPs) in the Early Permian coincided with the demise of the Variscan and the Southern Tianshan orogens, respectively. The Early Triassic Siberian LIP was formed in the wake of the Western Altaid orogeny in the Late Permian.

  2. Paleocene–Eocene warming and biotic response in the epicontinental West Siberian Sea

    Frieling, J.; Iakovleva, A.I.; Reichart, G.-J.; Aleksandrova, G.N.; Gnibidenko, Z.N.; Schouten, S.; Sluijs, A.

    2014-01-01

    We present a Paleocene–Eocene (ca. 60–52 Ma) sea-surface temperature record from sediments deposited in the epicontinental West Siberian Sea. TEX86 paleothermometry indicates long-term late Paleocene (~17 °C ca. 59 Ma) to early Eocene (26 °C at 52 Ma) sea-surface warming, consistent with trends

  3. Historical records of organic matter supply and degradation status in the East Siberian Sea

    Bröder, Lisa; Tesi, Tommaso; Andersson, August

    2016-01-01

    biomarkers were used to construct two centennial records in the East Siberian Sea. Differences in topsoil and Pleistocene Ice Complex Deposit permafrost concentrations, modeled using δ13C and δ14C, were larger between inner and outer shelf than the changes over time. Similarly, lignin-derived phenol...

  4. Anthropogenic impacts on habitat structure and species richness in the west Siberian Arctic

    Olga Khitun; Olga Rebristaya

    2002-01-01

    Intensive technogenous invasion in the West Siberian Arctic during the last two decades in connection with gas and oil exploration, along with the constant growth of domestic reindeer herds, has caused dramatic changes in arctic ecosystems. Loss of biodiversity on the species level has not yet been documented in the region on a whole, but changes in ecosystems in...

  5. Paleocene-Eocene warming and biotic response in the epicontinental West Siberian Sea

    Frieling, Joost|info:eu-repo/dai/nl/338017909; Iakovleva, Alina I.; Reichart, Gert Jan|info:eu-repo/dai/nl/165599081; Aleksandrova, Galina N.; Gnibidenko, Zinaida N.; Schouten, Stefan|info:eu-repo/dai/nl/137124929; Sluijs, Appy|info:eu-repo/dai/nl/311474748

    2014-01-01

    We present a Paleocene-Eocene (ca. 60-52 Ma) sea-surface temperature record from sediments deposited in the epicontinental West Siberian Sea. TEX86 paleothermometry indicates long-term late Paleocene (~17 °C ca. 59 Ma) to early Eocene (26 °C at 52 Ma) sea-surface warming, consistent with trends

  6. Metabolic influences on circadian rhythmicity in Siberian and Syrian hamsters exposed to long photoperiods.

    Challet, E; Kolker, D E; Turek, F W

    2000-01-01

    Calorie restriction and other situations of reduced glucose availability in rodents alter the entraining effects of light on the circadian pacemaker located in the suprachiasmatic nuclei. Siberian and Syrian hamsters are photoperiodic species that are sexually active when exposed to long summer-like photoperiods, while both species show opposite changes in body mass when transferred from long to short or short to long days. Because metabolic cues may fine tune the photoperiodic responses via the suprachiasmatic nuclei, we tested whether timed calorie restriction can alter the photic synchronization of the light-entrainable pacemaker in these two hamster species exposed to long photoperiods. Siberian and Syrian hamsters were exposed to 16 h:8 h light:dark cycles and received daily hypocaloric (75% of daily food intake) or normocaloric diet (100% of daily food intake) 4 h after light onset. Four weeks later, hamsters were transferred to constant darkness and fed ad libitum. The onset of the nocturnal pattern of locomotor activity was phase advanced by 1.5 h in calorie-restricted Siberian hamsters, but not in Syrian hamsters. The lack of phase change in calorie-restricted Syrian hamsters was also observed in individuals exposed to 14 h:10 h dim light:dark cycles and fed with lower hypocaloric food (i.e. 60% of daily food intake) 2 h after light onset. Moreover, in hamsters housed in constant darkness and fed ad lib., light-induced phase shifts of the locomotor activity in Siberian hamsters, but not in Syrian hamsters were significantly reduced when glucose utilization was blocked by pretreatment with 500 mg/kg i.p. 2-deoxy-D-glucose. Taken together, these results show that the photic synchronization of the light-entrainable pacemaker can be modulated by metabolic cues in Siberian hamsters, but not in Syrian hamsters maintained on long days.

  7. Borrelia burgdorferi Sensu Lato in Siberian chipmunks (Tamias sibiricus) introduced in suburban forests in France.

    Vourc'h, Gwenaël; Marmet, Julie; Chassagne, Michelle; Bord, Séverine; Chapuis, Jean-Louis

    2007-01-01

    Numerous vertebrate reservoirs have been described for Borrelia burgdorferi sensu lato (sl), which includes the etiological agents of Lyme Borreliosis (LB). The Siberian chipmunk (Tamias sibiricus) is a rodent originating from Asia, where it is suspected to be a B. burgdorferi reservoir. It has been intentionally released into the wild in Europe since the 1970s, but has not yet been subject to any study regarding its association with the LB agent. In this paper we studied Siberian chipmunk infestation with the LB vector (Ixodes ricinus) and infection prevalence by LB spirochetes in a suburban introduced population. We compared these findings with known competent reservoir hosts, the bank vole (Myodes [clethrionomys] glareolus) and wood mouse (Apodemus sylvaticus). All Siberian chipmunks were infested with larvae and larval abundance was higher in this species (mean number of larvae [95% Confidence Interval]: 73.5 [46.0, 117.2]) than in the two other rodent species (bank voles: 4.4 [3.0, 6.3] and wood mice: 10.2 [4.9, 21.2]). Significant factors affecting abundance of larvae were host species and sampling season. Nymphs were most prevalent on chipmunks (86.2%, mean: 5.1 [3.3, 8.0]), one vole carried only two nymphs, and none of the mice had any nymphs. Nymph abundance in chipmunks was affected by sampling season and sex. Furthermore, the infection prevalence of B. burgdorferi sl in the Siberian chipmunk was the highest (33.3%) and predominantly of B. afzelii. The infection prevalence was 14.1% in bank voles, but no wood mouse was found to be infected. Our results suggest that the Siberian chipmunk may be an important reservoir host for LB.

  8. Characterization of degenerative changes in the temporomandibular joint of the bengal tiger (Panthera tigris tigris) and siberian tiger (Panthera tigris altaica).

    Murphy, M K; Arzi, B; Vapniarsky-Arzi, N; Athanasiou, K A

    2013-11-01

    The articulation of the temporomandibular joint (TMJ) is composed of the temporal bone dorsally, the mandibular condyle ventrally and a fibrous articular disc. The TMJ disc plays an essential role in distributing load between the two articular surfaces. Degeneration of the disc in the presence of joint pathology has been shown in man; however, TMJ pathology has not been documented previously in tigers (Panthera tigris). The mandibular condyle and TMJ disc of a Bengal tiger (P. tigris tigris) and a Siberian tiger (P. tigris altaica) were evaluated grossly and the TMJ disc was characterized biochemically and mechanically. Characterization of the TMJ disc verified region- and direction-dependent biochemical and mechanical properties, reflective of the functional demands on the joint. Degenerative joint disease was observed in both cases and this was more severe in the Siberian tiger. Simultaneous evaluation of joint pathology, biochemical composition and mechanical properties of the TMJ disc revealed a loss in functional properties (tensile anisotropy) of the disc as joint pathology advanced from moderate to severe. TMJ degeneration may compromise the ability of the animal to eat and thrive and may be a factor contributing to the endangered status of these species. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Mitochondrial genome diversity in the Tubalar, Even, and Ulchi: contribution to prehistory of native Siberians and their affinities to Native Americans.

    Sukernik, Rem I; Volodko, Natalia V; Mazunin, Ilya O; Eltsov, Nikolai P; Dryomov, Stanislav V; Starikovskaya, Elena B

    2012-05-01

    To fill remaining gaps in mitochondrial DNA diversity in the least surveyed eastern and western flanks of Siberia, 391 mtDNA samples (144 Tubalar from Altai, 87 Even from northeastern Siberia, and 160 Ulchi from the Russian Far East) were characterized via high-resolution restriction fragment length polymorphism/single nucleotide polymorphisms analysis. The subhaplogroup structure was extended through complete sequencing of 67 mtDNA samples selected from these and other related native Siberians. Specifically, we have focused on the evolutionary histories of the derivatives of M and N haplogroups, putatively reflecting different phases of settling Siberia by early modern humans. Population history and phylogeography of the resulting mtDNA genomes, combined with those from previously published data sets, revealed a wide range of tribal- and region-specific mtDNA haplotypes that emerged or diversified in Siberia before or after the last glacial maximum, ∼18 kya. Spatial distribution and ages of the "east" and "west" Eurasian mtDNA haploclusters suggest that anatomically modern humans that originally colonized Altai derived from macrohaplogroup N and came from Southwest Asia around 38,000 years ago. The derivatives of macrohaplogroup M, which largely emerged or diversified within the Russian Far East, came along with subsequent migrations to West Siberia millennia later. The last glacial maximum played a critical role in the timing and character of the settlement of the Siberian subcontinent. Copyright © 2012 Wiley Periodicals, Inc.

  10. Quantum Distinction: Quantum Distinctiones!

    Zeps, Dainis

    2009-01-01

    10 pages; How many distinctions, in Latin, quantum distinctiones. We suggest approach of anthropic principle based on anthropic reference system which should be applied equally both in theoretical physics and in mathematics. We come to principle that within reference system of life subject of mathematics (that of thinking) should be equated with subject of physics (that of nature). For this reason we enter notions of series of distinctions, quantum distinction, and argue that quantum distinct...

  11. Asian and Siberian ginseng as a potential modulator of immune function: an in vitro cytokine study using mouse macrophages.

    Wang, Huamin; Actor, Jeffrey K; Indrigo, Jessica; Olsen, Margaret; Dasgupta, Amitava

    2003-01-01

    Ginseng is a widely used herbal product in China, other Asian countries, and in the Unites States. There is a traditional belief that ginseng stimulates immune functions. In this study, the innate effects of Asian and Siberian ginsengs on cytokines and chemokines produced by cultured macrophages were examined. The effects of Asian and Siberian ginseng on cytokines and chemokines produced by cultured macrophages were examined. Mouse macrophages (J774A.1) were incubated with Asian or Siberian ginseng at varying concentrations (1, 10, 100, and 1000 microg/ml) for 24 h and then harvested for RNA isolation. The expression levels of IL-1beta, IL-12, TNF-alpha, MIP-1 alpha, and MIP-2 mRNA were measured by quantitative PCR. Our data showed that Asian ginseng induced a statistically significant increase in IL-12 expression at both mRNA and protein levels. However, the minor twofold increase is probably biologically insignificant. No significant increase of IL-12 by Siberian ginseng was observed at any dose level studied. No significant change in IL-1beta, IL-15, TNF-alpha, or MIP-1alpha mRNA was observed by either Asian or Siberian ginseng treatment. Our data showed statistically significant differential regulation of IL-12 by Asian ginseng. Siberian ginseng did not show a statistically significant increase. We conclude that both Asian ginseng and Siberian ginseng cannot significantly stimulate innate macrophage immune functions that influence cellular immune responses. Therefore, contrary to the popular belief, Asian and Siberian ginseng may not stimulate immune function.

  12. Carbon mineralization in Laptev and East Siberian sea shelf and slope sediment

    V. Brüchert

    2018-01-01

    Full Text Available The Siberian Arctic Sea shelf and slope is a key region for the degradation of terrestrial organic material transported from the organic-carbon-rich permafrost regions of Siberia. We report on sediment carbon mineralization rates based on O2 microelectrode profiling; intact sediment core incubations; 35S-sulfate tracer experiments; pore-water dissolved inorganic carbon (DIC; δ13CDIC; and iron, manganese, and ammonium concentrations from 20 shelf and slope stations. This data set provides a spatial overview of sediment carbon mineralization rates and pathways over large parts of the outer Laptev and East Siberian Arctic shelf and slope and allows us to assess degradation rates and efficiency of carbon burial in these sediments. Rates of oxygen uptake and iron and manganese reduction were comparable to temperate shelf and slope environments, but bacterial sulfate reduction rates were comparatively low. In the topmost 50 cm of sediment, aerobic carbon mineralization dominated degradation and comprised on average 84 % of the depth-integrated carbon mineralization. Oxygen uptake rates and anaerobic carbon mineralization rates were higher in the eastern East Siberian Sea shelf compared to the Laptev Sea shelf. DIC ∕ NH4+ ratios in pore waters and the stable carbon isotope composition of remineralized DIC indicated that the degraded organic matter on the Siberian shelf and slope was a mixture of marine and terrestrial organic matter. Based on dual end-member calculations, the terrestrial organic carbon contribution varied between 32 and 36 %, with a higher contribution in the Laptev Sea than in the East Siberian Sea. Extrapolation of the measured degradation rates using isotope end-member apportionment over the outer shelf of the Laptev and East Siberian seas suggests that about 16 Tg C yr−1 is respired in the outer shelf seafloor sediment. Of the organic matter buried below the oxygen penetration depth, between 0.6 and 1.3

  13. The evidence of apelin has the bidirectional effects on feeding regulation in Siberian sturgeon (Acipenser baerii).

    Hao, Jin; Liu, Qing; Zhang, Xin; Wu, Yuanbing; Zhu, Jieyao; Qi, Jinwen; Tang, Ni; Wang, Shuyao; Wang, Hong; Chen, Defang; Li, Zhiqiong

    2017-08-01

    Apelin is a peptide, mainly produced in the brain, which participates in several physiologic effects. However, knowledge about the mechanism of appetite regulation in teleosts, including the role of apelin is not well understood. The aim of this study is to explore the effect of feeding status on the expression of apelin mRNA in the whole brain and the effects of injection of apelin on food intake in Siberian sturgeon (Acipenser baerii). In this study, we first cloned the apelin cDNA sequence of the Siberian sturgeon. We obtained a 1046-bp cDNA fragment, including a 237-bp open reading frame (ORF) that encoded 78 amino acids. Apelin was widely distributed in 11 tissues related to feeding regulation, with the highest expression in thewhole brain, followed by the spleen and trunk kidney. In addition, we measured the effects of periprandial (preprandial and postprandial) change, fasting and re-feeding on apelin mRNA expression in whole brain. The level of apelin mRNA was significantly decreased 1h after feeding. The results of the fasting experiment showed that the expression of apelin mRNA in the brain was significantly reduced after 1day of fasting but consistently increased throughout the 15-day food deprivation period. When the 15-day fasted fish were re-fed, apelin mRNA expression in the brain was significantly increased as compared to that of the control. These results suggest that apelin may play a bidirectional role in the regulation of food intake in the Siberian sturgeon. In order to further examine the effect of apelin on feeding regulation in Siberian sturgeons, acute and chronic intraperitoneal (i.p.) injection experiments were performed and food intakes were recorded. Results showed that acute i.p. injection of apelin-13 reduced food intake, however, chronic i.p. injection apelin-13 increased the food intake for 7days in Siberian sturgeons. In conclusion, our results show that apelin has a bidirectional effect on feeding regulation in Siberian sturgeons

  14. Results of Paleomagnetic Investigation of Angara - Taseeva Depression and Central Part of Tunguska Syncline (Siberian Trap Province, Russia)

    Latyshev, A.; Veselovskiy, R. V.; Pavlov, V.

    2014-12-01

    Results of paleomagnetic investigation of two regions of Siberian Trap province (Angara - Taseeva depression and central part of Tunguska syncline) are performed here. Our work was dedicated to the estimation of dynamics and duration of magmatic activity during Siberian Traps emplacement. The conclusions are based on paleomagnetic study of large dolerite sills in the periphery of Siberian Trap province, tuffaceous deposits, small intrusions and lava flows of Tunguska syncline, and on geochronological data (Ivanov et al., 2013; Reichow et al., 2009). The presented data show that formation of Siberian Traps in these regions took place as several short bursts of magmatic activity led to large sill intrusions and eruptions of tuffs. This data are in agreement with the pulsating character of magmatic activity in the Northern part of Siberian platform (Pavlov et al., 2014). The most powerful burst of magmatic activity in Angara-Taseeva syncline is supposed to be synchronous to the main phase of volcanic eruptions in the Northern part of Siberian platform and emplacement of ore-bearing intrusions in Noril'sk district. This study was funded by grant RFBR # 14-05-31447.

  15. 99.9% Spin-Flip Efficiency in the Presence of a Strong Siberian Snake

    Morozov, V.S.; Blinov, B.B.; Etienne, Z.B.; Krisch, A.D.; Leonova, M.A.; Lin, A.M.T.; Lorenzon, W.; Peters, C.C.; Sivers, D.W.; Wong, V.K.; Yonehara, K.; Anferov, V. A.; Schwandt, P.; Stephenson, E.J.; Przewoski, B. von; Sato, H.

    2003-01-01

    We recently studied the spin-flipping efficiency of an rf-dipole magnet using a 120-MeV horizontally polarized proton beam stored in the Indiana University Cyclotron Facility Cooler Ring, which contained a full Siberian snake. We flipped the spin by ramping the rf dipole's frequency through an rf-induced depolarizing resonance. By adiabatically turning on the rf dipole, we minimized the beam loss, while preserving almost all of the beam's polarization. After optimizing the frequency ramp parameters, we used up to 400 multiple spin flips to measure a spin-flip efficiency of 99.93 ± 0.02%. This result indicates that spin flipping should be possible in very-high-energy polarized storage rings, where Siberian snakes are certainly needed and only dipole rf-flipper magnets are practical

  16. Adiabatic partial Siberian snake turn-on with no beam depolarization

    Phelps, R.A.; Anferov, V.A.; Chu, C.M.; Courant, E.D.; Crandell, D.A.; Derbenev, Y.S.; Kaufman, W.A.; Koulsha, A.V.; Krisch, A.D.; Nurushev, T.S.; Raczkowksi, D.B.; Sund, S.E.; Wong, V.K.; Caussyn, D.D.; Ellison, T.J.P.; Lee, S.Y.; Sperisen, F.; Stephenson, E.J.; von Przewoski, B.; Baiod, R.; Khiari, F.Z.; Ratner, L.G.; Sato, H.

    1994-01-01

    A recent experiment in the IUCF cooler ring studied the adiabatic turn-on of a partial Siberian snake at 370 MeV, where the spin tune, ν s is 21/2 for all snake strengths. The snake consisted of two rampable warm solenoid magnets in series with a superconducting solenoid; this combination allowed varying the snake strength between about 0 and 25% at 370 MeV. We measured the beam polaraization after varying the snake either 1, 2, or 10 times; we found with good precision that no polarization was lost. This supports the conjecture that a Siberian snake can be ramped adiabatically at an energy where the spin tune is a half integer

  17. Adiabatic Siberian snake turn-on and acceleration through depolarizing resonances

    Koulsha, A.V.; Anferov, V.A.; Baiod, R.

    1993-01-01

    The authors plan to install in the IUCF Cooler Ring a rampable partial (30%) Siberian snake to test if the spin polarization is preserved during adiabatic turn-on. They also plan to use this ramped snake to accelerate polarized protons to 370 MeV while passing through two depolarizing resonances. The Siberian snake will consist of two small rampable warm solenoids placed symmetrically on either side of the exciting cold 2 T·m solenoid which would run dc at about 0.5 T·m. Ramping each warm magnet from about -0.25T·m to + 0.25 T·m. Recent experiments showed that turning on the snake in 100 msec at 370 MeV causes no serious beam loss

  18. PALEOARCHEAN MAFIC ROCKS OF THE SOUTHWESTERN SIBERIAN CRATON: PRELIMINARY GEOCHRONOLOGY AND GEOCHEMICAL CHARACTERIZATION

    A. V. Ivanov

    2017-01-01

    Full Text Available The Siberian craton consists of Archean blocks, which were welded up into the same large unit by ca 1.9 Ga [Gladkochub et al., 2006; Rojas-Agramonte et al., 2011]. The history of the constituent Archean blocks is mosaic because of limited number of outcrops, insufficient sampling coverage because of their location in remote regions and deep forest and difficulties with analytical studies of ancient rocks, which commonly underwent metamorphic modifications and secondary alterations. In this short note, we report data on discovery of unusual for Archean mafic rocks of ultimate fresh appearance. These rocks were discovered within southwestern Siberian craton in a region near a boundary between Kitoy granulites of the Sharyzhalgai highgrade metamorphic complex and Onot green-schist belt (Fig. 1. Here we present preliminary data on geochronology of these rocks and provide their geochemical characterization.

  19. ANALYSIS OF SURGERIES DUE TO PULMONARY TUBERCULOSIS IN SIBERIAN AND FAR EASTERN FEDERAL DISTRICTS

    N. G. Grischenko

    2017-01-01

    Full Text Available The pool of TB infection in Siberian and Far Eastern Federal Districts is still full of complicated cases: among those being followed up by TB dispensaries, there are many patients suffering from fibrous cavernous TB as well as any clinical forms of tuberculosis with multiple drug resistance.The situation can be improved through activated use of surgical treatment (along with the other interventions, first of all among those mentioned above. There is significant international and Russian experience of managing tuberculosis patients using surgery as a part of comprehensive treatment.Surgical services of special medical units in the regions of Siberian and Far Eastern Federal Districts possess certain potential to increase the number surgeries for such complicated cases. 

  20. Tectonics of East Siberian Sea Basin and its influence on petroleum systems

    Karpov, Yury; Antonina, Stoupakova; Anna, Suslova; Mariia, Agasheva

    2016-04-01

    The East Siberian Sea basin (ESSB) is the largest part of the Siberian Arctic shelf, extending for over 1000 km from New Siberian Islands archipelago to Wrangel Island. Nowadays East Siberian Sea margin is considered as a region with probable high petroleum potential. This part of Russian Arctic shelf is the least studied. The major problems in geological investigation of East Siberian Sea shelf are absence of deep wells in area and low seismic exploration maturity. Only general conclusions on its geology and hydrocarbon systems can be drawn based on limited seismic, gravity and magnetic data, supported by projection of onshore geological data to offshore. So, that's why now only complex geological and seismic stratigraphy interpretations are provided. Today we have several concepts and can summarize the tectonic history of the basin. The basin is filled with siliclastic sediments. In the deepest depocentres sediments thickness exceed 8 km in average. Seismic data was interpreted using methods of seismic stratigraphy. Stratigraphic interpretation was possible to achieve because seismic reflections follow chronostratigraphic correlations. Finally, main seismic horizons were indicated. Each indicated horizon follows regional stratigraphic unconformity. In case of absence of deep wells in ESSB, we can only prove possible source rocks by projection of data about New Siberian Islands archipelago source rocks on offshore. The petroleum potential of these rocks was investigated by several authors [1, 2, 3]. Perspective structures, investigated in ESSB were founded out by comparing seismogeological cross-sections with explored analogs in other Russian and foreign onshore and offshore basins. The majority of structures could be connected with stratigraphic and fault traps. New data on possible petroleum plays was analyzed, large massif of data on geology and tectonic history of the region was collected, so now we can use method of basin modelling to evaluate hydrocarbon

  1. [Industrial production of the LDRD "Siberia-N" digital radiographic devices].

    Baru, S E; Ukraintsev, Iu G

    2004-01-01

    It is envisaged, as a key task, in the Federal Program on Tuberculosis Monitoring, that preventive measures and early TB detection is a priority. Fluorography, which is important for the recognition of pulmonary tuberculosis at its early stages, has been used in the diagnostics of pulmonary pathologies. However, according to the statistics provided by the Russian Ministry of Healthcare, around 80% of available medical equipment is now worn and obsolete. Owing to a fruitful research activity related with designing a digital low-dose X-Ray unit (Siberia-N) carried out by the Budker Institute of Nuclear Physics, Siberian Branch of the Russian Academy of Sciences (Novosibirsk), a certain progress can be stated in perfecting the fluorography equipment in Russia. The above unit incorporates all advanced achievements in the field of digital X-Ray diagnostics.

  2. Optical properties of Colored Dissolved Organic Matter (CDOM) on the East Siberian shelf

    Semiletov, I. P.; Pugach, S.; Pipko, I.

    2015-12-01

    The Great Siberian Rivers integrate meteorological and hydrological changes in their watersheds and play a significant role in the physical and biogeochemical regime of the Arctic Ocean. Given the magnitude of Siberian Arctic dissolved organic matter (DOM) export and the uncertain extent to which it is degraded to greenhouse gases, intensified studies to better quantify and understand this large carbon pool and processes acting on it are urgently needed. The East Siberian Arctic shelf is characterized by the highest rate of coastal erosion and significant volume of the riverine discharge which derived terrigenous DOM in the Arctic Ocean. DOM plays a significant role in freshwater and marine aquatic ecosystems including its effects on nutrients and carbon cycling. The colored fraction of DOM, CDOM, directly affects the quantity and spectral quality of available light, thereby impaction both primary production and UV exposure in aquatic ecosystems. Since 2003 we measure CDOM in the East Siberian Arctic Seas (ESAS) in situ using the WETStar fluorometer which doesn't require prefiltration of sample. Combined analysis of CDOM and DOC data obtained at near-annual basis in (2003-2011) demonstrate a high degree of correlation between these parameters. For all the measured samples taken during the ISSS cruises (2003, 2004, 2005, 2008, 2011), there is an overall linear relationship between DOC concentration, CDOM, and salinity. Here we report the spatial-time variability of river-borne DOM in the ESAS using CDOM as a proxy parameter. Higher absorption coefficients (a254), spectral slope parameter over range 275-295 nm (S275-295) and CDOM concentrations reflect the dominant contribution of terrigenous DOM. It is shown that the attenuation light coefficient in the shallow ESAS is mostly determined by riverine CDOM.

  3. State Institutes of the Siberian Khanate and their Reflection in Archaeological Materials

    Sergey F. Tataurov

    2016-09-01

    Full Text Available The article is devoted to the analysis of the state institutes of the Siberian khanate and their reflection in the archaeological materials received during archaeological studying of sites of this period. There are considered processes of a class formation and formation of the stratified society. It is based on the criteria expressed in the works by known Siberian archaeologist N.P. Matveeva. In article the assessment is given to a level of development of productive forces of the population of the state, it is pointed out value of resettlement processes and development of trade relations both in the khanate, and with the adjacent states. The special attention is paid to emergence of the cities of the khanate, their role in centralization of the power, in development of interstate and interstate means of communication, trade. There is given appreciation of fortification systems of the cities and boundary towns of the khanate and is drawn the conclusion about participation in construction of the experts invited from Central Asia. There are analyzes questions of property and social stratification and reflection of this process in a funeral ceremony. The assumption become that as additional criteria of level of statehood of the Siberian khanate can act personal markers of the power – the press, headdresses, the weapon, etc. Criterion of level of centralization of the power for the Siberian khanate is the professional army which consisted from the tatars, hired groups and a militia. Fortification systems of protection of borders of the khanate in the south of Baraby and in Tarsky Priirtyshje also point to the high level of the khan’s power. In the conclusion it is said that archaeological materials fill missing information of written sources and their attraction in historical reconstruction of the tyurko-tatar statehood is one of indispensable conditions of similar researches.

  4. Peptic Ulcer Disease and Helicobacter pylori Infection in Different Siberian Ethnicities.

    Tsukanov, Vladislav V; Kasparov, Edward V; Tonkikh, Julia L; Shtygasheva, Olga V; Butorin, Nikolay N; Amelchugova, Olga S; Vasyutin, Alexander V; Bronnikova, Elena P; Fassan, Matteo; Rugge, Massimo

    2017-02-01

    The high prevalence of Helicobacter pylori (H. pylori) infection in eastern Siberia is consistently established. In the same geographic area, however, fragmentary information is available on the epidemiology of the peptic ulcer disease (PUD). To assess the prevalence of H. pylori infection (including CagA status) and PUD in different eastern Siberian ethnicities. An endoscopy population of 3149 eastern Siberian dyspeptic patients was considered [1727 Europoids and 1422 Mongoloids (Evenks = 792; Khakases = 630)]. H. pylori status was assessed by urease test and/or serum anti-H. pylori IgG and/or histology. CagA status was serologically assessed (anti-CagA antibodies). All the Siberian ethnicities featured high rates of H. pylori infection (Europoids = 87.1%, Evenks = 88.6%, Khakases = 85.4%). Among the 1504 H. pylori-positive Europoids, the prevalence of CagA-positive status (68.7%) was significantly higher than that featured by the 1240 H. pylori-positive Mongoloid ethnicities (46.9%; p Peptic ulcer disease significantly prevailed among Europoids (prevalence among Europoid Evenks and Khakases: 8.9% and 8.3%, respectively; prevalence among Mongoloid Evenks and Khakases = 1.0% and 4.4%, respectively). eastern Siberian populations feature consistent high rates of H. pylori infection, but different prevalence of peptic ulcer disease. In particular, Europoids featured a prevalence of both CagA-positive status and peptic ulcer disease significantly higher than that of the Mongoloid ethnicities. These results suggest that both environmental factors (coexisting with the H. pylori infection) and host-related variables modulate the clinicopathological expression of the H. pylori -associated gastric diseases. © 2016 John Wiley & Sons Ltd.

  5. Siberian Regional Identity in the Context of Historical Consciousness (Content Analysis of Tomsk Regional Media

    A V Bocharov

    2011-12-01

    Full Text Available The article presents a model to study the Siberian regional identity in the context of historical consciousness, as well as the results of its practical application in the content analysis of the publications by the Tomsk regional media. On the basis of the content analysis procedures the author demonstrates how, through historical memory, the regional identity is formed and manifested in the regional media in various spheres of society.

  6. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

    Gilbert, M Thomas P; Drautz, Daniela I; Lesk, Arthur M

    2008-01-01

    We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis...... to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep....

  7. Geological Structure of the Basement of Western and Eastern Parts of the West-Siberian Plain

    Ivanov, Kirill S.; Erokhin, Yuriy V.; Ponomarev, Vladimir S.; Pogromskaya, Olga E.; Berzin, Stepan V.

    2016-01-01

    The U-Pb dating (SHRIMP-II on zircon) was obtained for the first time from the basement of the West Siberian Plain in the Western half of the region. It is established that a large part of the protolith of the metamorphic depth in the Shaim-Kuznetsov meganticlinorium contained sedimentary late- and middle-Devonian rocks (395-358 million years).…

  8. Adrenal hormones mediate melatonin-induced increases in aggression in male Siberian hamsters (Phodopus sungorus).

    Demas, Gregory E; Polacek, Kelly M; Durazzo, Alfredo; Jasnow, Aaron M

    2004-12-01

    Among the suite of seasonal adaptations displayed by nontropical rodents, some species demonstrate increased territorial aggression in short compared with long day lengths despite basal levels of testosterone. The precise physiological mechanisms mediating seasonal changes in aggression, however, remain largely unknown. The goal of the present study was to examine the role of melatonin, as well as adrenal hormones, in the regulation of seasonal aggression in male Siberian hamsters (Phodopus sungorus). In Experiment 1, male Siberian hamsters received either daily (s.c.) injections of melatonin (15 microg/day) or saline 2 h before lights out for 10 consecutive days. In Experiment 2, hamsters received adrenal demedullations (ADMEDx), whereas in Experiment 3 animals received adrenalectomies (ADx); control animals in both experiments received sham surgeries. Animals in both experiments subsequently received daily injections of melatonin or vehicle as in Experiment 1. Animals in all experiments were tested using a resident-intruder model of aggression. In Experiment 1, exogenous melatonin treatment increased aggression compared with control hamsters. In Experiment 2, ADMEDx had no effect on melatonin-induced aggression. In Experiment 3, the melatonin-induced increase in aggression was significantly attenuated by ADx. Collectively, the results of the present study demonstrate that short day-like patterns of melatonin increase aggression in male Siberian hamsters and suggest that increased aggression is due, in part, to changes in adrenocortical steroids.

  9. “The History and Culture of the Western Siberian Tatars”: Some Notes about the Book

    Z.A. Tychinskikh

    2017-03-01

    Full Text Available The article presents a collective monograph “The History and Culture of the Western Siberian Tatars” published in 2015 by Sh. Marjani Institute of History of Tatarstan Academy of Sciences. This book is the first academic work, which integrated and multidimensionally accumulated almost all materials (of demography, genetics, linguistics, history, ethnography and ethnosociology available in modern science related to the formation and development of the Turkic-Tatar population of Western Siberia from ancient times to the early 21st century. The monograph is distinguished by the ethnoterritorial approach: the authors focus on the entire Turkic-Tatar population of Western Siberia, which was formed in different historical periods and includes two main components – population called in ethnographic science the “Siberian Tatars” and the group of Tatars who migrated (mainly from the Volga region to the Siberian region during the 16th–20th centuries. The book contains a large number of illustrations, which were collected during the expeditions of the authors in the rural settlements of the Tatars of Western Siberia, during archaeological excavations, in numerous archives and museums in Russia. Many photos are presented for the first time.

  10. Sources and characteristics of terrestrial carbon in Holocene-scale sediments of the East Siberian Sea

    Keskitalo, Kirsi; Tesi, Tommaso; Bröder, Lisa; Andersson, August; Pearce, Christof; Sköld, Martin; Semiletov, Igor P.; Dudarev, Oleg V.; Gustafsson, Örjan

    2017-09-01

    Thawing of permafrost carbon (PF-C) due to climate warming can remobilise considerable amounts of terrestrial carbon from its long-term storage to the marine environment. PF-C can be then be buried in sediments or remineralised to CO2 with implications for the carbon-climate feedback. Studying historical sediment records during past natural climate changes can help us to understand the response of permafrost to current climate warming. In this study, two sediment cores collected from the East Siberian Sea were used to study terrestrial organic carbon sources, composition and degradation during the past ˜ 9500 cal yrs BP. CuO-derived lignin and cutin products (i.e., compounds solely biosynthesised in terrestrial plants) combined with δ13C suggest that there was a higher input of terrestrial organic carbon to the East Siberian Sea between ˜ 9500 and 8200 cal yrs BP than in all later periods. This high input was likely caused by marine transgression and permafrost destabilisation in the early Holocene climatic optimum. Based on source apportionment modelling using dual-carbon isotope (Δ14C, δ13C) data, coastal erosion releasing old Pleistocene permafrost carbon was identified as a significant source of organic matter translocated to the East Siberian Sea during the Holocene.

  11. Evaluation of methane emissions from West Siberian wetlands based on inverse modeling

    Kim, H-S; Inoue, G [Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047 (Japan); Maksyutov, S; Machida, T [National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 (Japan); Glagolev, M V [Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991 (Russian Federation); Patra, P K [Research Institute for Global Change/JAMSTEC, 3173-25 Showa-cho, Kanazawa-ku, Yokohama, Kanagawa 236-0001 (Japan); Sudo, K, E-mail: heonsook.kim@gmail.com [Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)

    2011-07-15

    West Siberia contains the largest extent of wetlands in the world, including large peat deposits; the wetland area is equivalent to 27% of the total area of West Siberia. This study used inverse modeling to refine emissions estimates for West Siberia using atmospheric CH{sub 4} observations and two wetland CH{sub 4} emissions inventories: (1) the global wetland emissions dataset of the NASA Goddard Institute for Space Studies (the GISS inventory), which includes emission seasons and emission rates based on climatology of monthly surface air temperature and precipitation, and (2) the West Siberian wetland emissions data (the Bc7 inventory), based on in situ flux measurements and a detailed wetland classification. The two inversions using the GISS and Bc7 inventories estimated annual mean flux from West Siberian wetlands to be 2.9 {+-} 1.7 and 3.0 {+-} 1.4 Tg yr{sup -1}, respectively, which are lower than the 6.3 Tg yr{sup -1} predicted in the GISS inventory, but similar to those of the Bc7 inventory (3.2 Tg yr{sup -1}). The well-constrained monthly fluxes and a comparison between the predicted CH{sub 4} concentrations in the two inversions suggest that the Bc7 inventory predicts the seasonal cycle of West Siberian wetland CH{sub 4} emissions more reasonably, indicating that the GISS inventory predicts more emissions from wetlands in northern and middle taiga.

  12. Global nickel anomaly links Siberian Traps eruptions and the latest Permian mass extinction.

    Rampino, Michael R; Rodriguez, Sedelia; Baransky, Eva; Cai, Yue

    2017-09-29

    Anomalous peaks of nickel abundance have been reported in Permian-Triassic boundary sections in China, Israel, Eastern Europe, Spitzbergen, and the Austrian Carnic Alps. New solution ICP-MS results of enhanced nickel from P-T boundary sections in Hungary, Japan, and Spiti, India suggest that the nickel anomalies at the end of the Permian were a worldwide phenomenon. We propose that the source of the nickel anomalies at the P-T boundary were Ni-rich volatiles released by the Siberian volcanism, and by coeval Ni-rich magma intrusions. The peaks in nickel abundance correlate with negative δ 13 C and δ 18 O anomalies, suggesting that explosive reactions between magma and coal during the Siberian flood-basalt eruptions released large amounts of CO 2 and CH 4 into the atmosphere, causing severe global warming and subsequent mass extinction. The nickel anomalies may provide a timeline in P-T boundary sections, and the timing of the peaks supports the Siberian Traps as a contributor to the latest Permian mass extinction.

  13. Visual pigment coexpression in all cones of two rodents, the Siberian hamster, and the pouched mouse.

    Lukáts, Akos; Dkhissi-Benyahya, Ouria; Szepessy, Zsuzsanna; Röhlich, Pál; Vígh, Béla; Bennett, Nigel C; Cooper, Howard M; Szél, Agoston

    2002-07-01

    To decide whether the identical topography of short- and middle-wavelength cone photoreceptors in two species of rodents reflects the presence of both opsins in all cone cells. Double-label immunocytochemistry using antibodies directed against short-wavelength (S)-and middle- to long-wavelength (M/L)-sensitive opsin were used to determine the presence of visual pigments in cones of two species of rodents, the Siberian hamster (Phodopus sungorus) and the pouched mouse (Saccostomus campestris) from South Africa. Topographical distribution was determined from retinal whole-mounts, and the colocalization of visual pigments was examined using confocal laser scanning microscopy. Opsin colocalization was also confirmed in consecutive semithin tangential sections. The immunocytochemical results demonstrate that in both the Siberian hamster and the pouched mouse all retinal cones contain two visual pigments. No dorsoventral gradient in the differential expression of the two opsins is observed. The retina of the Siberian hamster and the pouched mouse is the first example to show a uniform coexpression of M and S cone opsins in all cones, without any topographical gradient in opsin expression. This finding makes these two species good models for the study of molecular control mechanisms in opsin coexpression in rodents, and renders them suitable as sources of dual cones for future investigations on the role and neural connections of this cone type.

  14. Chronic peroxisome proliferator-activated receptor gamma (PPARgamma) activation of epididymally derived white adipocyte cultures reveals a population of thermogenically competent, UCP1-containing adipocytes molecularly distinct from classic brown adipocytes

    Petrovic, Natasa; Walden, Tomas B; Shabalina, Irina G

    2009-01-01

    The recent insight that brown adipocytes and muscle cells share a common origin and in this respect are distinct from white adipocytes has spurred questions concerning the origin and molecular characteristics of the UCP1-expressing cells observed in classic white adipose tissue depots under certain...... physiological or pharmacological conditions. Examining precursors from the purest white adipose tissue depot (epididymal), we report here that chronic treatment with the peroxisome proliferator-activated receptor gamma agonist rosiglitazone promotes not only the expression of PGC-1alpha and mitochondriogenesis...... associated with classic brown adipocytes (Zic1, Lhx8, Meox2, and characteristically PRDM16) or for myocyte-associated genes (myogenin and myomirs (muscle-specific microRNAs)) and retain white fat characteristics such as Hoxc9 expression. Co-culture experiments verify that the UCP1-expressing cells...

  15. Green synthesis of multifunctional silver and gold nanoparticles from the oriental herbal adaptogen: Siberian ginseng

    Abbai R

    2016-07-01

    Full Text Available Ragavendran Abbai,1,* Ramya Mathiyalagan,1,* Josua Markus,1 Yeon-Ju Kim,2 Chao Wang,2 Priyanka Singh,2 Sungeun Ahn,2 Mohamed El-Agamy Farh,2 Deok Chun Yang1,2 1Ginseng Bank, Graduate School of Biotechnology, 2Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea *These authors contributed equally to this work Abstract: Pharmacologically active stem of the oriental herbal adaptogen, Siberian ginseng, was employed for the ecofriendly synthesis of Siberian ginseng silver nanoparticles (Sg-AgNPs and Siberian ginseng gold nanoparticles (Sg-AuNPs. First, for metabolic characterization of the sample, liquid chromatography-tandem mass spectrometry analysis (indicated the presence of eleutherosides A and E, total phenol content, and total reducing sugar were analyzed. Second, the water extract of the sample mediated the biological synthesis of both Sg-AgNPs and Sg-AuNPs that were crystalline face-centered cubical structures with a Z-average hydrodynamic diameter of 126 and 189 nm, respectively. Moreover, Fourier transform infrared analysis indicated that proteins and aromatic hydrocarbons play a key role in the formation and stabilization of Sg-AgNPs, whereas phenolic compounds accounted for the synthesis and stability of Sg-AuNPs. 3-(4,5-Dimethyl-2-thiazolyl-2,5-diphenyl-2H tetrazolium bromide (MTT assay determined that Sg-AgNPs conferred strong cytotoxicity against MCF7 (human breast cancer cell line and was only slightly toxic to HaCaT (human keratinocyte cell line at 10 µg·mL-1. However, Sg-AuNPs did not display cytotoxic effects against both of the cell lines. The disc diffusion assay indicated a dose-dependent increase in the zone of inhibition of Staphylococcus aureus (ATCC 6538, Bacillus anthracis (NCTC 10340, Vibrio parahaemolyticus (ATCC 33844, and Escherichia coli (BL21 treated with Sg-AgNPs, whereas Sg-AuNPs did not show inhibitory activity. In addition, the 2,2-diphenyl-1

  16. Proteomic Analysis Reveals Distinct Metabolic Differences Between Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) and Macrophage Colony Stimulating Factor (M-CSF) Grown Macrophages Derived from Murine Bone Marrow Cells.

    Na, Yi Rang; Hong, Ji Hye; Lee, Min Yong; Jung, Jae Hun; Jung, Daun; Kim, Young Won; Son, Dain; Choi, Murim; Kim, Kwang Pyo; Seok, Seung Hyeok

    2015-10-01

    Macrophages are crucial in controlling infectious agents and tissue homeostasis. Macrophages require a wide range of functional capabilities in order to fulfill distinct roles in our body, one being rapid and robust immune responses. To gain insight into macrophage plasticity and the key regulatory protein networks governing their specific functions, we performed quantitative analyses of the proteome and phosphoproteome of murine primary GM-CSF and M-CSF grown bone marrow derived macrophages (GM-BMMs and M-BMMs, respectively) using the latest isobaric tag based tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Strikingly, metabolic processes emerged as a major difference between these macrophages. Specifically, GM-BMMs show significant enrichment of proteins involving glycolysis, the mevalonate pathway, and nitrogen compound biosynthesis. This evidence of enhanced glycolytic capability in GM-BMMs is particularly significant regarding their pro-inflammatory responses, because increased production of cytokines upon LPS stimulation in GM-BMMs depends on their acute glycolytic capacity. In contrast, M-BMMs up-regulate proteins involved in endocytosis, which correlates with a tendency toward homeostatic functions such as scavenging cellular debris. Together, our data describes a proteomic network that underlies the pro-inflammatory actions of GM-BMMs as well as the homeostatic functions of M-BMMs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Overexpression of human fatty acid transport protein 2/very long chain acyl-CoA synthetase 1 (FATP2/Acsvl1) reveals distinct patterns of trafficking of exogenous fatty acids

    Melton, Elaina M. [Department of Biochemistry, University of Nebraska, Lincoln, NE (United States); Center for Cardiovascular Sciences, Albany Medical College, Albany, NY (United States); Cerny, Ronald L. [Department of Chemistry, University of Nebraska, Lincoln, NE (United States); DiRusso, Concetta C. [Department of Biochemistry, University of Nebraska, Lincoln, NE (United States); Black, Paul N., E-mail: pblack2@unl.edu [Department of Biochemistry, University of Nebraska, Lincoln, NE (United States)

    2013-11-01

    Highlights: •Roles of FATP2 in fatty acid transport/activation contribute to lipid homeostasis. •Use of 13C- and D-labeled fatty acids provide novel insights into FATP2 function. •FATP2-dependent trafficking of FA into phospholipids results in distinctive profiles. •FATP2 functions in the transport and activation pathways for exogenous fatty acids. -- Abstract: In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells expressing FATP2 to gain further insights into how this protein functions in fatty acid transport and intracellular fatty acid trafficking. Our previous studies showed the expression of FATP2 modestly increased C16:0-CoA and C20:4-CoA and significantly increased C18:3-CoA and C22:6-CoA after 4 h. The increases in C16:0-CoA and C18:3-CoA suggest FATP2 must necessarily partner with a long chain acyl CoA synthetase (Acsl) to generate C16:0-CoA and C18:3-CoA through vectorial acylation. The very long chain acyl CoA synthetase activity of FATP2 is consistent in the generation of C20:4-CoA and C22:6-CoA coincident with transport from their respective exogenous fatty acids. The trafficking of exogenous fatty acids into phosphatidic acid (PA) and into the major classes of phospholipids (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidyserine (PS)) resulted in distinctive profiles, which changed with the expression of FATP2. The

  18. Overexpression of human fatty acid transport protein 2/very long chain acyl-CoA synthetase 1 (FATP2/Acsvl1) reveals distinct patterns of trafficking of exogenous fatty acids

    Melton, Elaina M.; Cerny, Ronald L.; DiRusso, Concetta C.; Black, Paul N.

    2013-01-01

    Highlights: •Roles of FATP2 in fatty acid transport/activation contribute to lipid homeostasis. •Use of 13C- and D-labeled fatty acids provide novel insights into FATP2 function. •FATP2-dependent trafficking of FA into phospholipids results in distinctive profiles. •FATP2 functions in the transport and activation pathways for exogenous fatty acids. -- Abstract: In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells expressing FATP2 to gain further insights into how this protein functions in fatty acid transport and intracellular fatty acid trafficking. Our previous studies showed the expression of FATP2 modestly increased C16:0-CoA and C20:4-CoA and significantly increased C18:3-CoA and C22:6-CoA after 4 h. The increases in C16:0-CoA and C18:3-CoA suggest FATP2 must necessarily partner with a long chain acyl CoA synthetase (Acsl) to generate C16:0-CoA and C18:3-CoA through vectorial acylation. The very long chain acyl CoA synthetase activity of FATP2 is consistent in the generation of C20:4-CoA and C22:6-CoA coincident with transport from their respective exogenous fatty acids. The trafficking of exogenous fatty acids into phosphatidic acid (PA) and into the major classes of phospholipids (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidyserine (PS)) resulted in distinctive profiles, which changed with the expression of FATP2. The

  19. Tamoxifen-inducible gene deletion reveals a distinct cell type associated with trabecular bone, and direct regulation of PTHrP expression and chondrocyte morphology by Ihh in growth region cartilage.

    Hilton, Matthew J; Tu, Xiaolin; Long, Fanxin

    2007-08-01

    Indian hedgehog (Ihh) controls multiple aspects of endochondral skeletal development by signaling to both chondrocytes and perichondrial cells. Previous efforts to delineate direct effects of Ihh on chondrocytes by Col2-Cre-mediated ablation of Smoothened (Smo, encoding a transmembrane protein indispensable for Ihh signaling) has been only partially successful, due to the inability to discriminate between chondrocytes and perichondrial cells. Here we report a transgenic line (Col2-Cre) expressing under the control of the Colalpha1(II) promoter an inert form of Cre that is activatable by exogenous tamoxifen (TM); TM administration at proper times during embryogenesis induced Cre activity in chondrocytes but not in the perichondrium. By using this mouse line, we deleted Smo within subsets of chondrocytes without affecting the perichondrium and found that Smo removal led to localized disruption of the expression of parathyroid hormone-related protein (PTHrP) and the morphology of chondrocytes. Unexpectedly, TM invariably induced Cre activity in a subset of cells associated with the trabecular bone surface of long bones. These cells, when genetically marked and cultured in vitro, were capable of producing bone nodules. Expression of the Col2-Cre transgene in these cells likely reflected the endogenous Colalpha1(II) promoter activity as similar cells were found to express the IIA isoform of Colalpha1(II) mRNA endogenously. In summary, the present study has not only provided evidence that Ihh signaling directly controls PTHrP expression and chondrocyte morphology in the growth region cartilage, but has also uncovered a distinct cell type associated with the trabecular bone that appears to possess osteogenic potential.

  20. Trace element transport in western Siberian rivers across a permafrost gradient

    Pokrovsky, Oleg S.; Manasypov, Rinat M.; Loiko, Sergey V.; Krickov, Ivan A.; Kopysov, Sergey G.; Kolesnichenko, Larisa G.; Vorobyev, Sergey N.; Kirpotin, Sergey N.

    2016-03-01

    Towards a better understanding of trace element (TE) transport in permafrost-affected Earth surface environments, we sampled ˜ 60 large and small rivers (important region. No statistically significant effect of the basin size on most TE concentrations was evidenced. Two groups of elements were distinguished: (1) elements that show the same trend throughout the year and (2) elements that show seasonal differences. The first group included elements decreasing northward during all seasons (Sr, Mo, U, As, Sb) marking the underground water influence of river feeding. The elements of the second group exhibited variable behavior in the course of the year. A northward increase during spring period was mostly pronounced for Fe, Al, Co, Zn and Ba and may stem from a combination of enhanced leaching from the topsoil and vegetation and bottom waters of the lakes (spring overturn). A springtime northward decrease was observed for Ni, Cu, Zr and Rb. The increase in element concentration northward was observed for Ti, Ga, Zr and Th only in winter, whereas Fe, Al, rare earth elements (REEs), Pb, Zr, and Hf increased northward in both spring and winter, which could be linked to leaching from peat and transport in the form of Fe-rich colloids. A southward increase in summer was strongly visible for Fe, Ni, Ba, Rb and V, probably due to peat/moss release (Ni, Ba, Rb) or groundwater feeding (Fe, V). Finally, B, Li, Cr, V, Mn, Zn, Cd, and Cs did not show any distinct trend from S to N. The order of landscape component impact on TE concentration in rivers was lakes > bogs > forest. The lakes decreased export of Mn and Co in summer and Ni, Cu, and Rb in spring, presumably due to biotic processes. The lakes enriched the rivers in insoluble lithogenic elements in summer and winter, likely due to TE mobilization from unfrozen mineral sediments. The rank of environmental factors on TE concentration in western Siberian rivers was latitude (three permafrost zones) > season > watershed size

  1. Methane oxidation associated to submerged brown-mosses buffers methane emissions from Siberian polygonal peatlands

    Liebner, Susanne; Zeyer, Josef; Knoblauch, Christian

    2010-05-01

    Circumpolar peatlands store roughly 18 % of the globally stored carbon in soils [based on 1, 2]. Also, northern wetlands and tundra are a net source of methane (CH4), an effective greenhouse gas (GHG), with an estimated annual CH4 release of 7.2% [3] or 8.1% [4] of the global total CH4 emission. Although it is definite that Arctic tundra significantly contributes to the global methane emissions in general, regional variations in GHG fluxes are enormous. CH4 fluxes of polygonal tundra within the Siberian Lena Delta, for example, were reported to be low [5, 6], particularly at open water polygonal ponds and small lakes [7] which make up around 10 % of the delta's surface. Low methane emissions from polygonal ponds oppose that Arctic permafrost thaw ponds are generally known to emit large amounts of CH4 [8]. Combining tools of biogeochemistry and molecular microbiology, we identified sinks of CH4 in polygonal ponds from the Lena Delta that were not considered so far in GHG studies from Arctic wetlands. Pore water CH4 profiling in polygonal ponds on Samoylov, a small island in the central part of the Lena Delta, revealed a pronounced zone of CH4 oxidation near the vegetation surface in submerged layers of brown-mosses. Here, potential CH4 oxidation was an order of magnitude higher than in non-submerged mosses and in adjacent bulk soil. We could additionally show that this moss associated methane oxidation (MAMO) is hampered when exposure of light is prevented. Shading of plots with submerged Scorpidium scorpioides inhibited MAMO leading to higher CH4 concentrations and an increase in CH4 fluxes by a factor of ~13. Compared to non-submerged mosses, the submerged mosses also showed significantly lower δ13C values indicating that they use carbon dioxide derived from methane oxidation for photosynthesis. Applying stable isotope probing of DNA, type II methanotrophs were identified to be responsible for the oxidation of CH4 in the submerged Scorpidium scorpioides. Our

  2. Will the Three Gorges Dam affect the underwater light climate of Vallisneria spiralis L. and food habitat of Siberian crane in Poyang Lake?

    Wu, G.; Leeuw, de J.; Skidmore, A.K.; Prins, H.H.T.; Best, E.P.H.; Liu, Y.

    2009-01-01

    Almost 95% of the entire population of the Siberian crane (Grus leucogeranus) winter in Poyang Lake, China, where they forage on the tubers of the submerged aquatic macrophyte Vallisneria spiralis. The Three Gorges Dam on the Yangtze River may possibly affect this food source of the Siberian crane

  3. Photoperiod- and Triiodothyronine-dependent Regulation of Reproductive Neuropeptides, Proinflammatory Cytokines, and Peripheral Physiology in Siberian Hamsters (Phodopus sungorus).

    Banks, Ruth; Delibegovic, Mirela; Stevenson, Tyler J

    2016-06-01

    Seasonal trade-offs in reproduction and immunity are ubiquitous in nature. The mechanisms that govern transitions across seasonal physiological states appear to involve reciprocal switches in the local synthesis of thyroid hormone. In long-day (LD) summer-like conditions, increased hypothalamic triiodothyronine (T3) stimulates gonadal development. Alternatively, short-day (SD) winter-like conditions increase peripheral leukocytes and enhance multiple aspects of immune function. These data indicate that the localized effects of T3 in the hypothalamus and leukocytes are photoperiod dependent. We tested the hypothesis that increased peripheral T3 in SD conditions would increase aspects of reproductive physiology and inhibit immune function, whereas T3 injections in LD conditions would facilitate aspects of immune function (i.e., leukocytes). In addition, we also examined whether T3 regulates hypothalamic neuropeptide expression as well as hypothalamic and splenic proinflammatory cytokine expression. Adult male Siberian hamsters were maintained in LD (15L:9D) or transferred to SD (9L:15D) for 8 weeks. A subset of LD and SD hamsters was treated daily with 5 µg T3 for 2 weeks. LD and SD controls were injected with saline. Daily T3 administration in SD hamsters (SD+T3) resulted in a rapid and substantial decrease in peripheral leukocyte concentrations and stimulated gonadal development. T3 treatment in LD (LD+T3) had no effect on testicular volumes but significantly increased leukocyte concentrations. Molecular analyses revealed that T3 stimulated interleukin 1β messenger RNA (mRNA) expression in the spleen and inhibited RFamide Related Peptide-3 mRNA expression in the hypothalamus. Moreover, there was a photoperiod-dependent decrease in splenic tumor necrosis factor-α mRNA expression. These findings reveal that T3 has tissue-specific and photoperiod-dependent regulation of seasonal rhythms in reproduction and immune function. © 2016 The Author(s).

  4. Southern montane populations did not contribute to the recolonization of West Siberian Plain by Siberian larch (Larix sibirica): a range-wide analysis of cytoplasmic markers.

    Semerikov, Vladimir L; Semerikova, Svetlana A; Polezhaeva, Maria A; Kosintsev, Pavel A; Lascoux, Martin

    2013-10-01

    While many species were confined to southern latitudes during the last glaciations, there has lately been mounting evidence that some of the most cold-tolerant species were actually able to survive close to the ice sheets. The contribution of these higher latitude outposts to the main recolonization thrust remains, however, untested. In the present study, we use the first range-wide survey of genetic diversity at cytoplasmic markers in Siberian larch (Larix sibirica; four mitochondrial (mt) DNA loci and five chloroplast (cp) DNA SSR loci) to (i) assess the relative contributions of southern and central areas to the current L. sibirica distribution range; and (ii) date the last major population expansion in both L. sibirica and adjacent Larix species. The geographic distribution of cpDNA variation was uninformative, but that of mitotypes clearly indicates that the southernmost populations, located in Mongolia and the Tien-Shan and Sayan Mountain ranges, had a very limited contribution to the current populations of the central and northern parts of the range. It also suggests that the contribution of the high latitude cryptic refugia was geographically limited and that most of the current West Siberian Plain larch populations likely originated in the foothills of the Sayan Mountains. Interestingly, the main population expansion detected through Approximate Bayesian Computation (ABC) in all four larch species investigated here pre-dates the LGM, with a mode in a range of 220,000-1,340,000 years BP. Hence, L. sibirica, like other major conifer species of the boreal forest, was strongly affected by climatic events pre-dating the Last Glacial Maximum. © 2013 John Wiley & Sons Ltd.

  5. Impact of climate change on radial growth of Siberian spruce and Scots pine in North-western Russia

    Lopatin E

    2007-01-01

    Full Text Available When adapting forest management practices to a changing environment, it is very important to understand the response of an unmanaged natural forest to climate change. The method used to identify major climatic factors influencing radial growth of Siberian spruce and Scots pine along a latitudinal gradient in north-western Russia is dendroclimatic analysis. A clear increasing long-term trend was identified in air temperature and precipitation. During the last 20 years, all meteorological stations experienced temperature increases, and 40 years ago precipitation began to increase. This is shown by the radial increment of Siberian spruce and Scots pine. Therefore, climate change could partly explain the increased forest productivity. The total variance explained by temperature varied from 22% to 41% and precipitation from 19% to 38%. The significant climatic parameters for radial increment in Komi Republic were identified, and the relation between temperature and precipitation in explained variance changes over time for Siberian spruce.

  6. Oxidative stress provokes distinct transcriptional responses in the stress-tolerant atr7 and stress-sensitive loh2 Arabidopsis thaliana mutants as revealed by multi-parallel quantitative real-time PCR analysis of ROS marker and antioxidant genes.

    Mehterov, Nikolay; Balazadeh, Salma; Hille, Jacques; Toneva, Valentina; Mueller-Roeber, Bernd; Gechev, Tsanko

    2012-10-01

    The Arabidopsis thaliana atr7 mutant is tolerant to oxidative stress induced by paraquat (PQ) or the catalase inhibitor aminotriazole (AT), while its original background loh2 and wild-type plants are sensitive. Both, AT and PQ, which stimulate the intracellular formation of H₂O₂ or superoxide anions, respectively, trigger cell death in loh2 but do not lead to visible damage in atr7. To study gene expression during oxidative stress and ROS-induced programmed cell death, two platforms for multi-parallel quantitative real-time PCR (qRT-PCR) analysis of 217 antioxidant and 180 ROS marker genes were employed. The qRT-PCR analyses revealed AT- and PQ-induced expression of many ROS-responsive genes mainly in loh2, confirming that an oxidative burst plays a role in the activation of the cell death in this mutant. Some of the genes were specifically regulated by either AT or PQ, serving as markers for particular types of ROS. Genes significantly induced by both AT and PQ in loh2 included transcription factors (ANAC042/JUB1, ANAC102, DREB19, HSFA2, RRTF1, ZAT10, ZAT12, ethylene-responsive factors), signaling compounds, ferritins, alternative oxidases, and antioxidant enzymes. Many of these genes were upregulated in atr7 compared to loh2 under non-stress conditions at the first time point, indicating that higher basal levels of ROS and higher antioxidant capacity in atr7 are responsible for the enhanced tolerance to oxidative stress and suggesting a possible tolerance against multiple stresses of this mutant. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  7. [Telomere length and phylogenetic relationship of Baikal and Siberian planarians (Turbellaria, Tricladida)].

    Koroleva, A G; Evtushenko, E V; Timoshkin, O A; Vershinin, A V; Kiril'chik, S V

    2013-01-01

    Dynamics of the telomeric DNA (tDNA) and the phylogeny of the Baikal and Siberian planarians have been studied based on the analysis of the 18S rDNA and beta-actin gene fragments. A relationship between tDNA and the planarians size has been demonstrated. Giant planarians with a minor exception have longer tDNA than little planarians. Phylogenetic affinity between the species that have the stretched tracks of tDNA, big size and similar habitats may indicate possible role of tDNA in the development of the indefinite regenerative capacity of planarians.

  8. Exploration of horizontal intrinsic spin resonances with two partial Siberian snakes

    F. Lin

    2007-04-01

    Full Text Available Two partial Siberian snakes were used to avoid all the spin imperfection and vertical intrinsic resonances in the alternating gradient synchrotron (AGS at Brookhaven National Laboratory. However, the horizontal betatron motion can cause polarization loss resulting from the nonvertical stable spin direction in the presence of two partial snakes. This type of resonance, called a horizontal intrinsic spin resonance, was observed and systematically studied in the AGS. A simplified analytic model and numerical simulation have been developed to compare with experimental data. Properties of the horizontal intrinsic resonance are discussed.

  9. Orbital parameters of proton and deuteron beams in the NICA collider with solenoid Siberian snakes

    Kovalenko, A D; Butenko, A V; Kekelidze, V D; Mikhaylov, V A; Kondratenko, M A; Filatov, Yu N; Kondratenko, A M

    2016-01-01

    Two solenoid Siberian snakes are required to obtain ion polarization in the “spin transparency” mode of the NICA collider. The field integrals of the solenoid snakes for protons and deuterons at maximum momentum of 13.5 GeV/c are equal to 2×50 T·m and 2×160 T·m respectively. The snakes introduce strong betatron oscillation coupling. The calculations of orbital parameters of proton and deuteron beams in NICA collider with solenoid snakes are presented. (paper)

  10. Spin Transparency Mode in the NICA Collider with Solenoid Siberian Snakes for Proton and Deuteron Beam

    Kovalenko, A. D.; Butenko, A. V.; Mikhaylov, V. A.; Kondratenko, M. A.; Kondratenko, A. M.; Filatov, Yu N.

    2017-12-01

    Two solenoid Siberian Snakes are required to obtain ion polarization in spin transparency mode of the NICA collider. The snake solenoids with a total field integral of 2×50 T·m are placed into the straight sections of the NICA collider. It allows one to control polarization of protons and deuterons up to 13.5 GeV/c and 4 GeV/c respectively. The snakes introduce a strong betatron oscillation coupling. The calculations of orbital parameters of proton and deuteron beams in the NICA collider with solenoid Snakes are presented.

  11. ETHNOCULTURAL CONTEXT IN “SIBERIAN TALES” OF V.G. KOROLENKO

    Oxana Ivanova

    2012-05-01

    Full Text Available The special features of ethnocultural context in the “Siberian Tales” of V.G. Korolenko based on the stories “Makar’s Dream”, “Sokolinets”,“Marusya’s wood house” are analyzed in this paper. The representatives of such nationalities as Yakuts, Russians and Tatars are regarded. The specific peculiarities of the representatives of these nationalities are pointed out. The dependence of the main national character features from the environment, severe climate and Yakut conditions is underlined.

  12. Endogenous lipid (cholesterol) pneumonia in three captive Siberian tigers (Panthera tigris altaica).

    Bollo, Enrico; Scaglione, Frine Eleonora; Chiappino, Laura; Sereno, Alessandra; Triberti, Orfeo; Schröder, Cathrin

    2012-05-01

    During the years 2009-2011, 7 Siberian tigers (Panthera tigris altaica), aged between 2 and 14 years, from the Safaripark of Pombia were referred for necropsy to the Department of Animal Pathology of the University of Turin (Italy). Three tigers, aged 10 (2 animals) and 14 years, had multifocal, irregularly distributed, white, soft, subpleural, 3-mm nodules scattered throughout the lungs. Histologically, there was a marked infiltration of macrophages, with foamy cytoplasm, and multinucleate giant cells interspersed with numerous clusters of cholesterol clefts. A mild lymphocytic infiltration was localized around the lesion. The findings were consistent with endogenous lipid pneumonia, which was considered an incidental finding of no clinical significance.

  13. Comparison of physiological load tolerances between the Siberian husky and the Czechoslovakian wolfdog, during sport training

    Dominika Gulda

    2018-03-01

    Full Text Available The purpose of the study was to determine the physiological load tolerances of two breeds of dogs used for sports, namely the Siberian husky and the Czechoslovakian wolfdog, on the basis of measurements of surface temperature and blood lactic acid levels.Two breeds - Czechoslovakian wolfdog (10 individuals and Siberian husky (10 individuals, 20 dogs - male, 4-6 years old, were selected for the study. All the qualified animals were previously examined by a veterinarian and considered to be healthy. The dogs tested were used in dogtrekking sport competitions. For both breeds, an attempt was made to test the dogtrekking harness for 5 km of non-stop track running. The animals trotted while being led by a guide. Three attempts were made for each dog at 48 hour intervals. All dogs were tested for two parameters, first before and then after the exercise – measuring surface temperature at selected points of the body as well as lactic acid concentration. A higher and statistically significant level of lactic acid was recorded in the case of Siberian husky. Before the run, the level of lactic acid was comparable in both breeds. The second parameter was the surface temperature measured at the selected measuring points. Significant statistical differences were noted for the wolfdog breed at P≤0.05 before the exercise and 10 minutes after resting, at the neck, rump and abdominal points. In addition, the same level of statistical significance was measured by surface thermography at the abdominal point, both before and immediately after the run. The high statistically significant increase (P≤0.01 in surface temperature was noted for muscles of the so-called rump, both before and after the exertion. There was no statistically significant difference in the back thermography in the wolfdog breed. In the Siberian husky breed, statistically significant differences (P≤0.05 were observed at the neck, rump and chest points, in confrontation with the

  14. Tracing river runoff and DOC over the East Siberian Shelf using in situ CDOM measurements

    Pugach, Svetlana; Semiletov, Igor; Pipko, Irina

    2010-05-01

    The Great Siberian Rivers integrate meteorological and hydrological changes in their watersheds and play a significant role in the physical and biogeochemical regime of the Arctic Ocean through transport of fresh water (FW) and carbon into the sea. Since 1994, the Laboratory of Arctic Research POI in cooperation with the IARC UAF investigate the fresh water and carbon fluxes in the Siberian Arctic land-shelf system with the special emphasize in the East Siberian Arctic shelf (ESAS) which represents the widest and shallowest continental shelf in the World Ocean, yet it is still poorly explored. The East Siberian Sea is influenced by water exchange from the eastern Laptev Sea (where local shelf waters are diluted mostly by Lena River discharge) and by inflow of Pacific waters from the Chukchi Sea. This region is characterized by the highest rate of coastal erosion and significant volume of the riverine discharge and exhibits the largest gradients in all oceanographic parameters observed for the entire Arctic Ocean. Here we demonstrate a connection among Chromophoric (or Colored) Dissolved Organic Matter (CDOM) which represents the colored fraction of Dissolved Organic Carbon (DOC), salinity, and pCO2. Our data have documented strong linear correlations between salinity and CDOM in the near shore zone strongly influenced by riverine runoff. Correlation coefficient between CDOM and salinity in surface waters was equal to -0.94, -0.94 and -0.95 for surface water stations in September of 2003, 2004, and 2005, respectively. Combined analysis of CDOM and DOC data demonstrated a high degree of correlation between these parameters (r=0.96). Such close connection between these characteristics of waters in this region makes it possible to restore the distribution of DOC according to our original CDOM data of the profiling systems, such as CTD-Seabird equipped by WETStar CDOM fluorimeter. It is shown that the CDOM can be used as a conservative tracer to follow the transport and

  15. TUBERCULOSIS IN SIBERIAN AND FAR EASTERN FEDERAL DISTRICTS (2007-2016

    T. V. Alekseeva

    2017-01-01

    Full Text Available The article describes changes in the main tuberculosis epidemiological indicators in Siberian and Far Eastern Federal Districts over the last decade. The rate of changes was analyzed for 21 regions within two districts, total number and structure of those followed up by phthisiologists in 2007-2016 were compared. TB situation has not significantly improved since the drug resistance and HIV infection become more and more frequent, providing an indirect impact on the epidemiological indicators. It is very difficult to treat such categories of patients and these difficulties do not allow enhancing treatment efficiency and cause an abrupt growth of the costs per one patient, both financial and organizational ones.

  16. Quantitative Non-canonical Amino Acid Tagging (QuaNCAT) Proteomics Identifies Distinct Patterns of Protein Synthesis Rapidly Induced by Hypertrophic Agents in Cardiomyocytes, Revealing New Aspects of Metabolic Remodeling*

    Liu, Rui; Kenney, Justin W.; Manousopoulou, Antigoni; Johnston, Harvey E.; Kamei, Makoto; Woelk, Christopher H.; Xie, Jianling; Schwarzer, Michael; Proud, Christopher G.

    2016-01-01

    Cardiomyocytes undergo growth and remodeling in response to specific pathological or physiological conditions. In the former, myocardial growth is a risk factor for cardiac failure and faster protein synthesis is a major factor driving cardiomyocyte growth. Our goal was to quantify the rapid effects of different pro-hypertrophic stimuli on the synthesis of specific proteins in ARVC and to determine whether such effects are caused by alterations on mRNA abundance or the translation of specific mRNAs. Cardiomyocytes have very low rates of protein synthesis, posing a challenging problem in terms of studying changes in the synthesis of specific proteins, which also applies to other nondividing primary cells. To study the rates of accumulation of specific proteins in these cells, we developed an optimized version of the Quantitative Noncanonical Amino acid Tagging LC/MS proteomic method to label and selectively enrich newly synthesized proteins in these primary cells while eliminating the suppressive effects of pre-existing and highly abundant nonisotope-tagged polypeptides. Our data revealed that a classical pathologic (phenylephrine; PE) and the recently identified insulin stimulus that also contributes to the development of pathological cardiac hypertrophy (insulin), both increased the synthesis of proteins involved in, e.g. glycolysis, the Krebs cycle and beta-oxidation, and sarcomeric components. However, insulin increased synthesis of many metabolic enzymes to a greater extent than PE. Using a novel validation method, we confirmed that synthesis of selected candidates is indeed up-regulated by PE and insulin. Synthesis of all proteins studied was up-regulated by signaling through mammalian target of rapamycin complex 1 without changes in their mRNA levels, showing the key importance of translational control in the rapid effects of hypertrophic stimuli. Expression of PKM2 was up-regulated in rat hearts following TAC. This isoform possesses specific regulatory

  17. NUMBER AND STRUCTURE OF MEDICAL STAFF IN THE SIBERIAN CITIES IN THE GREAT PATRIOTIC WAR OF 1941-1945

    Yuliya A. Davidova

    2013-01-01

    Full Text Available A dynamics of the number of medical personnel Siberian cities in the Great Patriotic war is analyzed in the article. The author studies quantity and structure of senior and low-grade medical personnel of healthcare institutions, shows its impact on medical and sanitarian anti-epidemic work, as well as considers methods of decision of personnel problem in the region. The study is based on analysis of documents of the State Archive of the Russian Federation, the Russian State Archive of Socio-Political History, the Russian State Archive of Economy and the Regional Archives of the Siberian cities.

  18. Impact of Climate Change on Siberian High and Wintertime Air Pollution in China in Past Two Decades

    Zhao, Shuyu; Feng, Tian; Tie, Xuexi; Long, Xin; Li, Guohui; Cao, Junji; Zhou, Weijian; An, Zhisheng

    2018-02-01

    China has suffered severe air pollutions during wintertime as national industrialization and urbanization have been increasingly developed in the past decades. Recent studies suggest that climate change has important impacts on extreme haze events in northern China. This study uses reanalysis datasets to analyze the trend and variability of Siberian High (SiH) intensity, and its relationship with the Arctic temperature and sea ice cover (SIC) in past two decades. The results show that Arctic is warming accompanied by a rapid decline of SIC, while Eurasia is cooling and SiH intensity is gradually enhancing. The statistics illustrates that the SiH has a significantly positive correlation to the temperature (R = 0.70), and a significant anticorrelation to the SIC (R = -0.69), and this is because the warming Arctic and the reducing SIC enhanced the SiH. The enhanced SiH leads to strengthened northerly winds in the North China Plain (NCP). The WRF-Chem model calculation reveals the strengthened northerly winds during the stronger SiH period in January 2016 produce a significant decrease in PM2.5 (particulate matter with aerodynamic diameter less than 2.5 µm) concentrations by 100-200 µg m-3 than that during the weaker one in January 2013. A sensitivity calculation figures out the reduction of PM2.5 concentrations due to a decrease of 50% in emissions is comparable to changes from the weak SiH condition to the strong SiH condition, suggesting that extreme climate variability in the past few years could have an equivalent impact as a consequence of a large emission reduction on wintertime air pollution in the NCP.

  19. Black-footed ferrets and Siberian polecats as ecological surrogates and ecological equivalents

    Biggins, D.E.; Hanebury, L.R.; Miller, B.J.; Powell, R.A.

    2011-01-01

    Ecologically equivalent species serve similar functions in different communities, and an ecological surrogate species can be used as a substitute for an equivalent species in a community. Siberian polecats (Mustela eversmanii) and black-footed ferrets (M. nigripes) have long been considered ecological equivalents. Polecats also have been used as investigational surrogates for black-footed ferrets, yet the similarities and differences between the 2 species are poorly understood. We contrasted activity patterns of radiotagged polecats and ferrets released onto ferret habitat. Ferrets tended to be nocturnal and most active after midnight. Polecats were not highly selective for any period of the day or night. Ferrets and polecats moved most during brightly moonlit nights. The diel activity pattern of ferrets was consistent with avoidance of coyotes (Canis latrans) and diurnal birds of prey. Similarly, polecat activity was consistent with avoidance of red foxes (Vulpes vulpes) in their natural range. Intraguild predation (including interference competition) is inferred as a selective force influencing behaviors of these mustelines. Examination of our data suggests that black-footed ferrets and Siberian polecats might be ecological equivalents but are not perfect surrogates. Nonetheless, polecats as surrogates for black-footed ferrets have provided critical insight needed, especially related to predation, to improve the success of ferret reintroductions. ?? 2011 American Society of Mammalogists.

  20. Surface forcing of non-stand-replacing fires in Siberian larch forests

    Chen, Dong; Loboda, Tatiana V.

    2018-04-01

    Wildfires are the dominant disturbance agent in the Siberian larch forests. Extensive low- to mediate-intensity non-stand-replacing fires are a notable property of fire regime in these forests. Recent large scale studies of these fires have focused mostly on their impacts on carbon budget; however, their potential impacts on energy budget through post-fire albedo changes have not been considered. This study quantifies the post-fire surface forcing for Siberian larch forests that experienced non-stand-replacing fires between 2001 and 2012 using the full record of MODIS MCD43A3 albedo product and a burned area product developed specifically for the Russian forests. Despite a large variability, the mean effect of non-stand-replacing fires imposed through albedo is a negative forcing which lasts for at least 14 years. However, the magnitude of the forcing is much smaller than that imposed by stand-replacing fires, highlighting the importance of differentiating between the two fire types in the studies involving the fire impacts in the region. The results of this study also show that MODIS-based summer differenced normalized burn ratio (dNBR) provides a reliable metric for differentiating non-stand-replacing from stand-replacing fires with an overall accuracy of 88%, which is of considerable importance for future work on modeling post-fire energy budget and carbon budget in the region.

  1. Photoperiod and acute energy deficits interact on components of the thyroid hormone system in hypothalamic tanycytes of the Siberian hamster

    Herwig, Annika; Wilson, Dana; Logie, Tracy J.; Boelen, Anita; Morgan, Peter J.; Mercer, Julian G.; Barrett, Perry

    2009-01-01

    In the Siberian hamster, seasonal weight loss occurs gradually over many weeks during autumn and winter. This is driven by a regulatory mechanism that is able to integrate duration of exposure to short days (SDs) with the size of body energy reserves. After food restriction in SDs, followed by ad

  2. NEW DATA ON AGE AND NATURE OF CARBONIZATION WITHIN SOUTHERN FLANK OF THE BAIKAL LEDGE OF THE SIBERIAN CRATON BASEMENT

    Yu. V. Danilova

    2017-01-01

    Full Text Available The Baikal ledge rock formations in the Siberian craton structure are included in the Akitkan mobile belt which is considered as the Late Paleoproterozoic independent island arc system moved up to the ancient basement during the terrains amalgamation 1.91–2.00 Ga ago (Fig. 1 [Rosen, 2003; Gladkochub et al., 2009; Didenko et al., 2013].

  3. The effect of thermal shock on morphological characteristics of blood cells in Siberian sturgeon (Acipenser baerii triploids

    Teresa Wlasow

    2011-01-01

    Full Text Available The aim of the study was to evaluate the effect of thermal shock on morphotic blood elements in Siberian sturgeon Acipenser baerii triploids. The thermal shock (37 °C for 2 min was applied in the 18th min after fertilization. Blood was sampled from parallel cultured ten triploids and ten diploids on day 70 after hatching. Ploidy was assessed with the cytogenetic method and measurements of cellular nuclei. In the blood of triploids, significant dominance of immature red blood cells, erythrocytes with a displaced nucleus, microcytes and erythroplastids were observed. The blood of triploids was also characterized by a reduced number of lymphocytes. The percentage of neutrophil and eosinophil granulocytes was elevated; increased share of neutrophil granulocytes with a 4-, 5- or 6-segmented nucleus and eosinophil granulocytes with a nucleus consisting of three and more segments was observed. Disturbances in the picture of red blood cells can be considered as an expression of intensification of end-stage changes in triploids. The response to these changes in the blood of triploid Siberian sturgeon is an increase in the share of polymorphonuclear PMN, cells counted as microphages. Frequent presence of immature red blood cells in triploid Siberian sturgeon is a process that aims at counterbalancing the loss among these blood cells. It is the first report on morphological changes and proportions among blood cells in triploid Siberian sturgeon.

  4. New paleomagnetic poles from Arctic Siberia support Indian Ocean option for the Neoproterozoic APWP of the Siberian craton.

    Pasenko, A.; Malyshev, S. V.

    2017-12-01

    Quantity and quality of paleomagnetic poles obtained so far for Neoproterozoic of Siberia are still insufficient even to outline the general trend of APWP of Siberia for this huge and very interesting time interval. Meanwhile, the solution of this problem is crucial for choice of polarity option for Siberian proterozoic paleomagnetic directions, for construction and testing of world paleotectonic and paleogeographic reconstructions. For example, whether or not the Siberian craton could be connected with Laurentia within the supercontinent Rodinia depends directly on paleomagnetic polarity option choice, which , in its turn, is determined by either we choose for neoproterozoic drift of Siberian paleomagnetic poles Pacific ocean trend [Smethurst et al., 1998] or Indian ocean [Pavlov et al., 2015] trend. To advance in solution of this problem we have carried out the paleomagnetic investigations of several sedimentary sections and sills of Arctic Siberia considered to be meso-neoproterozoic in age. In particular we have studied the terrigenous Udza and Unguohtah Formations and basic sills of the Udzha Uplift; the carbonate Khaipakh Formation of the Olenek Uplift; the carbonate Burovaya Formation of the Turukhansk Uplift; basic sills of the Kparaulakh Mountains.In this report we present the paleomagnetic poles obtained, discuss their bearing on construction of the adequate Siberian neoproterozoic APWP and show that our new data rather support the Indian ocean option.This research were supported by Grant from RF President #MK-739.2017.5

  5. [50 years anniversary of Research Institute for Occupational Medicine and Human Ecology with Siberian Division of RAMSc].

    Rukavishnikov, V S; Shaiakhmetov, S F; Gus'kova, T M

    2010-01-01

    The article covers main steps of establishment and development of Research Institute for Occupational medicine and Human ecology with Siberian Division of RAMSc over 50 years of activities, major results of research, contribution of the Institute personnel into development of hygienic science and practical medicine in Siberia.

  6. Vibrio cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico

    Alam, Munirul; Islam, M. Tarequl; Rashed, Shah Manzur; Johura, Fatema-tuz; Bhuiyan, Nurul A.; Delgado, Gabriela; Morales, Rosario; Mendez, Jose Luis; Navarro, Armando; Watanabe, Haruo; Hasan, Nur-A; Colwell, Rita R.; Cravioto, Alejandro

    2012-01-01

    Vibrio cholerae O1 classical (CL) biotype caused the fifth and sixth pandemics, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the seventh pandemic in Asia in the 1970s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia and although it had never been reported from Latin America, V. cholerae CL and ET biotypes, including a hybrid ET, were found associated with areas of cholera endemicity in Mexico between 199...

  7. Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma

    Nepal, Chirag; O'Rourke, Colm J; Oliveira, Douglas Vnp

    2018-01-01

    Intrahepatic cholangiocarcinoma (iCCA) remains a highly heterogeneous malignancy that has eluded effective patient stratification to date. The extent to which such heterogeneity can be influenced by individual driver mutations remains to be evaluated. Here, we analyzed genomic (whole-exome sequen...

  8. Metabolomics reveals distinct neurochemical profiles associated with stress resilience

    Brooke N. Dulka

    2017-12-01

    Full Text Available Acute social defeat represents a naturalistic form of conditioned fear and is an excellent model in which to investigate the biological basis of stress resilience. While there is growing interest in identifying biomarkers of stress resilience, until recently, it has not been feasible to associate levels of large numbers of neurochemicals and metabolites to stress-related phenotypes. The objective of the present study was to use an untargeted metabolomics approach to identify known and unknown neurochemicals in select brain regions that distinguish susceptible and resistant individuals in two rodent models of acute social defeat. In the first experiment, male mice were first phenotyped as resistant or susceptible. Then, mice were subjected to acute social defeat, and tissues were immediately collected from the ventromedial prefrontal cortex (vmPFC, basolateral/central amygdala (BLA/CeA, nucleus accumbens (NAc, and dorsal hippocampus (dHPC. Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS was used for the detection of water-soluble neurochemicals. In the second experiment, male Syrian hamsters were paired in daily agonistic encounters for 2 weeks, during which they formed stable dominant-subordinate relationships. Then, 24 h after the last dominance encounter, animals were exposed to acute social defeat stress. Immediately after social defeat, tissue was collected from the vmPFC, BLA/CeA, NAc, and dHPC for analysis using UPLC-HRMS. Although no single biomarker characterized stress-related phenotypes in both species, commonalities were found. For instance, in both model systems, animals resistant to social defeat stress also show increased concentration of molecules to protect against oxidative stress in the NAc and vmPFC. Additionally, in both mice and hamsters, unidentified spectral features were preliminarily annotated as potential targets for future experiments. Overall, these findings suggest that a metabolomics approach can identify functional groups of neurochemicals that may serve as novel targets for the diagnosis, treatment, or prevention of stress-related mental illness. Keywords: Metabolomics, Biomarkers, Resilience, Stress, Oxidative stress, Social defeat

  9. Intra-stand variation of cone structure and seed production in Siberian stone pine: pattern and use for breeding

    V.S. Akimov

    2013-12-01

    Full Text Available Siberian stone pine (Pinus sibirica Du Tour in Russia is primarily valued as a nut-bearing species. Therefore, intra-standvariation in its cone structure and seed production have been actively studied during the last 50 years. However, these studies arepoorly related to practical breeding. We used a novel system of traits to characterize yearly seed crops at the different levels of itsstructural organization. The purpose is to analyze the results of long-term observations of the intra-stand variation of the reproductivefeatures complex, and to reveal the pattern and character of its diversity. This information would be useful to develop the method ofsearching the initial material for breeding. The research plot is established in the Nizhne-Sechenovo forest located 25 km fromTomsk in the south part of the boreal zone (170 years old, mean height 22 m, mean d.b.h. 60 cm. The number of sampled trees variedbetween 40-120 among years. The registration of seed crop and analysis of its structure was conducted every year from 1990 to 2005. Theintra-stand variation of the traits' level was determined as a standard deviation in percent from the simple average. The level ofvariability rose sharply and the correlations between them decreased in the years of the low crops. The results concerning variation in seedand cone traits are listed in the next table. The number of full seeds depended rather on losses in the processes of development (r =0.80*-0.85* than on their starting number (r =0.55*-0.60*. The mass of one seed with sound endosperm rose with an increase in the ratio ofthe ovules, which were lost at the earlier stagesof development (r = 0.20-0.25* and the flat seed ratio (r = 0.35*-0.40*. In year-to-year dynamics, the number of cones per tree ispositively connected with the number of filled seeds per cone (r = 0.78* and with other indices characterizing 'the crop quality'.The breeding rank of trees by all important

  10. Distribution, densities, and ecology of Siberian cranes in the Khroma River region of northern Yakutia in northeastern Russia

    Bysykatova, Inga P.; Krapu, Gary L.; Germogenov, Nicolai I.; Buhl, Deborah A.; Aborn, David

    2014-01-01

    The Siberian crane (Grus leucogeranus) is the third rarest crane species in the world with a breeding range now centered on 3 core areas and a buffer zone in the arctic of northern Yakutia in northeastern Russia. During 16 July-2 August 2009, we undertook ground surveys within the Khroma River core breeding area, surrounding buffer zone, and lands lying to the west of the known rbeeding range to estimate densities and determine habitat use and social status of Siberian cranes. A total of 142 Siberian cranes were sighted (including 55 pairs) at 54 locations with 32 cranes (including 13 pairs) sighted outside the currently known breeding range in the lower drainages of the Syalakh and Syuryuktyakh Rivers. After adjusting for a probability of detection of 0.484 (95% CI = 0.281-0.833), Siberian crane densities in the Khroma core area and the buffer zone averaged 0.0921 cranes/km2 and 0.0363 cranes/km2, respectively. A majority of cranes (n = 93 [65%]) occurred in complexes of large basin wetlands, with use centered in those having extensive beds of pendant grass (Arctophila fulva). Of the 142 cranes seen, 110 (77%) were paired, 21 (15%) were singles, and 11 (8%) were in groups of 3-5. The Khroma core supports 1 of 2 large concentrations of breeding Siberian cranes remaining in the wild; therefore, we recommend that consideration be given to designating a nature reserve that would encompass the Khroma core, adjacent buffer zone, and lands to the west (including coastal tundra areas along the lower drainages of the Syalah and Syuryuktyah Rivers). Further research is needed to gain additional insight into Siberian crane distribution and numbers on lands beyond the currently delineated western boundary of the Siberian crane breeding range in the Ust-Yana District of northern Yakutia. Important gaps remain in information needed to effectively guide conservation efforts for the Eastern Population, and recent advances in remote tracking technology offer potential

  11. Smoke aerosol chemistry and aging of Siberian biomass burning emissions in a large aerosol chamber

    Kalogridis, A.-C.; Popovicheva, O. B.; Engling, G.; Diapouli, E.; Kawamura, K.; Tachibana, E.; Ono, K.; Kozlov, V. S.; Eleftheriadis, K.

    2018-07-01

    Vegetation open fires constitute a significant source of particulate pollutants on a global scale and play an important role in both atmospheric chemistry and climate change. To better understand the emission and aging characteristics of smoke aerosols, we performed small-scale fire experiments using the Large Aerosol Chamber (LAC, 1800 m3) with a focus on biomass burning from Siberian boreal coniferous forests. A series of burn experiments were conducted with typical Siberian biomass (pine and debris), simulating separately different combustion conditions, namely, flaming, smoldering and mixed phase. Following smoke emission and dispersion in the combustion chamber, we investigated aging of aerosols under dark conditions. Here, we present experimental data on emission factors of total, elemental and organic carbon, as well as individual organic compounds, such as anhydrosugars, phenolic and dicarboxylic acids. We found that total carbon accounts for up to 80% of the fine mode (PM2.5) smoke aerosol. Higher PM2.5 emission factors were observed in the smoldering compared to flaming phase and in pine compared to debris smoldering phase. For low-temperature combustion, organic carbon (OC) contributed to more than 90% of total carbon, whereas elemental carbon (EC) dominated the aerosol composition in flaming burns with a 60-70% contribution to the total carbon mass. For all smoldering burns, levoglucosan (LG), a cellulose decomposition product, was the most abundant organic species (average LG/OC = 0.26 for pine smoldering), followed by its isomer mannosan or dehydroabietic acid (DA), an important constituent of conifer resin (DA/OC = 0.033). A levoglucosan-to-mannosan ratio of about 3 was observed, which is consistent with ratios reported for coniferous biomass and more generally softwood. The rates of aerosol removal for OC and individual organic compounds were investigated during aging in the chamber in terms of mass concentration loss rates over time under dark

  12. Nutrient cycling and ecosystem metabolism in boreal streams of the Central Siberian Plateau

    Diemer, L.; McDowell, W. H.; Prokushkin, A. S.

    2013-12-01

    Arctic boreal streams are undergoing considerable change in carbon and nutrient biogeochemistry due to degrading permafrost and increasing fire activity. Recent studies show that fire increases transport of inorganic solutes from the boreal landscape to arctic streams in some regions; couple this with expected greater labile dissolved organic carbon (DOC) from deepening active layers, enhanced biomass production, and increased annual precipitation and boreal streams may experience greater in-stream primary production and respiration in the coming century. Little is known about the spatial and temporal dynamics of inorganic nutrients in relation to C availability in headwater streams of a major Arctic region, the Central Siberian Plateau. Our preliminary data of Central Siberian headwater streams show NO3 and PO4 concentrations near or below detection limits (e.g. nine samples taken in spring from a small stream near the Russian settlement of Tura averaged 10 μg/L NO3-N and 9.7 μg/L PO4-P), and recent studies in Central Siberia suggest that bioavailable organic matter and inorganic nutrients such as NO3 will likely increase with climate warming. We examined the fate of nutrients in Central Siberian streams using Tracer for Spiraling Curve Characterization (TASCC) additions of NO3, NH4, and PO4 along with conservative tracer, NaCl, in spring at high and low discharges in streams underlain by continuous permafrost in Central Siberia. We also sampled two sites in spring every 2 hours overnight for 24 hours to document any diel patterns in DOC and inorganic nutrients. Our results thus far show that NO3 uptake length may be strongly correlated with DOC concentration (a function of fire activity). Preliminary results also show that despite high discharge and cold temperatures (4-8°C) in mid to late spring, there appears to be biological activity stimulating a diel signal for NO3 with maximum concentration corresponding to low light (11 PM). Investigating the primary

  13. Deglacial remobilization of permafrost carbon to sediments along the East Siberian Arctic Seas

    Martens, J.; Wild, B.; Bröder, L.; Andersson, A.; Pearce, C.; O'Regan, M.; Jakobsson, M.; Tesi, T.; Muschitiello, F.; Sköld, M.; Semiletov, I. P.; Dudarev, O.; Gustafsson, O.

    2017-12-01

    Current climate change is expected to thaw large quantities of permafrost carbon (PF-C) and expose it to degradation which emits greenhouse gases (i.e. CO2 and CH4). Warming causes a gradual deepening of the seasonally thawed active layer surface of permafrost soils, but also the abrupt collapse of deeper Ice Complex Deposits (ICD), especially along Siberian coastlines. It was recently hypothesized that past warming already induced large-scale permafrost degradation after the last glacial, which ultimately amplified climate forcing. We here assess the mobilization of PF-C to East Siberian Arctic Sea sediments during these warming periods. We perform source apportionment using bulk carbon isotopes (ΔΔ14C, δ13C) together with terrestrial biomarkers (CuO-derived lignin phenols) as indicators for PF-C transfer. We apply these techniques to sediment cores (SWERUS-L2) from the Chukchi Sea (4-PC1) and the southern Lomonosov Ridge (31-PC1). We found that PF-C fluxes during the Bølling-Allerød warming (14.7 to 12.7 cal ka BP), the Younger Dryas cooling (12.7 to 11.7 cal ka BP) and the early Holocene warming (until 11 cal ka BP) were overall higher than mid and late Holocene fluxes. In the Chukchi Sea, PF-C burial was 2x higher during the deglaciation (7.2 g m-2 a-1) than in the mid and late Holocene (3.6 g m-2 a-1), and ICD were the dominant source of PF-C (79.1%). Smaller fractions originated from the active layer (9.1%) and marine sources (11.7%). We conclude that thermo-erosion of ICD released large amounts of PF-C to the Chukchi Sea, likely driven by climate warming and the deglacial sea level rise. This contrasts to earlier analyses of Laptev Sea sediments where active layer material from river transport dominated the carbon flux. Preliminary data on lignin phenol concentrations of Lomonosov Ridge sediments suggest that the postglacial remobilization of PF-C was one order of magnitude higher (10x) than during both the preceding glacial and the subsequent Holocene

  14. Opposing effects of fire severity on climate feedbacks in Siberian larch forests

    Loranty, M. M.; Alexander, H. D.; Natali, S.; Kropp, H.; Mack, M. C.; Bunn, A. G.; Davydov, S. P.; Erb, A.; Kholodov, A. L.; Schaaf, C.; Wang, Z.; Zimov, N.; Zimov, S. A.

    2017-12-01

    Boreal larch forests in northeastern Siberia comprise nearly 25% of the continuous permafrost zone. Structural and functional changes in these ecosystems will have important climate feedbacks at regional and global scales. Like boreal ecosystems in North America, fire is an important determinant of landscape scale forest distribution, and fire regimes are intensifying as climate warms. In Siberian larch forests are dominated by a single tree species, and there is evidence that fire severity influences post-fire forest density via impacts on seedling establishment. The extent to which these effects occur, or persist, and the associated climate feedbacks are not well quantified. In this study we use forest stand inventories, in situ observations, and satellite remote sensing to examine: 1) variation in forest density within and between fire scars, and 2) changes in land surface albedo and active layer dynamics associated with forest density variation. At the landscape scale we observed declines in Landsat derived albedo as forests recovered in the first several decades after fire, though canopy cover varied widely within and between individual fire scars. Within an individual mid-successional fire scar ( 75 years) we observed canopy cover ranging from 15-90% with correspondingly large ranges of albedo during periods of snow cover, and relatively small differences in albedo during the growing season. We found an inverse relationship between canopy density and soil temperature within this fire scar; high-density low-albedo stands had cooler soils and shallower active layers, while low-density stands had warmer soils and deeper active layers. Intensive energy balance measurements at a high- and low- density site show that canopy cover alters the magnitude and timing of ground heat fluxes that affect active layer properties. Our results show that fire impacts on stand structure in Siberian larch forests affect land surface albedo and active layer dynamics in ways that

  15. Dissolved organic matter and its optical characteristics in the Laptev and East Siberian seas: spatial distribution and interannual variability (2003-2011)

    Pugach, Svetlana P.; Pipko, Irina I.; Shakhova, Natalia E.; Shirshin, Evgeny A.; Perminova, Irina V.; Gustafsson, Örjan; Bondur, Valery G.; Ruban, Alexey S.; Semiletov, Igor P.

    2018-02-01

    The East Siberian Arctic Shelf (ESAS) is the broadest and shallowest continental shelf in the world. It is characterized by both the highest rate of coastal erosion in the world and a large riverine input of terrigenous dissolved organic matter (DOM). DOM plays a significant role in marine aquatic ecosystems. The chromophoric fraction of DOM (CDOM) directly affects the quantity and spectral quality of available light, thereby impacting both primary production and ultraviolet (UV) exposure in aquatic ecosystems. A multiyear study of CDOM absorption, fluorescence, and spectral characteristics was carried out over the vast ESAS in the summer-fall seasons. The paper describes observations accomplished at 286 stations and 1766 in situ high-resolution optical measurements distributed along the nearshore zone. Spatial and interannual CDOM dynamics over the ESAS were investigated, and driving factors were identified. It was shown that the atmospheric circulation regime is the dominant factor controlling CDOM distribution on the ESAS. This paper explores the possibility of using CDOM and its spectral parameters to identify the different biogeochemical regimes in the surveyed area. The analysis of CDOM spectral characteristics showed that the major part of the Laptev and East Siberian seas shelf is influenced by terrigenous DOM carried in riverine discharge. Western and eastern provinces of the ESAS with distinctly different DOM optical properties were also identified; a transition between the two provinces at around 165-170° E, also consistent with hydrological and hydrochemical data, is shown. In the western ESAS, a region of substantial river impact, the content of aromatic carbon within DOM remains almost constant. In the eastern ESAS, a gradual decrease in aromaticity percentage was observed, indicating contribution of Pacific-origin waters, where allochthonous DOM with predominantly aliphatic character and much smaller absorption capacity predominates. In addition, we

  16. EARLY STAGE OF THE CENTRAL ASIAN OROGENIC BELT BUILDING: EVIDENCES FROM THE SOUTHERN SIBERIAN CRATON

    D. P. Gladkochub

    2017-01-01

    Full Text Available The origin of the Central-Asian Orogenic Belt (CAOB, especially of its northern segment nearby the southern margin of the Siberian craton (SC is directly related to development and closure of the Paleo-Asian Ocean (PAO. Signatures of early stages of the PAO evolution are recorded in the Late Precambrian sedimentary successions of the Sayan-Baikal-Patom Belt (SBPB on the southern edge of SC. These successions are spread over 2000 km and can be traced along this edge from north-west (Sayan area to south-east (Baikal area and further to north-east (Patom area. Here we present the synthesis of all available and reliable LA-ICP-MS U-Pb geochronological studies of detrital zircons from these sedimentary successions.

  17. Advanced inorganic fluorides. Proceedings of the Second International Siberian workshop INTERSIBFLUORINE-2006

    Volkov, V.V.; Mit'kin, V.N.; Bujnovskij, A.S.; Sofronov, V.L.

    2006-01-01

    Proceedings of the Second International Siberian workshop ISIF-2006 on modern inorganic fluorides contain full author's texts of 82 plenary reports and posters on the main trends in chemistry and technology of inorganic fluorides and their various applications. The following new trends are reflected in the ISIF-2006 Proceedings versus the ISIF-2003 ones: production and use of of nano-sized systems and materials based on fluoride phases and fluorinating systems; chemistry of fluorofullerenes, fluorides of graphite and carbon materials; development of research and technical principles of economically viable process of depleted uranium hexafluoride conversion; vitrifying systems based on metal fluorides possessing valuable functional optical properties; mechanochemical processes and phenomena in chemistry of inorganic fluorides [ru

  18. Modeling sub-sea permafrost in the East Siberian Arctic Shelf: the Dmitry Laptev Strait

    Nicolsky, D; Shakhova, N

    2010-01-01

    The present state of sub-sea permafrost modeling does not agree with certain observational data on the permafrost state within the East Siberian Arctic Shelf. This suggests a need to consider other mechanisms of permafrost destabilization after the recent ocean transgression. We propose development of open taliks wherever thaw lakes and river paleo-valleys were submerged shelf-wide as a possible mechanism for the degradation of sub-sea permafrost. To test the hypothesis we performed numerical modeling of permafrost dynamics in the Dmitry Laptev Strait area. We achieved sufficient agreement with the observed distribution of thawed and frozen layers to suggest that the proposed mechanism of permafrost destabilization is plausible.

  19. A 4.7 tesla metre solenoid for a partial Siberian snake

    Ratner, L.; Leonhardt, W.; Otter, A.; Ellstrom, L.

    1993-11-01

    We describe the engineering design of a 4.7 T-m solenoid magnet which will be installed at the Brookhaven National Laboratory AGS for a partial Siberian Snake Experiment which is an interlaboratory collaboration. The magnet has an overall length of 2.5 m, a clear bore of 15 cm and operates at a peak field of 2 T. It is pulsed at 3 second intervals with a peak current of 9500 A dc driven from a 150 V power supply. The construction uses conventional hollow copper coils but the return flux yokes are made from 1/8 inch plates bolted together. On assembly the flux yokes and endplates are clamped tightly to the coil to prevent any movement during the current pulse. The fabrication experience and test data will be presented. The magnet was installed in the summer of 1993. (author). 3 refs., 1 tab., 1 fig

  20. Stratigraphic, regional unconformity analysis and potential petroleum plays of East Siberian Sea Basin

    Karpov, Yury; Stoupakova, Antonina; Suslova, Anna; Agasheva, Mariia

    2017-04-01

    The East Siberian Sea basin (ESSB) one of the most unexplored part of the Russian Arctic shelf, extending for over 1000 km from New Siberian Islands archipelago to Wrangel Island. This region is considered as a region with probable high petroleum potential. Within the ESSB several phases of orogeny are recognized [1]: Elsmerian orogeny in Early Devonian, Early Brooks orogeny in Early Cretaceous, Late Brooks orogeny in Late Cretaceous. Two generations of the basins could be outlined. Both of these generations are controlled by the basement domains [1]: Paleozoic (post-Devonian) to Mesozoic basins preserved north of the Late Mesozoic frontal thrusts; Aptian-Albian to Quaternary basins, postdating the Verkhoyansk-Brookian orogeny, and evolving mainly over the New-Siberian-Chukchi Fold Belt. Basin is filled with siliclastic sediments and in the deepest depocentres sediments thickness exceeds 8-10 km in average. Seismic data was interpreted using methods of seismic stratigraphy. Finally, main seismic horizons were indicated and each horizon follows regional stratigraphic unconformities: mBU - in base of Cenozoic, BU - in base of Upper Cretaceous, LCU - in base of Cretaceous, JU - in middle of Jurassic, F - in top of Basement. In ESSB, we can identify Permian, Triassic, Jurassic, Cretaceous, Paleogene and Neogene seismic stratigraphy complexes. Perspective structures, investigated in ESSB were founded out by comparing seismogeological cross-sections with explored analogs in other onshore and offshore basins [2, 3, 4]. The majority of structures could be connected with stratigraphic and fault traps. The most perspective prospects are probably connected with grabens and depressions, where thickness of sediments exceed 10 km. Reservoirs in ESSB are proposed by regional geological explorations on New Siberian Islands Archipelago and Wrangel Island. Potential seals are predominantly assigned to Jurassic and Cretaceous periods. Thick clinoform units of various geometry and

  1. A 4.7 tesla metre solenoid for a partial Siberian snake

    Ratner, L; Leonhardt, W [Brookhaven National Lab., Upton, NY (United States); Otter, A; Ellstrom, L

    1993-11-01

    We describe the engineering design of a 4.7 T-m solenoid magnet which will be installed at the Brookhaven National Laboratory AGS for a partial Siberian Snake Experiment which is an interlaboratory collaboration. The magnet has an overall length of 2.5 m, a clear bore of 15 cm and operates at a peak field of 2 T. It is pulsed at 3 second intervals with a peak current of 9500 A dc driven from a 150 V power supply. The construction uses conventional hollow copper coils but the return flux yokes are made from 1/8 inch plates bolted together. On assembly the flux yokes and endplates are clamped tightly to the coil to prevent any movement during the current pulse. The fabrication experience and test data will be presented. The magnet was installed in the summer of 1993. (author). 3 refs., 1 tab., 1 fig.

  2. Variety, State and Origin of Drained Thaw Lake Basins in West-Siberian North

    Kirpotin, S.; Polishchuk, Y.; Bryksina, N.; Sugaipova, A.; Pokrovsky, O.; Shirokova, L.; Kouraev, A.; Zakharova, E.; Kolmakova, M.; Dupre, B.

    2009-04-01

    Drained thaw lake basins in Western Siberia have a local name "khasyreis" [1]. Khasyreis as well as lakes, ponds and frozen mounds are invariable element of sub-arctic frozen peat bogs - palsas and tundra landscapes. In some areas of West-Siberian sub-arctic khasyreis occupy up to 40-50% of total lake area. Sometimes their concentration is so high that we call such places ‘khasyrei's fields". Khasyreis are part of the natural cycle of palsa complex development [1], but their origin is not continuous and uniform in time and, according to our opinion, there were periods of more intensive lake drainage and khasyrei development accordingly. These times were corresponding with epochs of climatic warming and today we have faced with one of them. So, last years this process was sufficiently activated in the south part of West-Siberian sub-arctic [2]. It was discovered that in the zone of continuous permafrost thermokarst lakes have expanded their areas by about 10-12%, but in the zone of discontinuous permafrost the process of their drainage prevails. These features are connected with the thickness of peat layers which gradually decreases to the North, and thus have reduced the opportunity for lake drainage in northern areas. The most typical way of khasyrei origin is their drainage to the bigger lakes which are always situated on the lower levels and works as a collecting funnels providing drainage of smaller lakes. The lower level of the big lake appeared when the lake takes a critical mass of water enough for subsidence of the lake bottom due to the melting of underlaying rocks [2]. Another one way of lake drainage is the lake intercept by any river. Lake drainage to the subsurface (underlaying rocks) as some authors think [3, 4] is not possible in Western Siberia, because the thickness of permafrost is at list 500 m here being safe confining bed. We mark out few stages of khasyrei development: freshly drained, young, mature and old. This row reflects stages of

  3. Community Organization of Siberian Coachmen in Late XVI – XVII Centuries

    Oleg V. Semenov

    2014-06-01

    Full Text Available The article, basing on the wide range of archival data, mostly introduced into scientific use for the first time, studies communal (secular and church organization of Siberian coachmen in late XVI – XVII centuries. The paper touches upon the issue, concerning the time of its establishment, thoroughly characterizes the structure, functions and officials. The features of interrelation between coachmen ‘world’ and state and other corporate communities of the region are showed. The conclusion that, despite the dependence on the authorities, the processes of bureaucratization and the growth of the villeinage trends, common for the country, coachmen played significant role in the social life of Siberia is made. They intensively protected their interests and forced the government to consider them.

  4. Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.

    Ricaut, François-Xavier; Keyser-Tracqui, Christine; Cammaert, Laurence; Crubézy, Eric; Ludes, Bertrand

    2004-04-01

    We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia. Copyright 2003 Wiley-Liss, Inc.

  5. Mechanical fasteners used in historical Siberian shipbuilding: perspectives for metallurgical analysis

    Goncharov, A. E.; Mednikov, D. M.; Karelin, N. M.; Nasyrov, I. R.

    2017-10-01

    Recent discoveries of shipwrecked vessels in the northern reaches of the river Yenisei led to a number of questions concerning the history of shipbuilding in Siberia and the technical features of the first vessels of the industrial era to navigate the Northern Sea Route and the Yenisei. One of these questions addresses the features of mechanical fasteners used in the construction of the Siberian vessels. The answer to this question may provide information on how the first vessels, constructed in Siberia during the 1870’s, were able to sail the high seas of the Arctic Ocean and reach European ports. In this paper, we provide a description of iron mechanical fasteners obtained from one shipwrecked vessel and discuss on the perspectives of a metallurgical analysis This research has been funded by a grant of the Russian Fund of Humanities Research (Russian Fund of Fundamental Research) and the Krasnoyarsk Regional Science Fund under Grant number 16-11-24010.

  6. Influence of the Siberian larch extract on the processes of peroxide oxidation of lipids in experiment

    Pateyuk Andrey

    2016-03-01

    Full Text Available In modern conditions wood processing is one of the primary branches of production in Transbaikal region. In connection with big squares of logging the question of processing and utilizing waste products directly on the spot is particularly acute. We researched the activity of water extract from sawdust of Siberian larch "Ekstrapinus" on the power exchange and processes of peroxide oxidation of lipids against immobilized stress in experiment. The data provided in the article prove that the use of Ekstrapinus extract reduces the pathological violations arising under stress. So, Ekstrapinus extract restores energy potential of cages when modeling stress, restores energy potential of cells, normalizes balance in the system "peroxide oxidation of lipids – antioxidant protection" and supports the balance of tiol in an animal organism in the state of stress. Considering absence of toxicity in the recommended doses, it is possible to recommend their application under stress.

  7. VICTIMIZATION BARRIERS OF SMALL BUSINESS (ON THE EXAMPLE OF SIBERIAN FEDERAL DISTRICT

    Альберт Станиславович Милевич

    2013-08-01

    Full Text Available The actuality of this article confirms the mainest idea: determination of basic factors of victimization businessmen in small business in Siberian District(SD. This article consider field and main explorations in victimization of entrepreneurs of small business at 5 regions SD. The representativeness of exploration shows sociological choice. In field study took part 100 respondents, all in all 487 reprenteurs.The primary research method had chosen in the way of survey. By the results were identified over 14 organizations and instances which were given bribes over 10 times. Moreover the exploration showed causes why businessmen forced to solve problems by not legal way.It is necessary to eliminate this victimization factors and program of victimological prophylaxis for successful development of small business of SD and it’s regions concretely. Decision of this problem would be showed in the next article.DOI: http://dx.doi.org/10.12731/2218-7405-2013-6-19

  8. Morbillivirus infection in a wild siberian tiger in the Russian Far East.

    Quigley, Kathy S; Evermann, James F; Leathers, Charles W; Armstrong, Douglas L; Goodrich, John; Duncan, Neil M; Miquelle, Dale G

    2010-10-01

    We report the first documented case of morbillivirus infection in a wild, free-ranging Siberian tiger (Panthera tigris altaica). The tigress entered a small village in the Russian Far East in an ambulatory but stuporous state with no apparent recognition or fear of humans. Her condition progressed rapidly with neurological signs, anorexia, and ultimately death. Histologic lesions included vacuolated to malacic white matter in the brain stem, cerebellum, and thalamus, with associated lymphocytic meningoencephalitis. Large, intranuclear, eosinophilic inclusions were within regional astrocytes, and the brain lesions were immunohistochemically positive when stained for canine distemper viral antigen. Hematologic and blood chemistry results were consistent with overwhelming systemic infection and starvation. The animal also was antibody-positive for canine distemper virus, feline panleukopenia, and feline coronavirus.

  9. Half-length model of a Siberian Snake magnet for RHIC

    Okamura, M; Kawaguchi, T; Katayama, T; Jain, A; Muratore, J; Morgan, G; Willen, E

    2000-01-01

    For the Relativistic Heavy Ion Collider (RHIC) Spin Project, super-conducting helical dipole magnets are being constructed. These magnets will be used in 'Siberian Snakes' and 'Spin Rotators', which manipulate spin direction of proton beams in RHIC. The dipole field in these magnets rotates 360 deg. and is required to reach a magnetic field strength of more than 4.0 T. The bore radius of the coils and the magnetic length of the magnets are 50 and 2400 mm, respectively. To ascertain the performance of these magnets, which are built using a new 'coil in a slot' technique, a half-length model has been fabricated and tested. The quench performance, field uniformity and rotation angle have been investigated. The measured values in the model magnet agreed well with field calculations. These results demonstrate the adequacy of the fabrication method adopted in the model magnet. (authors)

  10. The cost to society of a methane outbreak from the East Siberian shelf (Invited)

    Wadhams, P.

    2013-12-01

    Peter Wadhams (Dept. of Applied Mathematics and Theoretical Physics, University of Cambridge) Chris Hope (Judge Institute, University of Cambridge) Gail Whiteman (Erasmus University, Rotterdam) The East Siberian Sea has been emitting an increasing volume of methane in the form of plumes in each of the recent summers that observations have been carried out by a US-Russian joint group led by I Semiletov and N Shakhova. We believe that the emissions are due to melt of offshore permafrost due to warming of sea temperatures associated with the summer retreat of the sea ice. The field observers believe that out of a reservoir of some 720 Gt it is possible that 50 Gt could be emitted rapidly, within a few years. We calculated in a paper in "Nature" what the impact of such an emission (occurring over 10 years) would be, and found a total economic cost over a century (using the Stern Review PAGE09 model) of 60 trillion dollars, and an additional warming of the climate of some 0.6 C by 2040. These results have aroused controversy, and to assist in further discussions of their implications we have carried out further analyses as follows: 1. We have considered smaller and larger emissions, and have considered the overall costs for emissions occurring more slowly over a longer period, and/or beginning at a later date. We find that costs are approximately proportional to volume of emission, and are actually increased if the emission date is delayed until later in the century. 2. A further field operation is being carried out in summer 2013, and we will carry out, in time for the AGU meeting, a further model calculation based on the latest opinions of Semiletov and Shakhova regarding the way in which the East Siberian Sea emission field is developing.

  11. An assessment of flux of radionuclide contamination through the large Siberian rivers to the Kara sea

    Maderich, V.; Dziuba, N.; Koshebutsky, V.; Zheleznyak, M.; Volkov, V.

    2004-01-01

    The activities of several nuclear reprocessing plants (Siberian Chemical Combine (SCC) and Mining, Chemical Combine (MCC) and Mayak Production Association (Mayak)) that are placed in the watersheds of large Siberian rivers Ob' and Yenisey may potentially cause contamination of the Arctic Ocean. An assessment of the levels of radionuclide discharges into the Kara Sea from existing and potential sources of techno-genic radioactivity, located within the watershed of the Ob' and Yenisey rivers is presented. In frame of EU INCO-COPERNICUS project RADARC a linked chain of 1D river model RIVTOX and 3D estuary model THREETOX was used to simulate impact of the previous and potential releases from the nuclear installations in the basins of Ob' and Yenisey rivers on radioactive contamination of the rivers and the Kara Sea. The RIVTOX includes the one-dimensional model of river hydraulics, suspended sediment and radionuclide transport in river channels. THREETOX includes a set of submodels: a hydrodynamics sub-model, ice dynamics-thermodynamics sub-model, suspended sediment transport and radionuclide transport submodels. The radionuclide transport model simulate processes in water, suspended sediments and in bottom sediments. These models were adapted to the Ob' river path from Mayak and SCC and Yenisey River from MCC. The simulations of 90 Sr and 137 Cs contamination for the period 1949-1994 were carried out for the Ob' and period 1959-1994 for the Yenisey. The use of model chain allowed to reconstruct contamination of water and sediments along the river path to estimate fluxes into the Kara Sea. It was shown strong initial contamination in early 50's the sediments in the Ob' were sources for secondary contamination of river and estuary. Based on chosen realistic scenarios, simulations have been performed in order to assess the potential risk of contamination from existing and potential sources of radionuclides into the Kara Sea through the Ob' and Yenisey rivers. (author)

  12. Susceptibility of the Siberian polecat to subcutaneous and oral Yersinia pestis exposure

    Castle, K.T.; Biggins, D.; Carter, L.G.; Chu, M.; Innes, Kim; Wimsatt, J.

    2001-01-01

    To determine if the Siberian polecat (Mustela eversmannii) represents a suitable model for the study of plague pathogenesis and prevention in the black-footed ferret (Mustela nigripes), polecats were exposed to 103, 107, or 1010 Yersinia pestis organisms by subcutaneous injection; an additional group was exposed to Y. pestis via ingestion of a plague-killed mouse. Plague killed 88% of polecats exposed to Y. pestis (71% mortality in the 103 group, 100% mortality in the 107 and 1010 groups, and 83% mortality in the mouse-fed group). Within the challenged group, mean day of death post-challenge ranged from 3.6 to 7.6 days; all polecats died on or before day 12 post-challenge. Animals receiving the lowest parenteral dose survived significantly longer than those receiving higher parenteral doses. Within challenged animals, mean survival time was lower in those presenting with significant weight loss by day 3, lethargy, and low fecal output; time to onset of lethargy and other signs was also related to risk of dying and/or plague dose. Six polecats developed serum antibody titers to the Y. pestis F1 protein. Three seropositive polecats survived the initial challenge and a subsequent exposure to a plague-killed mouse, while two seropositive animals later died. This study confirms that the Siberian polecat is susceptible to plague and suggests that this species will offer an appropriate surrogate for black-footed ferrets in future plague studies and related vaccine trials.

  13. Fermentation of Arabinoxylan-Oligosaccharides, Oligofructose and their Monomeric Sugars by Hindgut Bacteria from Siberian Sturgeon and African Catfish in Batch Culture in vitro

    Geraylou, Z.; Rurangwa, E.; Wiele, van der T.; Courtin, C.M.; Delcour, J.A.; Buyse, J.; Ollevier, F.

    2014-01-01

    The in vitro fermentation of two Non-Digestible Oligosaccharide (NDO) preparations, Arabinoxylan- Oligosaccharides (AXOS) and Oligofructose (OF), and their respective monomeric sugars, xylose and fructose, were investigated by hindgut microbiota of two major aquaculture fish species, Siberian

  14. THE SOUTHERN FRAGMENT OF THE SIBERIAN CRATON: “LANDSCAPE” HISTORY OVER TWO BILLION YEARS

    Arkady M. Stanevich

    2010-01-01

    Full Text Available In the state-of-the-art geology, concepts of evolution of interrelated geodynamic and biotic events throughout the history of the Earth have been developed (Fig. 1. Research results on sediments, bio-stratigraphy and geodynamics of the southern fragment of the Siberian craton (SSC, Fig. 2 provide for more or less reliable assessments of the status and evolution of ancient landscapes and biotas from the Lower Proterozoic to the Cenozoic.In the Lower Proterozoic, the geodynamic regime of the Urik-Iyskiy graben was similar to those of the westernpacific island-arc systems, which resulted in the orogen formation and established post-orogen granitoids of 1.86 bln years of age. At the beginning of the Early Riphean, volcano-sedimentary masses were accumulated in continental basins (Fig. 2, 3A. Collision orogenesis also resulted in the occurrence of the terrigeno-volcanogenic complex of the Akitkanskaya suite in the Western Pribaikalie and the transecting Irelskiy granitoids, aged 1.86 bln years, at the edge of the craton. Later on, most probably before the Riphean, peneplanation took place, and a shallow peripheral sea was formed with highly-mature sediments of the Purpolskaya suite. Different environments are reconstructed in the KodarUdokan zone. Sediments of the Udokanskaya suite, varying in thicknesses from 11 to 14 km, suggest a complicated evolution of sedimentation in the peripheral marine basin. Dozens of radiochronological datings of granitoids of the Chuiskiy and Kodarskiy complex which transect the Udokanskaya suite are within the range from 1.7 to 2.0 bln years. From the deposit composition and texture, it can be suggested that the middle, Chineiskaya sub-suite was formed under island-arc conditions; and glacial phenomena occurred in the late Udokan time.Further geological history of the SSC can be described only within the period after the Late Riphean sedimentations (see Fig. 3Б, В. The SSC evolution in the Neo-Proterozoic began with

  15. Touch communicates distinct emotions.

    Hertenstein, Matthew J; Keltner, Dacher; App, Betsy; Bulleit, Brittany A; Jaskolka, Ariane R

    2006-08-01

    The study of emotional signaling has focused almost exclusively on the face and voice. In 2 studies, the authors investigated whether people can identify emotions from the experience of being touched by a stranger on the arm (without seeing the touch). In the 3rd study, they investigated whether observers can identify emotions from watching someone being touched on the arm. Two kinds of evidence suggest that humans can communicate numerous emotions with touch. First, participants in the United States (Study 1) and Spain (Study 2) could decode anger, fear, disgust, love, gratitude, and sympathy via touch at much-better-than-chance levels. Second, fine-grained coding documented specific touch behaviors associated with different emotions. In Study 3, the authors provide evidence that participants can accurately decode distinct emotions by merely watching others communicate via touch. The findings are discussed in terms of their contributions to affective science and the evolution of altruism and cooperation. (c) 2006 APA, all rights reserved

  16. Trace element distribution in peridotite xenoliths from Tok, SE Siberian craton: A record of pervasive, multi-stage metasomatism in shallow refractory mantle

    Ionov, Dmitri A.; Chazot, Gilles; Chauvel, Catherine; Merlet, Claude; Bodinier, Jean-Louis

    2006-03-01

    Spinel peridotite xenoliths in alkali basalts at Tok, SE Siberian craton range from fertile lherzolites to harzburgites and wehrlites; olivine-rich (70-84%) rocks are dominant. REE patterns in the lherzolites range from nearly flat for fertile rocks (14-17% cpx) to LREE-enriched; the enrichments are positively correlated with modal olivine, consistent with high-permeability of olivine-rich rocks during melt percolation. Clinopyroxene in olivine-rich Tok peridotites typically has convex-upward trace element patterns (La/Nd PM 1); the LREE-enrichments are positively correlated with phosphorus abundances and are mainly hosted by accessory phosphates and P-rich cryptocrystalline materials. In addition to apatite, some Tok xenoliths contain whitlockite (an anhydrous, halogen-poor and Na-Mg-rich phosphate), which is common in meteorites and lunar rocks, but has not been reported from any terrestrial mantle samples. Some olivine-rich peridotites have generations of clinopyroxene with distinct abundances of Na, LREE, Sr and Zr. The mineralogical and trace element data indicate that the lithospheric mantle section represented by the xenoliths experienced a large-scale metasomatic event produced by upward migration of mafic silicate melts followed by percolation of low- T, alkali-rich melts and fluids. Chromatographic fractionation and fractional crystallisation of the melts close to the percolation front produced strong LREE-enrichments, which are most common in the uppermost mantle and are related to carbonate- and P 2O 5-rich derivatives of the initial melt. Reversal and gradual retreat of the percolation front during thermal relaxation to ambient geotherm ("retrograde" metasomatism) caused local migration and entrapment of small-volume residual fluids and precipitation of volatile-rich accessory minerals. A distinct metasomatic episode, which mainly produced "anhydrous" late-stage interstitial materials was concomitant with the alkali basaltic magmatism, which brought

  17. The 40Ar-39Ar dating of the metasomatites in the deep-fault zones of margin suture system of Siberian platform

    Savel'eva, V.B.; Travin, A.V.; Zyryanov, A.S.

    2003-01-01

    For clarifying the time sequence of metasomatites formation of diverse geochemical types in deep-fault zones of margin suture system of Siberian platform the 40 Ar- 39 Ar-isotope dating of their rock-forming minerals was performed. It was ascertained that formation of major metasomatic formations in the Baikal and Sayan branches of the margin suture system of Siberian platform was asynchronous, the time lag being in excess of 100 bl. years [ru

  18. The Chara-Sina dyke swarm in the structure of the Middle Paleozoic Vilyui rift system (Siberian Craton)

    Kiselev, A. I.; Konstantinov, K. M.; Yarmolyuk, V. V.; Ivanov, A. V.

    2016-11-01

    The formation of the Vilyui rift system in the eastern Siberian Craton was finished with breakdown of the continent and formation of its eastern margin. A characteristic feature of this rift system is the radial distribution of dyke swarms of basic rocks. This peculiarity allows us to relate it to the breaking processes above the mantle plume, the center of which was located in the region overlain in the modern structure by the foreland of the Verkhoyan folded-thrust belt. The Chara-Sina dyke swarm is the southern part of a large area of Middle Paleozoic basaltic magmatism in the eastern Siberian Craton. The OIB-like geochemical characteristics of dolerite allow us to suggest that the melting substrate for Middle Paleozoic basaltic magmatism was represented by a relatively homogeneous, mid-depleted mantle of the plume with geochemical parameters similar to those of OIB.

  19. The crust and mantle beneath the Siberian provinces: a preliminary model based on new receiver function analysis

    Soliman, Mohammad Youssof Ahmad; Artemieva, Irina; Thybo, Hans

    2012-01-01

    The new receiver function (RF) study complements the existing seismic data on the crustal and upper mantle structure at the margins of the Siberian craton and the West Siberian Basin. So far, RF studies of Siberia have been largely restricted to the Baikal rift zone (Gao et al., 2004; Liu and Gao......, 2006; Anan'in et al., 2009). However, available seismic data allow to apply the RF approach to other tectonic structures of the region. We calculate the RF using the LQT method (Vinnik, 1977; Kind et al. 1995) in the version by Yuan et al. (1997). This method involves rotating the earth...... the deconvolved signals using the appropriate moveout corrections which account for the dependence of Ps arrivals on P wave slowness. The results of RF analysis of the crustal and mantle structure are interpreted in terms of tectonic and geodynamic evolution of different provinces of Siberia that range from...

  20. Spin motion at and near orbital resonance in storage rings with Siberian snakes I. At orbital resonance

    Barber, D.P.; Vogt, M.

    2006-12-01

    Here, and in a sequel, we invoke the invariant spin field to provide an in-depth study of spin motion at and near low order orbital resonances in a simple model for the effects of vertical betatron motion in a storage ring with Siberian Snakes. This leads to a clear understanding, within the model, of the behaviour of the beam polarization at and near so-called snake resonances in proton storage rings. (orig.)

  1. Photoperiod-Induced Increases in Bone Mineral Apposition Rate in Siberian Hamsters and the Involvement of Seasonal Leptin Changes

    Marie Kokolski; Francis J. Ebling; James R. Henstock; Susan I. Anderson

    2017-01-01

    The adipokine leptin regulates energy balance, appetite, and reproductive maturation. Leptin also acts on bone growth and remodeling, but both osteogenic and anti-osteogenic effects have been reported depending on experimental conditions. Siberian hamsters (Phodopus sungorus) have natural variation in circulating leptin concentrations, where serum leptin is significantly decreased during the short day (SD)-induced winter state. In summer long day (LD) photoperiods, appetite and body adiposity...

  2. SIBERIAN POLICE BUREAUCRACY IN THE STATE APPARATUS OF ABSOLUTISM IN THE FIRST HALF OF THE 19TH CENTURY

    И А Коновалов

    2017-12-01

    Full Text Available Based on the pre-revolutionary legislation and archive materials, the article comprehen-sively considers the process of the formation of the Siberian police bureaucracy in the early 19thcentury. The objectives of the article are as follows: the reconstruction and comprehension of both positive and negative experienceaccumulated by the prerevolutionary regional govern-ment bodies, as well as of the peculiarities of the Siberian police bureaucracy; the explanation of the nature of the interrelations between the government and the population of the outskirts of the Russian Empire; the identifi cation of those aspects in the activities of local authorities, which for various reasons rarely come into the view of researchers. The author concludes that in the fi rst half of the 19thcenturythe State administration was not separated from police activi-ties, the administrative and police authorities in the region were de facto merged. A specifi c feature of the Siberian administration was the greater autonomy of the political machinery rather than in the country’s centre. It was conditioned by the remoteness from the centre and by the absence of nobilityassociations in the region.Due to this, the controlling,judicial and trustee functions,exercised by the nobilityin the centre,in Siberia were assigned to civil ser-vants. The mainconclusion is that the powers of the administrative and police authorities in the region had their own features and were much wider than in the central provinces of the Russian Empire.

  3. Stress state reconstruction and tectonic evolution of the northern slope of the Baikit anteclise, Siberian Craton, based on 3D seismic data

    Moskalenko, A. N.; Khudoley, A. K.; Khusnitdinov, R. R.

    2017-05-01

    In this work, we consider application of an original method for determining the indicators of the tectonic stress fields in the northern Baikit anteclise based on 3D seismic data for further reconstruction of the stress state parameters when analyzing structural maps of seismic horizons and corresponded faults. The stress state parameters are determined by the orientations of the main stress axes and shape of the stress ellipsoid. To calculate the stress state parameters from data on the spatial orientations of faults and slip vectors, we used the algorithms from quasiprimary stress computation methods and cataclastic analysis, implemented in the software products FaultKinWin and StressGeol, respectively. The results of this work show that kinematic characteristics of faults regularly change toward the top of succession and that the stress state parameters are characterized by different values of the Lode-Nadai coefficient. Faults are presented as strike-slip faults with normal or reverse component of displacement. Three stages of formation of the faults are revealed: (1) partial inversion of ancient normal faults, (2) the most intense stage with the predominance of thrust and strike-slip faults at north-northeast orientation of an axis of the main compression, and (3) strike-slip faults at the west-northwest orientation of an axis of the main compression. The second and third stages are pre-Vendian in age and correlate to tectonic events that took place during the evolution of the active southwestern margin of the Siberian Craton.

  4. Photoperiodic regulation of glycogen metabolism, glycolysis, and glutamine synthesis in tanycytes of the Siberian hamster suggests novel roles of tanycytes in hypothalamic function.

    Nilaweera, Kanishka; Herwig, Annika; Bolborea, Matei; Campbell, Gill; Mayer, Claus D; Morgan, Peter J; Ebling, Francis J P; Barrett, Perry

    2011-11-01

    The objective of this study is to investigate the impact of photoperiod on the temporal and spatial expression of genes involved in glucose metabolism in the brain of the seasonal mammal Phodopus sungorus (Siberian hamster). In situ hybridization was performed on brain sections obtained from male hamsters held in long photoperiod (high body weight and developed testes) or short photoperiod (reduced body weight with testicular regression). This analysis revealed upregulation in expression of genes involved in glycogen and glucose metabolism in short photoperiod and localized to the tanycyte layer of the third ventricle. On the basis of these data and a previously identified photoperiod-dependent increase in activity of neighboring hypothalamic neurons, we hypothesized that the observed expression changes may reflect alteration in either metabolic fuel or precursor neurotransmitter supply to surrounding neurons. Gene expression analysis was performed for genes involved in lactate and glutamate transport. This analysis showed that the gene for the lactate transporter MCT2 and glutamate transporter GLAST was decreased in the tanycyte layer in short photoperiod. Expression of mRNA for glutamine synthetase, the final enzyme in the synthesis of the neuronal neurotransmitter precursor, glutamine, was also decreased in short photoperiod. These data suggest a role for tanycytes in modulating glutamate concentrations and neurotransmitter supply in the hypothalamic environment. Copyright © 2011 Wiley-Liss, Inc.

  5. Polycyclic Aromatic Hydrocarbons In Aerosol and Snow Cover of Siberian Towns (east Siberia)

    Gorshkov, A.; Marinayte, I.

    Contamination of the atmosphere above Siberian towns has a few peculiarities: (i) level of pollution is presumably determined by discharges of large enterprises sur- rounded by company towns; (ii) long (up to 150 days) winter is characterized by the highest concentrations of pollutants within the near-ground atmospheric layer due to pronounced anti-cyclonic circulation of the atmosphere; (iii) polycyclic aromatic hydrocarbons (PAH) are specific minor components of the aerosols. Relatively high PAH concentrations in aerosol of Siberian towns are caused by the presence of ad- ditional intensive sources of PAH (besides those traditional: gas discharges of met- allurgy, heat-and-power engineering enterprises, and motor transport). These are the discharges of low power (produc- ing plant (50000 residents) - are presented in the report. Daily and seasonal dynamics of aerosol pollution and level of PAH accumulation in snow covers during 1996 U 2001 are estimated. The highest PAH concentrations (total concentrations of identi- fied compounds) are up to 300 ng/m3 in aerosol and up to 16 mg/m2 in snow cover. At day and night temperatures lowering up to -30 oe -40 01057;, the maximum of PAH concentration is observed in the daytime due to displacement of the tempera-ture in- version. When temperature increases, two SclassicalT maximums are observed during & cedil;the morning and the evening hours. It was shown that the effect of Scity air circula- & cedil;tionT caused by air masses transportation above a city from its center to out-skirts (within the near-ground air layer U to its center) does not contribute to efficient level- ing of PAH concentrations. The level of PAH accumulation in snow cover in different citySs sites and within one citySs region is ranging up to 10 times during a season. Calculated benz[a]pyren fluxes allow us to conclude that contamination of the atmo- sphere above Irkutsk (2.5 mkg/m2 per week) is comparable with that above large cities of Western

  6. East Siberian Sea, an Arctic region of very high biogeochemical activity

    L. G. Anderson

    2011-06-01

    Full Text Available Shelf seas are among the most active biogeochemical marine environments and the East Siberian Sea is a prime example. This sea is supplied by seawater from both the Atlantic and Pacific Oceans and has a substantial input of river runoff. All of these waters contribute chemical constituents, dissolved and particulate, but of different signatures. Sea ice formation during the winter season and melting in the summer has a major impact on physical as well as biogeochemical conditions. The internal circulation and water mass distribution is significantly influenced by the atmospheric pressure field. The western region is dominated by input of river runoff from the Laptev Sea and an extensive input of terrestrial organic matter. The microbial decay of this organic matter produces carbon dioxide (CO2 that oversaturates all waters from the surface to bottom relative to atmospheric level, even when primary production, inferred from low surface water nutrients, has occurred. The eastern surface waters were under-saturated with respect to CO2 illustrating the dominance of marine primary production. The drawdown of dissolved inorganic carbon equals a primary production of ~0.8 ± 2 mol C m−2, which when multiplied by half the area of the East Siberian Sea, ~500 000 km2, results in an annual primary production of 0.4 (± 1 × 1012 mol C or ~4 (± 10 × 1012 gC. Microbial decay occurs through much of the water column, but dominates at the sediment interface where the majority of organic matter ends up, thus more of the decay products are recycled to the bottom water. High nutrient concentrations and fugacity of CO2 and low oxygen and pH were observed in the bottom waters. Another signature of organic matter decomposition, methane (CH4, was observed in very high but variable concentrations. This is due to its seabed sources of glacial origin or modern production from

  7. Sources, degradation and transport of terrigenous organic carbon on the East Siberian Arctic Shelf Seas

    Tesi, Tommaso; Semiletov, Igor; Dudarev, Oleg; Gustafsson, Örjan

    2013-04-01

    Recent studies suggest that the present hydrological regime increase observed in the Arctic rivers is mainly the consequence of the changes in permafrost conditions as a result of climate warming. Given the enormous amount of carbon stored in coastal and terrestrial permafrost the potentially increased supply from this large carbon pool to the coastal Arctic Ocean, possibly associated with a translocated release to the atmosphere as CO2, is considered a plausible scenario in a warming climate. However, there is not sufficient information regarding the reactivity of terrigenous material once supplied to the Arctic Ocean. In this study, we address this critical issue by examining the organic composition of surface sediments collected over extensive scales on the East Siberian Arctic Shelf (ESAS) as part of the International Siberian Shelf Study (ISSS). The ESAS represents by far the largest shelf of the Arctic Ocean. Samples were collected from the inner- to the outer-shelf following the sediment transport pathway in a region between the Lena and the Kolyma rivers. The analytical approach includes the characterization of marine and land-derived carbon using a large number of molecular biomarkers obtained by alkaline CuO oxidation such as lignin-phenols, cutin-derived products, p-hydroxy benzenes, benzoic acids, fatty acids, and dicarboxylic acids. Our results indicated high concentrations of terrigenous material in shallow sediments and a marked decrease of terrestrial biomarkers with increasing distance from the coastline. In parallel, lignin-based degradation proxies suggested highly altered terrigenous carbon in mid- and outer-shelf sediments compared to coastal sediments. Furthermore, the ratio of cutin-derived products over lignin significantly increased along the sediment transport pathway. Considering that cutin is considered to be intrinsically more reactive compared to lignin, high values of this ratio off the coastal region were interpreted as selective

  8. DNA-Bank of the Siberian Group Chemical Enterprises workers and Seversk city residents

    Freidin, M. B.; Goncharova, I. A.; Karpov, A. B.; Takhauov, R. M.

    2004-01-01

    According to the mostr common definition a DNA-bank is a system of a genetic material storage. Applying to nuclear-chemical plant workers, DNA-bank creation is determined by the necessity to preserve a hereditary material of these people and their descendants for the further evaluation of consequences fo technogenic factors action on human genome using a contemporary conceptual and applied advances of genetics. In the frameworks of the study of technogenic factors indluence on human genome and genetic-caused disorders development the Seversk Biophysical Research Center is being created DNA-bank of Siberian Group of Chemical Enterprises workers exposed to radiation, their descendants, and ZATO Seversk and Tomsk city inhabitants. The DNA-bank will be a basis for all major research laboratory projects: analysis of molecular basis of individual radiosensitivity; analysis of technogenic factors role in congenital malformations and hereditary diseases development in nuclear-chemical plant workers offspring; elaboration of genotype-specific tes-systems of cancer prognosis and development of cardiovascular and other common disorders connected with the effect of technogenic factors. The DNA-bank creation is a technological issue aggravated by ethical problems. Whereas the DNA isolation is not a problem today, ethical complication id debated widely in the world. These questions strongly arise in a view of advances of Human Genome Project. Information consent on DNA usage is imperative today. Also questions on DNA property (who is its owner a doner or a banker) and of a confidentiality, which maintenance is a doubtable question in a case of multiple genetic testing, are not solved today. At present, the Genomic Medicine Laboratory disposes the DNA samples of more than 400 Sevesk and Tomsk inhabitants affected with breast and lung cancer. More than 800 blood samples of main manufacture of the Siberian Group of Chemical Enterprises workers are collected. About 1500 DNA samples

  9. Paleomagnetism of Early Paleozoic Rocks from the de Long Archipelago and Tectonics of the New Siberian Islands Terrane

    Metelkin, D. V.; Chernova, A. I.; Matushkin, N. Y.; Vernikovskiy, V. A.

    2017-12-01

    The De Long archipelago is located to the north of the Anjou archipelago as a part of a large group between the Laptev Sea and the East Siberian Sea - the New Siberian Islands and consists of Jeannette Island, Bennett Island and Henrietta Island. These islands have been shown to be part of a single continental terrane, whose tectonic history was independent of other continental masses at least since the Ordovician. Paleomagnetic and precise geological data for the De Long archipelago were absent until recently. Only in 2013 special international field trips to the De Long Islands could be organized and geological, isotope-geochronological and paleomagnetic studies were carried out.On Jeannette Island a volcanic-sedimentary sequence intruded by mafic dikes was described. The age of these dikes is more likely Early Ordovician, close to 480 Ma, as evidenced by the results of our 40Ar/39Ar and paleomagnetic investigations of the dolerites as well as the result from detrital zircons in the host rocks published before. On Bennett Island, there are widespread Cambrian-Ordovician mainly terrigenous rocks. Paleomagnetic results from these rocks characterize the paleogeographic position of the De Long archipelago at 465 Ma and perhaps at 530 Ma, although there is no evidence for the primary origin of magnetization for the latter. On Henrietta Island the Early Cambrian volcanic-sedimentary section was investigated. A paleomagnetic pole for 520 Ma was obtained and confirmed by new 40Ar/39Ar results. Adding to our previous paleomagnetic data for the Anjou archipelago the extended variant of the apparent polar wander path for the New Siberian Island terrane was created. The established paleolatitudes define its location in the equatorial and subtropical zone no higher than 40 degrees during the Early Paleozoic. Because there are no good confirmations for true polarity and related geographic hemisphere we present two possibilities for tectonic reconstruction. But both these

  10. The Socio-Political Crisis of the Siberian Region in the Post-February Period of the 1917 Revolution

    Mikhail I. Vtorushin

    2017-12-01

    Full Text Available The paper considers the problem of the Siberian region general crisis of the 1917 spring. The internal and external contradictions of the transformation process of socio-economic and political relations in Siberia are examined in terms of the post-February all- Russian revolutionary crisis development. The understanding of the socio-political Russian crisis in the spring of 1917, emerging after the February political coup, is essential in studying the revolutionary соnversion process of the early twentieth century Russian society, as this crisis has generally become the turning point in the country’s history and objectively led to the October political coup. The Russian revolutionary crisis constituents, its foreign and domestic manifestations require careful investigation in the issue formulation presented in the paper. The development specifics of the revolutionary crisis in the spring of 1917 in the trans-Uralian agricultural colony of the Russian Empire is of scientific interest, as well as the finding of its anti-crisis development scenarios in the paper presented period. The development of the nationwide crisis in Russia in the early twentieth century, due to the complex and contradictory processes of Russian society modernization in completing the industrial civilization and transition to the imperialist development stage, was complicated by the “Siberian historical issues” in the Siberian region. A set of these issues include the incompleteness of the regional peasantry land management, the contradictions between the old peasantry and Stolypin migrants, and also between the peasantry and the privileged regional Cossacks, the agricultural products export problems from Siberia to domestic and foreign markets, or marketing crisis, the contradictions between the regional and metropolis bourgeoisie, or the issue of the Siberians economic inequality, the local industry underdevelopment and the complete dependence of the local

  11. Paleo-eskimo mtDNA genome reveals matrilineal discontinuity in Greenland

    Gilbert, Marcus Thomas Pius; Kivisild, Toomas; Grønnow, Bjarne

    2008-01-01

    a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian......The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced...

  12. Multilevel landscape utilization of the Siberian flying squirrel: Scale effects on species habitat use.

    Remm, Jaanus; Hanski, Ilpo K; Tuominen, Sakari; Selonen, Vesa

    2017-10-01

    Animals use and select habitat at multiple hierarchical levels and at different spatial scales within each level. Still, there is little knowledge on the scale effects at different spatial levels of species occupancy patterns. The objective of this study was to examine nonlinear effects and optimal-scale landscape characteristics that affect occupancy of the Siberian flying squirrel, Pteromys volans , in South- and Mid-Finland. We used presence-absence data ( n  = 10,032 plots of 9 ha) and novel approach to separate the effects on site-, landscape-, and regional-level occupancy patterns. Our main results were: landscape variables predicted the placement of population patches at least twice as well as they predicted the occupancy of particular sites; the clear optimal value of preferred habitat cover for species landscape-level abundance is a surprisingly low value (10% within a 4 km buffer); landscape metrics exert different effects on species occupancy and abundance in high versus low population density regions of our study area. We conclude that knowledge of regional variation in landscape utilization will be essential for successful conservation of the species. The results also support the view that large-scale landscape variables have high predictive power in explaining species abundance. Our study demonstrates the complex response of species occurrence at different levels of population configuration on landscape structure. The study also highlights the need for data in large spatial scale to increase the precision of biodiversity mapping and prediction of future trends.

  13. Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis.

    Hwang, Hwan-Su; Lee, Hyoshin; Choi, Yong Eui

    2015-03-14

    Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant. In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes involved in the saponin biosynthetic pathway. The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.

  14. Poleward upgliding Siberian atmospheric rivers over sea ice heat up Arctic upper air.

    Komatsu, Kensuke K; Alexeev, Vladimir A; Repina, Irina A; Tachibana, Yoshihiro

    2018-02-13

    We carried out upper air measurements with radiosondes during the summer over the Arctic Ocean from an icebreaker moving poleward from an ice-free region, through the ice edge, and into a region of thick ice. Rapid warming of the Arctic is a significant environmental issue that occurs not only at the surface but also throughout the troposphere. In addition to the widely accepted mechanisms responsible for the increase of tropospheric warming during the summer over the Arctic, we showed a new potential contributing process to the increase, based on our direct observations and supporting numerical simulations and statistical analyses using a long-term reanalysis dataset. We refer to this new process as "Siberian Atmospheric Rivers (SARs)". Poleward upglides of SARs over cold air domes overlying sea ice provide the upper atmosphere with extra heat via condensation of water vapour. This heating drives increased buoyancy and further strengthens the ascent and heating of the mid-troposphere. This process requires the combination of SARs and sea ice as a land-ocean-atmosphere system, the implication being that large-scale heat and moisture transport from the lower latitudes can remotely amplify the warming of the Arctic troposphere in the summer.

  15. Climate-Induced Mortality of Siberian Pine and Fir in the Lake Baikal Watershed, Siberia

    Kharuk, Viacheslav I.; Im, Sergei T.; Petrova, IIya A.; Golyukov, Alexei S.; Ranson, Kenneth J.; Yagunov, Mikhail N.

    2016-01-01

    Siberian pine (Pinus sibirica) and fir (Abies sibirica) (so called "dark needle conifers", DNC) showed decreased radial growth increment within the Lake Baikal watershed since the 1980s with increasing mortality recorded since the year 2000. Tree ring width was strongly correlated with vapor pressure deficit, aridity and root zone moisture. Water stress from droughts made trees more susceptible to insect attacks causing mortality in about 10% of DNC stands within the Lake Baikal watershed. Within Siberia DNC mortality increased in the southern part of the DNC range. Biogeographically, tree mortality was located within the DNC - forest-steppes transition. Tree mortality was significantly correlated with drought and soil moisture anomalies. Within the interior of the DNC range mortality occurred within relief features with high water stress risk (i.e., steep convex south facing slopes with shallow well-drained soils). In general, DNC mortality in Siberia was induced by increased aridity and severe drought (inciting factors) in synergy with biotic attacks (contributing factor). In future climate scenarios with predicted increase in aridity DNC could be eliminated from the southern part of its current range and will be replaced by drought-resistant conifers and broadleaf species (e.g., Larix sibirica, Pinus silvestris, and Betula pubescence).

  16. Prospective targets of geological exploration in the Siberian platform and criteria of their feasibility

    D.V. Milyaev

    2017-06-01

    Full Text Available The relevance of the study is due to the reducing number of prospective blocks remaining unlicensed in Eastern Siberia and the need for feasibility study of the remaining potentially attractive blocks. The aim of the study is evaluation of the resource potential and allocation of new prospective license blocks in Eastern Siberia based on geological and economic criteria. The methods and instruments used in the study. To perform the economic analysis of resources and to assess the efficiency and risks of subsoil exploration and development, the authors used the results of in-house regional geological and geophysical modelling and economic research. A feasibility study of each potential pool was conducted on the author’s automated complex GeoProfi. The authors used probabilistic analysis and the cash flow discounting method to draw up an expert forecast. The results of the study. The study covers the present state and development prospects of oil and gas fields in the Siberian Platform within the Krasnoyarsk Territory, the Irkutsk Region, and the Sakha (Yakutia Republic. The top priority petroleum zones were analysed. A feasibility study of selected areas was conducted. The income density and feasible recoverable reserves density were mapped. The critical parameters that indicate unprofitable targets were calculated. The most feasible subsoil blocks were determined based on the correlation of economic and probability parameters.

  17. PROJECT OF THE TRANS-SIBERIAN RAILWAY RECONSTRUCTION AS AN OBJECT OF SOCIAL EFFICIENCY EVALUATION

    Kibalov E. B.

    2015-06-01

    Full Text Available We consider the problem of social efficiency evaluation concerning the project of the Trans-Siberian Railway reconstruction. This project is to be realized in the situation of strategic (fundamental uncertainty. Existing tools are not sufficient for solving this problem (because of qualitatively different nature of the project as compared with those abroad, much higher degree of uncertainty, and the lack of estimates for a number of necessary norms. Our study aims at development of an approach that would be adequate to the problem under consideration. We developed a two-level model for investment decision-making for appraisal and selection of a variant of the large-scale project. The upper level of this model bases on the macroeconomic approach (with the use of a specialized version of the Inter-Sector Inter-Region Optimization Model; the lower level bases on the microeconomic approach. As opposed to the foreign practice, the efficiency evaluation and selection of a variant of the transport project is top-down. End-to-end taking uncertainty into account is implemented. A tool for this is the scenario approach on the upper level, and the fuzzy set theory at the lower one.

  18. Remote sensing of photosynthetic-light-use efficiency of a Siberian boreal forest

    Nichol, C.J.; Grace, J.; Shibistova, O.; Matsubara, S.

    2002-01-01

    The relationship between a physiological index called the photochemical reflectance index (PRI) and photosynthetic light-use-efficiency (LUE) of a Siberian boreal forest during the winter-spring transition, or green-up period, was investigated in 2000. During this time the photosynthetic apparatus was considered under stress as a result of extremes of temperature (from -20 to 35 deg C) coupled with a high radiation load. Reflectance measurements of four stands were made from a helicopter-mounted spectro radiometer and PRI was calculated from these data. Eddy covariance towers were operating at the four stands and offered a means to calculate LUE. A significant linear relationship was apparent between PRI, calculated from the helicopter spectral data, and LUE, calculated from the eddy covariance data, for the four sites sampled. Reflectance measurements were also made of a Scots pine stand from the eddy covariance tower. Needles were also sampled during the time of spectral data acquisition for xanthophyll pigment determination. Strong linear relationships were observed among PRI, the epoxidation state of the xanthophyll cycle (EPS) and LUE over the green-up period and the diurnal cycle at the canopy scale

  19. Monitoring of Siberian biomass burning smoke from AHI on board geostationary satellite Himawari-8

    Sano, I.; Mukai, S.; Yoshida, A.; Nakata, M.; Minoura, H.; Holben, B. N.

    2016-12-01

    High frequency aerosol measurements are demanded for evaluation of the model simulations, monitoring the atmospheric qualities such as Particulate Matter (PM2.5), and so on. Geostationary satellite provides us with the high frequency information of the atmosphere. Japanese Meteorological Agency (JMA) launched the Himawari-8 geostationary satellite in 2014 and has prepared Himawari-9 for launching in 2016. Both satellites carry new generation imagers named Advanced Himawari Imager (AHI). They have 16 multi-channels from short visible to thermal infrared wavelengths with 1 km IFOV for visible and 2 km for infrared. Each observation is done within 10 minutes for the Earth full disk. Then high frequency Earth observations are realized. AHI has frequently observed biomass burning plume around East Siberia and its transportation according to weather system. This work retrieves aerosol properties due to the Siberian smoke plume and its movements based on the measurements with AHI. The results are compared with ground based measurements which have newly deployed at an AERONET/Niigata site in Japan. It is shown here that continuous measurements of aerosols from geostationary satellite combination with the polar orbiting satellite provide us with much detail information of aerosol.

  20. Identification of a new mineralized tissue in the notochord of reared Siberian sturgeon (Acipenser baerii).

    Leprévost, Amandine; Azaïs, Thierry; Trichet, Michael; Sire, Jean-Yves

    2017-11-01

    In a study aiming to improve knowledge on the mineralization of the axial skeleton in reared Siberian sturgeon (Acipenser baerii Brandt, 1869), we discovered a new mineralized tissue within the notochord. To our knowledge, such a structure has never been reported in any vertebrate species with the exception of the pathological mineralization of the notochord remains in degenerative intervertebral disks of mammals. Here, we describe this enigmatic tissue using X-ray microtomography, histological analyses and solid state NMR-spectroscopy. We also performed a 1-year monitoring of the mineral content (MC) of the notochord in relation with seasonal variations of temperature. In all specimens studied from 2-year-old juveniles onwards, this mineralized structure was found within a particular region of the notochord called funiculus. This feature first appears in the abdominal region then extends posteriorly with ageing, while the notochord MC also increases. The mineral phase is mainly composed of amorphous calcium phosphate, a small amount of which changes into hydroxyapatite with ageing. The putative role of this structure is discussed as either a store of minerals available for the phosphocalcic metabolism, or a mechanical support in a species with a poorly mineralized axial skeleton. A pathological feature putatively related to rearing conditions is also discussed. © 2017 Wiley Periodicals, Inc.

  1. Photoperiod and aggression induce changes in ventral gland compounds exclusively in male Siberian hamsters.

    Rendon, Nikki M; Soini, Helena A; Scotti, Melissa-Ann L; Weigel, Ellen R; Novotny, Milos V; Demas, Gregory E

    2016-05-01

    Chemical communication is a critical component of social behavior as it facilitates social encounters, allows for evaluation of the social partner, defines territories and resources, and advertises information such as sex and physiological state of an animal. Odors provide a key source of information about the social environment to rodents; however, studies identifying chemical compounds have thus far focused primarily on few species, particularly the house mouse. Moreover, considerably less attention has been focused on how environmental factors, reproductive phenotype, and behavioral context alter these compounds outside of reproduction. We examined the effects of photoperiod, sex, and social context on chemical communication in the seasonally breeding Siberian hamster. We sampled ventral gland secretions in both male and female hamsters before and after an aggressive encounter and identified changes in a range of volatile compounds. Next, we investigated how photoperiod, reproductive phenotype, and aggression altered ventral gland volatile compound composition across the sexes. Males exhibited a more diverse chemical composition, more sex-specific volatiles, and showed higher levels of excretion compared to females. Individual volatiles were also differentially excreted across photoperiod and reproductive phenotype, as well as differentially altered in response to an aggressive encounter. Female volatile compound composition, in contrast, did not differ across photoperiods or in response to aggression. Collectively, these data contribute to a greater understanding of context-dependent changes in chemical communication in a seasonally breeding rodent. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Effects of Burn Severity and Environmental Conditions on Post-Fire Regeneration in Siberian Larch Forest

    Thuan Chu

    2017-03-01

    Full Text Available Post-fire forest regeneration is strongly influenced by abiotic and biotic heterogeneity in the pre- and post-fire environments, including fire regimes, species characteristics, landforms, hydrology, regional climate, and soil properties. Assessing these drivers is key to understanding the long-term effects of fire disturbances on forest succession. We evaluated multiple factors influencing patterns of variability in a post-fire boreal Larch (Larix sibirica forest in Siberia. A time-series of remote sensing images was analyzed to estimate post-fire recovery as a response variable across the burned area in 1996. Our results suggested that burn severity and water content were primary controllers of both Larch forest recruitment and green vegetation cover as defined by the forest recovery index (FRI and the fractional vegetation cover (FVC, respectively. We found a high rate of Larch forest recruitment in sites of moderate burn severity, while a more severe burn was the preferable condition for quick occupation by vegetation that included early seral communities of shrubs, grasses, conifers and broadleaf trees. Sites close to water and that received higher solar energy during the summer months showed a higher rate of both recovery types, defined by the FRI and FVC, dependent on burn severity. In addition to these factors, topographic variables and pre-fire condition were important predictors of post-fire forest patterns. These results have direct implications for the post-fire forest management in the Siberian boreal Larch region.

  3. West Siberian basin hydrogeology - regional framework for contaminant migration from injected wastes

    Foley, M.G.

    1994-05-01

    Nuclear fuel cycle activities of the former Soviet Union (FSU) have resulted in massive contamination of the environment in western Siberia. We are developing three-dimensional numerical models of the hydrogeology and potential contaminant migration in the West Siberian Basin. Our long-term goal at Pacific Northwest Laboratory is to help determine future environmental and human impacts given the releases that have occurred to date and the current waste management practices. In FY 1993, our objectives were to (1) refine and implement the hydrogeologic conceptual models of the regional hydrogeology of western Siberia developed in FY 1992 and develop the detailed, spatially registered digital geologic and hydrologic databases to test them, (2) calibrate the computer implementation of the conceptual models developed in FY 1992, and (3) develop general geologic and hydrologic information and preliminary hydrogeologic conceptual models relevant to the more detailed models of contaminated site hydrogeology. Calibration studies of the regional hydrogeologic computer model suggest that most precipitation entering the ground-water system moves in the near-surface part of the system and discharges to surface waters relatively near its point of infiltration. This means that wastes discharged to the surface and near-surface may not be isolated as well as previously thought, since the wastes may be carried to the surface by gradually rising ground waters

  4. Chronic exposure to dim light at night suppresses immune responses in Siberian hamsters.

    Bedrosian, Tracy A; Fonken, Laura K; Walton, James C; Nelson, Randy J

    2011-06-23

    Species have been adapted to specific niches optimizing survival and reproduction; however, urbanization by humans has dramatically altered natural habitats. Artificial light at night (LAN), termed 'light pollution', is an often overlooked, yet increasing disruptor of habitats, which perturbs physiological processes that rely on precise light information. For example, LAN alters the timing of reproduction and activity in some species, which decreases the odds of successful breeding and increases the threat of predation for these individuals, leading to reduced fitness. LAN also suppresses immune function, an important proxy for survival. To investigate the impact of LAN in a species naive to light pollution in its native habitat, immune function was examined in Siberian hamsters derived from wild-caught stock. After four weeks exposure to dim LAN, immune responses to three different challenges were assessed: (i) delayed-type hypersensitivity (DTH), (ii) lipopolysaccharide-induced fever, and (iii) bactericide activity of blood. LAN suppressed DTH response and reduced bactericide activity of blood after lipopolysaccharide treatment, in addition to altering daily patterns of locomotor activity, suggesting that human encroachment on habitats via night-time lighting may inadvertently compromise immune function and ultimately fitness.

  5. Counselor Identity: Conformity or Distinction?

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  6. MODEL RECONSTRUCTION OF THE VEGETATION COVER OF THE SOUTH OF THE WEST SIBERIAN PLAIN FROM THE LATE PALEOLITHIC PERIOD UNTIL THE LATE XIX CENTURY

    М. А. Kharitonenkov

    2016-06-01

    Full Text Available Model reconstruction of vegetation cover of the south of the West Siberian Plain from the late Pleistocene to the modern era has been carried out on the basis of the associated chronological analysis of paleontological, archaeological and paleoclimate data. We have determined the starting point of active vegetation transformation in the south of the West Siberian Plain as a result of tradition-bound exploitation of natural resources. Periods of maximum anthropogenic load – peak and relative recession – on vegetation cover, acting as a further determinant factor, have been determined in this study for the first time. Comprehensive analysis and new understanding of palynological, paleozoological, archaeological and paleoclimate data in terms of theoretical synecology confirmed the notions on the determinant role of the anthropogenic factor in the transformation of the Pleistocene forest-meadow-steppe vegetation into contemporary communities of the southern taiga, the subtaiga and the forest-steppe of the West Siberian Plain.

  7. The contribution of the representatives of the Siberian (Tomsk mining and geological school to the developmet of mineral raw material base in Russia and Abroad

    П. С. Чубик

    2017-12-01

    Full Text Available This paper is devoted to the maturation and development of Siberian (Tomsk mining and geological school - one of the leading schools in Russia, which was created in the first third of the 20th century in Tomsk Technological Institute by V.A.Obruchev and M.A.Usov known to be outstanding Russian and Soviet geoscientists and members of the Russian Academy of Science. The article touches upon the participation of representatives of Siberian (Tomsk mining and geological school to the exploration and development of mineral and raw material base of Siberia, Russia’s Far East, Central Asia. The information about the most important geological discoveries made by nurslings of Siberian (Tomsk mining and geological school is provided.

  8. The Siberian Students in Research, Cultural and Social Life of the Region in the Late XIX – Early XX centuries

    Oksana V. Ustinova

    2017-03-01

    Full Text Available The article is devoted to the study of the role and place of students in the Siberian scientific-research and cultural-educational life of the region. It is shown that high moral ideals and a desire to help people in need be useful to its edge and to society in general – describe the ideas, common in the student's environment at the turn of XIX – XX centuries. Based on the analysis of archival materials and scientific literature, it was found that the students showed during this period, an increased desire to participate in social and cultural life of Siberia and the whole country. However, this participation in different ways manifested in the minds and actions of young people. Some students, actively engage in the cultural life of the region, entered in the companies involved in charity work, academic research, literary and theatrical art, medicine, advanced study of philosophy, technical processes, etc. At universities created various thematic interest groups, on a territorial basis – numerous fraternities, a nobility of purpose in the form of moral and material support of their members. However, some Siberian students in their own way understood his own mission in social processes, including under the form of participation in legal societies, clubs or fraternities in the activities of political and campaign focus, in the meetings discussing ideas about the possibilities of revolution, as expected, from their point of view, progress and prosperity in case of their implementation. Also in this period, there are illegal organizations that engage some students of Siberian universities. The activities of such organizations is highly political in nature.

  9. Widespread Expansion of Boreal Shrublands in the Siberian Low Arctic Is Linked to Cryogenic Disturbance and Geomorphology

    Frost, G. V.; Epstein, H. E.; Walker, D. A.

    2012-12-01

    Declassified imagery from the KH-4B "Corona" and KH-7 "Gambit" Cold War satellite surveillance systems (1963-1972) are a unique, high-resolution dataset that establishes a baseline for landcover-change studies in the Russian Arctic spanning 6 decades. We co-registered Corona/Gambit and modern high-resolution imagery for seven ~65 km2 Low Arctic sites in northwest Siberia and Chukotka and quantified changes in the extent of tall shrublands dominated by Siberian alder (Alnus fruticosa) using a point-intercept sampling approach. We made ground observations at two sites to identify important geomorphic processes and physiographic units associated with shrub expansion. Alder shrubland cover increased at all sites; relative to the 1960s extent, shrubland extent increased by 5-31% at the northwest Siberian sites and by 9% at both Chukotkan sites,. In northwest Siberia, alder expansion was closely linked to cryogenic disturbances related to patterned-ground and active-layer detachments. At the Chukotkan sites, most alder expansion occurred on hillslope colluvium and floodplains; we also observed modest increases in Siberian dwarf pine (Pinus pumila). The close correspondence between expanding shrub patches and disturbance processes indicates that sparsely-vegetated, mineral-rich seedbeds strongly facilitate alder recruitment, and that the spatio-temporal attributes of disturbance mechanisms are a key determinant of landscape susceptibility to shrub expansion. Shrub expansion, in turn, initiates a cascade of effects on permafrost thermal regime and disturbance, promoting the accumulation of biomass and potentially buffering permafrost from climate warming.; Recently-established alder shrubs growing on non-sorted circles in patterned ground near Obskaya, northwest Siberia.

  10. Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations.

    Hsieh, PingHsun; Hallmark, Brian; Watkins, Joseph; Karafet, Tatiana M; Osipova, Ludmila P; Gutenkunst, Ryan N; Hammer, Michael F

    2017-11-01

    Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that humans first occupied Siberia at least 45,000 years ago; yet our understanding of the demographic history of modern indigenous Siberians remains incomplete. In this study, we use whole-exome sequencing data from the Nganasans and Yakuts to infer the evolutionary history of these two indigenous Siberian populations. Recognizing the complexity of the adaptive process, we designed a model-based test to systematically search for signatures of polygenic selection. Our approach accounts for stochasticity in the demographic process and the hitchhiking effect of classic selective sweeps, as well as potential biases resulting from recombination rate and mutation rate heterogeneity. Our demographic inference shows that the Nganasans and Yakuts diverged ∼12,000-13,000 years ago from East-Asian ancestors in a process involving continuous gene flow. Our polygenic selection scan identifies seven candidate gene sets with Siberian-specific signals. Three of these gene sets are related to diet, especially to fat metabolism, consistent with the hypothesis of adaptation to a fat-rich animal diet. Additional testing rejects the effect of hitchhiking and favors a model in which selection yields small allele frequency changes at multiple unlinked genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Hypothalamic ventricular ependymal thyroid hormone deiodinases are an important element of circannual timing in the Siberian hamster (Phodopus sungorus.

    Annika Herwig

    Full Text Available Exposure to short days (SD induces profound changes in the physiology and behaviour of Siberian hamsters, including gonadal regression and up to 30% loss in body weight. In a continuous SD environment after approximately 20 weeks, Siberian hamsters spontaneously revert to a long day (LD phenotype, a phenomenon referred to as the photorefractory response. Previously we have identified a number of genes that are regulated by short photoperiod in the neuropil and ventricular ependymal (VE cells of the hypothalamus, although their importance and contribution to photoperiod induced physiology is unclear. In this refractory model we hypothesised that the return to LD physiology involves reversal of SD expression levels of key hypothalamic genes to their LD values and thereby implicate genes required for LD physiology. Male Siberian hamsters were kept in either LD or SD for up to 39 weeks during which time SD hamster body weight decreased before increasing, after more than 20 weeks, back to LD values. Brain tissue was collected between 14 and 39 weeks for in situ hybridization to determine hypothalamic gene expression. In VE cells lining the third ventricle, expression of nestin, vimentin, Crbp1 and Gpr50 were down-regulated at 18 weeks in SD photoperiod, but expression was not restored to the LD level in photorefractory hamsters. Dio2, Mct8 and Tsh-r expression were altered by SD photoperiod and were fully restored, or even exceeded values found in LD hamsters in the refractory state. In hypothalamic nuclei, expression of Srif and Mc3r mRNAs was altered at 18 weeks in SD, but were similar to LD expression values in photorefractory hamsters. We conclude that in refractory hamsters not all VE cell functions are required to establish LD physiology. However, thyroid hormone signalling from ependymal cells and reversal of neuronal gene expression appear to be essential for the SD refractory response.

  12. Hypothalamic over-expression of VGF in the Siberian hamster increases energy expenditure and reduces body weight gain.

    Lewis, Jo E; Brameld, John M; Hill, Phil; Cocco, Cristina; Noli, Barbara; Ferri, Gian-Luca; Barrett, Perry; Ebling, Francis J P; Jethwa, Preeti H

    2017-01-01

    VGF (non-acronymic) was first highlighted to have a role in energy homeostasis through experiments involving dietary manipulation in mice. Fasting increased VGF mRNA in the Arc and levels were subsequently reduced upon refeeding. This anabolic role for VGF was supported by observations in a VGF null (VGF-/-) mouse and in the diet-induced and gold-thioglucose obese mice. However, this anabolic role for VGF has not been supported by a number of subsequent studies investigating the physiological effects of VGF-derived peptides. Intracerebroventricular (ICV) infusion of TLQP-21 increased resting energy expenditure and rectal temperature in mice and protected against diet-induced obesity. Similarly, ICV infusion of TLQP-21 into Siberian hamsters significantly reduced body weight, but this was due to a decrease in food intake, with no effect on energy expenditure. Subsequently NERP-2 was shown to increase food intake in rats via the orexin system, suggesting opposing roles for these VGF-derived peptides. Thus to further elucidate the role of hypothalamic VGF in the regulation of energy homeostasis we utilised a recombinant adeno-associated viral vector to over-express VGF in adult male Siberian hamsters, thus avoiding any developmental effects or associated functional compensation. Initially, hypothalamic over-expression of VGF in adult Siberian hamsters produced no effect on metabolic parameters, but by 12 weeks post-infusion hamsters had increased oxygen consumption and a tendency to increased carbon dioxide production; this attenuated body weight gain, reduced interscapular white adipose tissue and resulted in a compensatory increase in food intake. These observed changes in energy expenditure and food intake were associated with an increase in the hypothalamic contents of the VGF-derived peptides AQEE, TLQP and NERP-2. The complex phenotype of the VGF-/- mice is a likely consequence of global ablation of the gene and its derived peptides during development, as well

  13. Summary of three dimensional pump testing of a fractured rock aquifer in the western Siberian Basin

    Nichols, R.L.; Looney, B.B.; Eddy-Dilek, C.A.; Drozhko, E.G.; Glalolenko, Y.V.; Mokrov, Y.G.; Ivanov, I.A.; Glagolev, A.V.; Vasil'kova, N.A.

    1996-01-01

    A group of scientists from the Savannah River Technology Center and Russia successfully completed a 17 day field investigation of a fractured rock aquifer at the MAYAK PA nuclear production facility in Russia. The test site is located in the western Siberian Basin near the floodplain of the Mishelyak river. The fractured rock aquifer is composed of orphyrites, tuff, tuffbreccia and lava and is overlain by 0.5--12 meters of elluvial and alluvial sediments. A network of 3 uncased wells (176, 1/96, and 2/96) was used to conduct the tests. Wells 176 and 2/96 were used as observation wells and the centrally located well 1/96 was used as the pumping well. Six packers were installed and inflated in each of the observation wells at a depth of up to 85 meters. The use of 6 packers in each well resulted in isolating 7 zones for monitoring. The packers were inflated to different pressures to accommodate the increasing hydrostatic pressure. A straddle packer assembly was installed in the pumping well to allow testing of each of the individual zones isolated in the observation wells. A constant rate pumping test was run on each of the 7 zones. The results of the pumping tests are included in Appendix A. The test provided new information about the nature of the fractured rock aquifers in the vicinity of the Mishelyak river and will be key information in understanding the behavior of contaminants originating from process wastes discharged to Lake Karachi. Results from the tests will be analyzed to determine the hydraulic properties of different zones within the fractured rock aquifer and to determine the most cost effective clean-up approach for the site

  14. Photoperiod history differentially impacts reproduction and immune function in adult Siberian hamsters.

    Prendergast, Brian J; Pyter, Leah M

    2009-12-01

    Seasonal changes in numerous aspects of mammalian immune function arise as a result of the annual variation in environmental day length (photoperiod), but it is not known if absolute photoperiod or relative change in photoperiod drives these changes. This experiment tested the hypothesis that an individual's history of exposure to day length determines immune responses to ambiguous, intermediate-duration day lengths. Immunological (blood leukocytes, delayed-type hypersensitivity reactions [DTH]), reproductive, and adrenocortical responses were assessed in adult Siberian hamsters (Phodopus sungorus) that had been raised initially in categorically long (15-h light/day; 15L) or short (9L) photoperiods and were subsequently transferred to 1 of 7 cardinal experimental photoperiods between 9L and 15L, inclusive. Initial photoperiod history interacted with contemporary experimental photoperiods to determine reproductive responses: 11L, 12L, and 13L caused gonadal regression in hamsters previously exposed to 15L, but elicited growth in hamsters previously in 9L. In hamsters with a 15L photoperiod history, photoperiods history, DTH responses were largely unaffected by increases in day length. Enhancement and suppression of blood leukocyte concentrations occurred at 13L in hamsters with photoperiod histories of 15L and 9L, respectively; however, prior exposure to 9L imparted marked hysteresis effects, which suppressed baseline leukocyte concentrations. Cortisol concentrations were only enhanced in 15L hamsters transferred to 9L and, in common with DTH, were unaffected by photoperiod treatments in hamsters with a 9L photoperiod history. Photoperiod history acquired in adulthood impacts immune responses to photoperiod, but manifests in a markedly dissimilar fashion as compared to the reproductive system. Prior photoperiod exposure has an enduring impact on the ability of the immune system to respond to subsequent changes in day length.

  15. West Siberian Basin hydrogeology: Site characterization of Mayak, Tomsk-7, and Krasnoyarsk-26

    Hoover, K.A.; Foley, M.G.; Allen, E.A.; Alexander, L.J.; McKinley, M.I.

    1997-01-01

    The former Soviet Union has extensive defense-related nuclear production facilities that have released large amounts of hazardous and radioactive waste materials into the air, surface water, and ground water in areas surrounding the production sites. The key sites of concern are Mayak, Tomsk-7, and Krasnoyarsk-26, all located within the West siberian Basin. The Pacific Northwest National Laboratory (PNNL), in cooperation with the Russian Ministry of Atomic Energy (Minatom), has been conducted contaminant-migration studies of Mayak, Tomsk-7, and Krasnoyarsk-26 in Western Siberia since 1993. The intent of this program is to maximize use of US and Russian site characterization, contaminant transport modeling, and remediation technology for the benefit of DOE and Minatom site-cleanup activities. Site characterization activities conducted during FY 1996 comprised evaluating the existing database, developing methods for synthesizing missing data, and designing an effective means of data and technology transfer. Comparison of the database, most of the contents of which have been acquired remotely with contaminant transport modeling data requirements allowed the authors to evaluate the utility of data acquired remotely for modeling purposes, and to identify gaps in the characterization of Russian waste-disposal sites. Identifying these gaps led to the second activity, which was to develop methods for synthesizing missing data from an evaluation of existing data. The authors tested these methods by evaluating geologic fracturing at the Mayak site. The third activity was the development of an effective procedure for data and technology transfer. The goal was to provide the site characterization database to Russian modelers in such a way that the data were easily transported, viewed, and manipulated for use in their models. This report summarizes the results of the three site characterization activities performed during FY 1996

  16. Archaeological Monuments of the Siberian Khanates: Search of the Markers of the Statehood.

    S.F. Tataurov

    2017-06-01

    Full Text Available Research objectives: To identify several sets of archaeological materials, which allow to unite all the Turkic-Tatar population of the forest-steppe zone of Western Siberia not only on the basis of socio-economic relations, but also on the principles of the existence of state entities. Research materials: Archaeological material (ceramics, weapons and funeral rite of warriors, ring-seals and attributes of supreme authority – helmets and tamgas. Results and novelty of the research: At present, the Turkic-Tatar state formations remain one of the most poorly studied issues in the medieval history of Western Siberia. An unformed base of archaeological sources could be added to a small amount of written documents. As a result, academic community is not able to make a full description of specific khanates – of their boundaries, administrative division and management, the level of development of state institutions, etc. Moreover, we do not have a chronological scale of cultural layers of any archaeological complex of this time including the capitals of khanates – Chimgi-Tura and Isker. Ordinary settlements and cemeteries remain with indefinite characteristics (cultural phenomena, which could allow to combine all these complexes into one whole, to become markers of the Siberian statehood. The author proposes to identify several sets of archaeological materials, which allow to unite all the Turkic-Tatar population of the forest-steppe zone of Western Siberia not only on the basis of socio-economic relations, but also on the principles of the existence of state entities. The author presents as these features ceramics, weapons and funeral rite of warriors, ring-seals and attributes of supreme authority – helmets and tamgas. It is possible that in the course of research this range of sources can be increased. Therefore, this work serves as an impulse for the development of scientific research in this direction.

  17. Aboveground Biomass Monitoring over Siberian Boreal Forest Using Radar Remote Sensing Data

    Stelmaszczuk-Gorska, M. A.; Thiel, C. J.; Schmullius, C.

    2014-12-01

    Aboveground biomass (AGB) plays an essential role in ecosystem research, global cycles, and is of vital importance in climate studies. AGB accumulated in the forests is of special monitoring interest as it contains the most of biomass comparing with other land biomes. The largest of the land biomes is boreal forest, which has a substantial carbon accumulation capability; carbon stock estimated to be 272 +/-23 Pg C (32%) [1]. Russian's forests are of particular concern, due to the largest source of uncertainty in global carbon stock calculations [1], and old inventory data that have not been updated in the last 25 years [2]. In this research new empirical models for AGB estimation are proposed. Using radar L-band data for AGB retrieval and optical data for an update of in situ data the processing scheme was developed. The approach was trained and validated in the Asian part of the boreal forest, in southern Russian Central Siberia; two Siberian Federal Districts: Krasnoyarsk Kray and Irkutsk Oblast. Together the training and testing forest territories cover an area of approximately 3,500 km2. ALOS PALSAR L-band single (HH - horizontal transmitted and received) and dual (HH and HV - horizontal transmitted, horizontal and vertical received) polarizations in Single Look Complex format (SLC) were used to calculate backscattering coefficient in gamma nought and coherence. In total more than 150 images acquired between 2006 and 2011 were available. The data were obtained through the ALOS Kyoto and Carbon Initiative Project (K&C). The data were used to calibrate a randomForest algorithm. Additionally, a simple linear and multiple-regression approach was used. The uncertainty of the AGB estimation at pixel and stand level were calculated approximately as 35% by validation against an independent dataset. The previous studies employing ALOS PALSAR data over boreal forests reported uncertainty of 39.4% using randomForest approach [2] or 42.8% using semi-empirical approach [3].

  18. Regional and landscape-scale variability of Landsat-observed vegetation dynamics in northwest Siberian tundra

    Frost, Gerald V; Epstein, Howard E; Walker, Donald A

    2014-01-01

    Widespread increases in Arctic tundra productivity have been documented for decades using coarse-scale satellite observations, but finer-scale observations indicate that changes have been very uneven, with a high degree of landscape- and regional-scale heterogeneity. Here we analyze time-series of the Normalized Difference Vegetation Index (NDVI) observed by Landsat (1984–2012), to assess landscape- and regional-scale variability of tundra vegetation dynamics in the northwest Siberian Low Arctic, a little-studied region with varied soils, landscape histories, and permafrost attributes. We also estimate spatio-temporal rates of land-cover change associated with expansion of tall alder (Alnus) shrublands, by integrating Landsat time-series with very-high-resolution imagery dating to the mid-1960s. We compiled Landsat time-series for eleven widely-distributed landscapes, and performed linear regression of NDVI values on a per-pixel basis. We found positive net NDVI trends (‘greening’) in nine of eleven landscapes. Net greening occurred in alder shrublands in all landscapes, and strong greening tended to correspond to shrublands that developed since the 1960s. Much of the spatial variability of greening within landscapes was linked to landscape physiography and permafrost attributes, while between-landscape variability largely corresponded to differences in surficial geology. We conclude that continued increases in tundra productivity in the region are likely in upland tundra landscapes with fine-textured, cryoturbated soils; these areas currently tend to support discontinuous vegetation cover, but are highly susceptible to rapid increases in vegetation cover, as well as land-cover changes associated with the development of tall shrublands. (paper)

  19. Light at night alters daily patterns of cortisol and clock proteins in female Siberian hamsters.

    Bedrosian, T A; Galan, A; Vaughn, C A; Weil, Z M; Nelson, R J

    2013-06-01

    Humans and other organisms have adapted to a 24-h solar cycle in response to life on Earth. The rotation of the planet on its axis and its revolution around the sun cause predictable daily and seasonal patterns in day length. To successfully anticipate and adapt to these patterns in the environment, a variety of biological processes oscillate with a daily rhythm of approximately 24 h in length. These rhythms arise from hierarchally-coupled cellular clocks generated by positive and negative transcription factors of core circadian clock gene expression. From these endogenous cellular clocks, overt rhythms in activity and patterns in hormone secretion and other homeostatic processes emerge. These circadian rhythms in physiology and behaviour can be organised by a variety of cues, although they are most potently entrained by light. In recent history, there has been a major change from naturally-occurring light cycles set by the sun, to artificial and sometimes erratic light cycles determined by the use of electric lighting. Virtually every individual living in an industrialised country experiences light at night (LAN) but, despite its prevalence, the biological effects of such unnatural lighting have not been fully considered. Using female Siberian hamsters (Phodopus sungorus), we investigated the effects of chronic nightly exposure to dim light on daily rhythms in locomotor activity, serum cortisol concentrations and brain expression of circadian clock proteins (i.e. PER1, PER2, BMAL1). Although locomotor activity remained entrained to the light cycle, the diurnal fluctuation of cortisol concentrations was blunted and the expression patterns of clock proteins in the suprachiasmatic nucleus and hippocampus were altered. These results demonstrate that chronic exposure to dim LAN can dramatically affect fundamental cellular function and emergent physiology. © 2013 British Society for Neuroendocrinology.

  20. Thermal Properties of West Siberian Sediments in Application to Basin and Petroleum Systems Modeling

    Romushkevich, Raisa; Popov, Evgeny; Popov, Yury; Chekhonin, Evgeny; Myasnikov, Artem; Kazak, Andrey; Belenkaya, Irina; Zagranovskaya, Dzhuliya

    2016-04-01

    Quality of heat flow and rock thermal property data is the crucial question in basin and petroleum system modeling. A number of significant deviations in thermal conductivity values were observed during our integral geothermal study of West Siberian platform reporting that the corrections should be carried out in basin models. The experimental data including thermal anisotropy and heterogeneity measurements were obtained along of more than 15 000 core samples and about 4 500 core plugs. The measurements were performed in 1993-2015 with the optical scanning technique within the Continental Super-Deep Drilling Program (Russia) for scientific super-deep well Tyumenskaya SG-6, parametric super-deep well Yen-Yakhinskaya, and deep well Yarudeyskaya-38 as well as for 13 oil and gas fields in the West Siberia. Variations of the thermal conductivity tensor components in parallel and perpendicular direction to the layer stratification (assessed for 2D anisotropy model of the rock studied), volumetric heat capacity and thermal anisotropy coefficient values and average values of the thermal properties were the subject of statistical analysis for the uppermost deposits aged by: T3-J2 (200-165 Ma); J2-J3 (165-150 Ma); J3 (150-145 Ma); K1 (145-136 Ma); K1 (136-125 Ma); K1-K2 (125-94 Ma); K2-Pg+Ng+Q (94-0 Ma). Uncertainties caused by deviations of thermal conductivity data from its average values were found to be as high as 45 % leading to unexpected errors in the basin heat flow determinations. Also, the essential spatial-temporal variations in the thermal rock properties in the study area is proposed to be taken into account in thermo-hydrodynamic modeling of hydrocarbon recovery with thermal methods. The research work was done with financial support of the Russian Ministry of Education and Science (unique identification number RFMEFI58114X0008).

  1. Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

    Sparkes, Robert B.; Doğrul Selver, Ayça; Gustafsson, Örjan; Semiletov, Igor P.; Haghipour, Negar; Wacker, Lukas; Eglinton, Timothy I.; Talbot, Helen M.; van Dongen, Bart E.

    2016-10-01

    Mobilisation of terrestrial organic carbon (terrOC) from permafrost environments in eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport or deposited across the wide East Siberian Arctic Shelf (ESAS). Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis-gas chromatography-mass spectrometry (py-GCMS) to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial phenols, aromatics and cyclopentenones to marine pyridines. There is good agreement between proportion phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p radiocarbon data for bulk OC (14COC) which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the aromatics group of compounds is likely sourced from old, aged terrOC, in contrast to the phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of phenols and pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and it shows that multiple river-ocean transects of surface sediments transition from river-dominated to coastal-erosion-dominated to marine-dominated signatures.

  2. [Some problems of the study and representation of Siberian flora biodiversity in connection with its conservation].

    Olonova, M V

    2007-01-01

    the Siberian flora.

  3. WAIST CIRCUMFERENCE AS INDICATOR COMPONENTS OF METABOLIC SYNDROME IN THE SIBERIAN POPULATION

    G. I. Simonova

    2014-01-01

    Full Text Available Object of research: to determine the cut-off point of waist circumference (WC identify the components of metabolic syndrome (MS in a large industrial center of Western Siberia.In the period from 2003 to 2005 in the screening population surveyed 9362 people, including 4268 men (45.6% and 5094 women (54.4%.The response rate was 61%. The study protocol included a sociodemographic data, measurement of blood pressure (BP, anthropometry (height, weight, WC, the definition of biochemical parameters. Statistical analysis was performed using the package SPSS. To determine the cut-off points of the used ROC model.In the group with ≥2 components of MS cut-off point WC from the men was 93.3 cm (sensitivity 72%, specificity 83%, women – 90.2 cm (sensitivity 72%, specificity 62%.The lowest cut-off point WC marked BP ≥ 130/85 mm Hg for men – 90 cm (sensitivity 66.8%, specificity 58.1%, for women – 86.5 cm (sensitivity 71.0%, specificity 55.7%. The highest cut-off point from the defined patients with diabetes for men was 99.0 cm (sensitivity 61%, specificity 70.2%, for women – cm (sensitivity 64.1%, specificity 65.9%.Conclusions: Cut-off point from the persons with the presence of ≥2 MS components in Siberian population 45–69 years, in accordance with the ROC analysis are 93.3 cm for men and 90.2 cm for women. The lowest cut-off point WC marked BP ≥ 130/85 mm Hg for men – 90 cm, for women – 86.5 cm. The highest cut-off point from the defined patients with diabetes for men was 99.0 cm, for women – 95 cm.

  4. Mortality of Siberian polecats and black-footed ferrets released onto prairie dog colonies

    Biggins, D.E.; Miller, B.J.; Hanebury, L.R.; Powell, R.A.

    2011-01-01

    Black-footed ferrets (Mustela nigripes) likely were extirpated from the wild in 19851986, and their repatriation depends on captive breeding and reintroduction. Postrelease survival of animals can be affected by behavioral changes induced by captivity. We released neutered Siberian polecats (M. eversmanii), close relatives of ferrets, in 19891990 on black-tailed prairie dog (Cynomys ludovicianus) colonies in Colorado and Wyoming initially to test rearing and reintroduction techniques. Captive-born polecats were reared in cages or cages plus outdoor pens, released from elevated cages or into burrows, and supplementally fed or not fed. We also translocated wild-born polecats from China in 1990 and released captive-born, cage-reared black-footed ferrets in 1991, the 1st such reintroduction of black-footed ferrets. We documented mortality for 55 of 92 radiotagged animals in these studies, mostly due to predation (46 cases). Coyotes (Canis latrans) killed 31 ferrets and polecats. Supplementally fed polecats survived longer than nonprovisioned polecats. With a model based on deaths per distance moved, survival was highest for wild-born polecats, followed by pen-experienced, then cage-reared groups. Indexes of abundance (from spotlight surveys) for several predators were correlated with mortality rates of polecats and ferrets due to those predators. Released black-footed ferrets had lower survival rates than their ancestral population in Wyoming, and lower survival than wild-born and translocated polecats, emphasizing the influence of captivity. Captive-born polecats lost body mass more rapidly postrelease than did captive-born ferrets. Differences in hunting efficiency and prey selection provide further evidence that these polecats and ferrets are not ecological equivalents in the strict sense. ?? 2011 American Society of Mammalogists.

  5. Dispersal limitation drives successional pathways in Central Siberian forests under current and intensified fire regimes.

    Tautenhahn, Susanne; Lichstein, Jeremy W; Jung, Martin; Kattge, Jens; Bohlman, Stephanie A; Heilmeier, Hermann; Prokushkin, Anatoly; Kahl, Anja; Wirth, Christian

    2016-06-01

    Fire is a primary driver of boreal forest dynamics. Intensifying fire regimes due to climate change may cause a shift in boreal forest composition toward reduced dominance of conifers and greater abundance of deciduous hardwoods, with potential biogeochemical and biophysical feedbacks to regional and global climate. This shift has already been observed in some North American boreal forests and has been attributed to changes in site conditions. However, it is unknown if the mechanisms controlling fire-induced changes in deciduous hardwood cover are similar among different boreal forests, which differ in the ecological traits of the dominant tree species. To better understand the consequences of intensifying fire regimes in boreal forests, we studied postfire regeneration in five burns in the Central Siberian dark taiga, a vast but poorly studied boreal region. We combined field measurements, dendrochronological analysis, and seed-source maps derived from high-resolution satellite images to quantify the importance of site conditions (e.g., organic layer depth) vs. seed availability in shaping postfire regeneration. We show that dispersal limitation of evergreen conifers was the main factor determining postfire regeneration composition and density. Site conditions had significant but weaker effects. We used information on postfire regeneration to develop a classification scheme for successional pathways, representing the dominance of deciduous hardwoods vs. evergreen conifers at different successional stages. We estimated the spatial distribution of different successional pathways under alternative fire regime scenarios. Under intensified fire regimes, dispersal limitation of evergreen conifers is predicted to become more severe, primarily due to reduced abundance of surviving seed sources within burned areas. Increased dispersal limitation of evergreen conifers, in turn, is predicted to increase the prevalence of successional pathways dominated by deciduous hardwoods

  6. Dim light at night disrupts the short-day response in Siberian hamsters.

    Ikeno, Tomoko; Weil, Zachary M; Nelson, Randy J

    2014-02-01

    Photoperiodic regulation of physiology, morphology, and behavior is crucial for many animals to survive seasonally variable conditions unfavorable for reproduction and survival. The photoperiodic response in mammals is mediated by nocturnal secretion of melatonin under the control of a circadian clock. However, artificial light at night caused by recent urbanization may disrupt the circadian clock, as well as the photoperiodic response by blunting melatonin secretion. Here we examined the effect of dim light at night (dLAN) (5lux of light during the dark phase) on locomotor activity rhythms and short-day regulation of reproduction, body mass, pelage properties, and immune responses of male Siberian hamsters. Short-day animals reduced gonadal and body mass, decreased spermatid nuclei and sperm numbers, molted to a whiter pelage, and increased pelage density compared to long-day animals. However, animals that experienced short days with dLAN did not show these short-day responses. Moreover, short-day specific immune responses were altered in dLAN conditions. The nocturnal activity pattern was blunted in dLAN hamsters, consistent with the observation that dLAN changed expression of the circadian clock gene, Period1. In addition, we demonstrated that expression levels of genes implicated in the photoperiodic response, Mel-1a melatonin receptor, Eyes absent 3, thyroid stimulating hormone receptor, gonadotropin-releasing hormone, and gonadotropin-inhibitory hormone, were higher in dLAN animals than those in short-day animals. These results suggest that dLAN disturbs the circadian clock function and affects the molecular mechanisms of the photoperiodic response. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Variability in understory evapotranspiration with overstory density in Siberian larch forests

    Tobio, A.; Loranty, M. M.; Kropp, H.; Pena, H., III; Alexander, H. D.; Natali, S.; Kholodov, A. L.

    2016-12-01

    , our results will help understand how fire regime shifts may alter understory contributions to ecosystem evapotranspiration in Siberian larch forests.

  8. Dissolved organic matter and its optical characteristics in the Laptev and East Siberian seas: spatial distribution and interannual variability (2003–2011

    S. P. Pugach

    2018-02-01

    Full Text Available The East Siberian Arctic Shelf (ESAS is the broadest and shallowest continental shelf in the world. It is characterized by both the highest rate of coastal erosion in the world and a large riverine input of terrigenous dissolved organic matter (DOM. DOM plays a significant role in marine aquatic ecosystems. The chromophoric fraction of DOM (CDOM directly affects the quantity and spectral quality of available light, thereby impacting both primary production and ultraviolet (UV exposure in aquatic ecosystems. A multiyear study of CDOM absorption, fluorescence, and spectral characteristics was carried out over the vast ESAS in the summer–fall seasons. The paper describes observations accomplished at 286 stations and 1766 in situ high-resolution optical measurements distributed along the nearshore zone. Spatial and interannual CDOM dynamics over the ESAS were investigated, and driving factors were identified. It was shown that the atmospheric circulation regime is the dominant factor controlling CDOM distribution on the ESAS. This paper explores the possibility of using CDOM and its spectral parameters to identify the different biogeochemical regimes in the surveyed area. The analysis of CDOM spectral characteristics showed that the major part of the Laptev and East Siberian seas shelf is influenced by terrigenous DOM carried in riverine discharge. Western and eastern provinces of the ESAS with distinctly different DOM optical properties were also identified; a transition between the two provinces at around 165–170° E, also consistent with hydrological and hydrochemical data, is shown. In the western ESAS, a region of substantial river impact, the content of aromatic carbon within DOM remains almost constant. In the eastern ESAS, a gradual decrease in aromaticity percentage was observed, indicating contribution of Pacific-origin waters, where allochthonous DOM with predominantly aliphatic character and much smaller absorption capacity

  9. Os-Hf-Sr-Nd isotope and PGE systematics of spinel peridotite xenoliths from Tok, SE Siberian craton: Effects of pervasive metasomatism in shallow refractory mantle

    Ionov, Dmitri A.; Shirey, Steven B.; Weis, Dominique; Brügmann, Gerhard

    2006-01-01

    Os-Hf-Sr-Nd isotopes and PGE were determined in peridotite xenoliths carried to the surface by Quaternary alkali basaltic magmas in the Tokinsky Stanovik Range on the Aldan shield. These data constrain the timing and nature of partial melting and metasomatism in the lithospheric mantle beneath SE Siberian craton. The xenoliths range from the rare fertile spinel lherzolites to the more abundant, strongly metasomatised olivine-rich (70-84%) rocks. Hf-Sr-Nd isotope compositions of the xenoliths are mainly within the fields of oceanic basalts. Most metasomatised xenoliths have lower 143Nd / 144Nd and 176Hf / 177Hf and higher 87Sr / 86Sr than the host basalts indicating that the metasomatism is older and has distinct sources. A few xenoliths have elevated 176Hf / 177Hf (up to 0.2838) and plot above the Hf-Nd mantle array defined by oceanic basalts. 187Os / 188Os in the poorly metasomatised, fertile to moderately refractory (Al2O3 ≥ 1.6%) Tok peridotites range from 0.1156 to 0.1282, with oldest rhenium depletion ages being about 2 Ga. The 187Os / 188Os in these rocks show good correlations with partial melting indices (e.g. Al2O3, modal cpx); the intercept of the Al-187Os / 188Os correlation with lowest Al2O3 estimates for melting residues (∼0.3-0.5%) has a 187Os / 188Os of ∼0.109 suggesting that these peridotites may have experienced melt extraction as early as 2.8 Gy ago. 187Os / 188Os in the strongly metasomatised, olivine-rich xenoliths (0.6-1.3% Al2O3) ranges from 0.1164 to 0.1275 and shows no apparent links to modal or chemical compositions. Convex-upward REE patterns and high abundances of heavy to middle REE in these refractory rocks indicate equilibration with evolved silicate melts at high melt / rock ratios, which may have also variably elevated their 187Os / 188Os. This inference is supported by enrichments in Pd and Pt on chondrite-normalised PGE abundance patterns in some of the rocks. The melt extraction ages for the Tok suite of 2.0 to 2.8 Ga are

  10. Effects of lecithin on growth and hematological indices in juveniles of Siberian sturgeon (Acipenser baeri Brandet 1869)

    Najafipour Moghadam, E.; Falahatkar, B.; Kalbassi, M.R.

    2011-01-01

    This study was carried out to evaluate the effects of dietary lecithin on growth performance and hematological indices in juveniles of Siberian sturgeon (Acipenser baeri). Fish with initial average weight of 32.9±0.3 grams were fed five isoproteic and isolipidic formulated diets with different soybean lecithin levels including 0, 2.5, 5, 7.5 and 10% in triplicate groups for 8 weeks. Results showed that lecithin supplementation to 7.5% significantly increased some growth indices such as body w...

  11. Distinction

    2010-01-01

    Pr Serge Haroche La Médaille d’or 2009 du CNRS est décernée au Pr Serge Haroche, titulaire de la chaire de Physique quantique depuis 2001. Serge Haroche est spécialiste de physique atomique et d’optique quantique. Il est l’un des fondateurs de l’électrodynamique quantique en cavité, domaine qui permet, par des expériences conceptuellement simples, d’éclairer les fondements de la théorie quantique et de réaliser des prototypes de systèmes de traitement quantique de l’information. Serge Haroche...

  12. Beyond annual budgets: carbon flux at different temporal scales in fire-prone Siberian Scots pine forests

    Wirth, C.; Czimczik, C.I.; Schulze, E.D.

    2002-01-01

    Along four chronosequences of fire-prone Siberian Scots pine forests we compared net primary production (NPP) and two different mass-based estimates of net ecosystem productivity (NEP C and NEP S ). NEP C quantifies changes in carbon pools along the chronosequences, whereas NEP S estimates the short-term stand-level carbon balance in intervals between fires. The chronosequences differed in the mean return interval of surface fires (unburned or moderately burned, 40 yr; heavily burned, 25 yr) and site quality (lichen versus Vaccinium type). Of the Vaccinium type (higher site quality) only a moderately burned chronosequence was studied. NEP C was derived from the rate of changes of two major carbon pools along the chronosequence time axes: (1) decomposition of old coarse woody debris (CWD) left from the previous generation after stand-replacing fire, and (2) accumulation of new carbon in biomass, CWD and soil organic layer by the regenerating stand. Young stands of all chronosequences were losing carbon at rates of -4 to -19 mol C/m 2 /yr (-48 to -228 g C/m 2 /yr). Depending on initial CWD pools and site-specific accumulation rates the stands became net carbon sinks after 12 yr (Vaccinium type) to 24 yr (lichen type) following the stand-replacing fire and offset initial carbon losses after 27 and 70 yr, respectively. Highest NEP C was reached in the unburned chronosequence (10.8 mol C/m 2 /yr or 130 g C/m 2 /yr). Maximum NEP C in the burned chronosequences ranged from 1.8 to 5.1 mol C/m 2 /yr (22 to 61 g C/m 2 /yr) depending on site quality and fire regime. Around a stand age of 200 yr NEP C was 1.6 ± 0.6 mol C/m 2 /yr (19 ± 7 g C/m 2 /yr) across all chronosequences. NEP S represents the current stand-level carbon accumulation in intervals between recurring surface fires and can be viewed as a mass-based analogue of net ecosystem exchange measured with flux towers. It was estimated based on measurements of current woody NPP, modelled decomposition of measured CWD

  13. Net ecosystem exchange and energy fluxes measured with the eddy covariance technique in a western Siberian bog

    P. Alekseychik

    2017-08-01

    Full Text Available Very few studies of ecosystem–atmosphere exchange involving eddy covariance data have been conducted in Siberia, with none in the western Siberian middle taiga. This work provides the first estimates of carbon dioxide (CO2 and energy budgets in a typical bog of the western Siberian middle taiga based on May–August measurements in 2015. The footprint of measured fluxes consisted of a homogeneous mixture of tree-covered ridges and hollows with the vegetation represented by typical sedges and shrubs. Generally, the surface exchange rates resembled those of pine-covered bogs elsewhere. The surface energy balance closure approached 100 %. Net CO2 uptake was comparatively high, summing up to 202 gC m−2 for the four measurement months, while the Bowen ratio was seasonally stable at 28 %. The ecosystem turned into a net CO2 source during several front passage events in June and July. The periods of heavy rain helped keep the water table at a sustainably high level, preventing a usual drawdown in summer. However, because of the cloudy and rainy weather, the observed fluxes might rather represent the special weather conditions of 2015 than their typical magnitudes.

  14. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog.

    Esther J Lee

    Full Text Available Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.

  15. Long-term trends in radial growth of Siberian spruce and Scots pine in Komi Republic (northwestern Russia)

    Lopatin, E. (Univ. of Joensuu (Finland)); Kolstroem, T. (Russian Academy of Sciences, Syktyvkar (Russian Federation)); Spiecker, H. (Univ. of Freiburg (Germany))

    2008-07-01

    Komi is situated on the eastern boundary of the European part of Russia, in the boreal region where large areas of natural forest still exist. Using radial growth measurements it was possible to attain positive long-term trends of growth in Scots pine (Pinus sylvestris) and Siberian spruce (Picea obovata) in the Komi Republic. Increases in the radial growth of Siberian spruce in the forest-tundra were 134% and in the northern taiga zone 35% over successive 50-year periods from 1901 to 1950 and from 1951 to 2000. Respectively, in the middle taiga zone a 76% increase in radial growth was found (over 100 years), whilst in the southern taiga zone the changes were not statistically significant. The increase in radial growth of Scots pine in the northern taiga zone was 32%. In the middle taiga zone the radial growth increase in Scots pine was 55% and in the southern taiga zone the changes were not statistically significant. The long-term growth trends of Komi were compared with those in other parts of Europe. (orig.)

  16. Late Cenozoic faulting and the stress state in the south-eastern segment of the Siberian platform

    V. A. Sankov

    2017-01-01

    Full Text Available We have studied the structural geology and geomorphology of the fault zones in the junction area of the Angara-Lena uplift and the Predbaikalsky trough. We have analyzed faults and folds and reconstructed paleostresses for this junction area named the Irkutsk amphitheatre. Our study shows that syn-fold (Middle Paleozoic faults include thrusts, reverse faults and strike-slip faults with reverse components, that occurred due to compression from the neighbouring folded region. Recently, contrary to compression, faulting took place under the conditions of extension of the sedimentary cover: most of these recent faults have been classified as normal faults. In the Late Cenozoic, the platform cover was subjected to brittle and partly plicative deformation due to the NW–SE-trending extension that is most clearly observed in the adjacent Baikal rift. Thus, the divergent boundary between the Siberian block of the North Eurasian plate and the Transbaikalia block of the Amur plate is a zone of dynamic influence, which occupies the area considerably exceeding the mountainous region on the Siberian platform. Important factors of faulting are differentiated vertical movements of the blocks comprising the platform. Such vertical movements might have been related to displacements of brine volumes. In the Late Cenozoic basins, movements along separate faults took place in the Late Pleistocene – Holocene.

  17. Low Amplitude of Geomagnetic Secular Variations Recorded in Traps of the Southern Siberian Platform: Very Fast Emplacement or Regional Remagnetization?

    Veselovskiy, R. V.; Latyshev, A. V.; Pavlov, V. E.

    2011-12-01

    We have studied the lowest part of the Permo-Triassic Siberian trap sequence which is located in the middle course of the Angara river (Southern Siberia). This sequenced is composed by 200m thick volcanoclastic rocks (tuffs with bombs of different composition) and includes numerous mafic subvolcanic bodies (dykes and sills). Altogether more than 20 sites representing tuffs, bombs, dykes and sills stretched along the valley of the Angara river over the distance more than 30 km have been sampled and studied. Obtained site mean paleomagnetic directions are tightly grouped, showing very lower scatter. Taking into account that amplitude of geomagnetic secular variation at the P-T boundary was about of same order as in Late Cenozoic (Pavlov et al., 2011) this lower scatter can be either a sequence of very fast traps emplacement which could have disastrous environmental impact or a result of subsequent regional remagnetization. The only geological event in the region which seems to be capable to cause this remagnetization is emplacement of Early Triassic sills in nearby areas. In such the case we should expect that mean paleomagnetic directions from these sills will be very close to these ones obtained from site presented in this report. We present results of paleomagnetic studies of these sills and make a choice in favor of one of discussed options. This work was supported by grants NSF EAR 0807585 ("The Siberian Traps and end-Permian extinction") and RFBR 09-05-01180, 10-05-00557.

  18. Quality and Distribution of Frozen Organic Matter (Old, Deep, Fossil Carbon) in Siberian Permafrost

    Schirrmeister, Lutz; Strauss, Jens; Wetterich, Sebastian; Grosse, Guido; Overduin, Pier Paul

    2013-04-01

    Holocene peaty deposits. Thus, we present one of the first in-depth studies of the complexity of OM distribution for the upper permafrost (to 100 m depth) in the northeastern Siberian Arctic, indicating that considerable variability of OM distribution between different stratigraphical units, between the same stratigraphical unit at different study sites, and even within stratigraphic units at the same site, are important factors that need to be taken into account in future inventories. Based on our own data and scarce published data on stratigraphical differences and the spatial variation of OC sequestered in late Quaternary permafrost deposits, we believe that knowledge about the quantities and qualities of this potentially significant OM pool is still too limited for extrapolating to larger spatial scales. However, combining TOC and ice content measurements with new bulk density estimates suggests that current carbon inventory values are too high.

  19. OPERATIONAL EXPERIENCE: UPGRADED MPC AND A SYSTEMS FOR THE RADIOCHEMICAL PLANT OF THE SIBERIAN CHEMICAL COMBINE

    RODRIGUEZ, C.; GOLOSKOKOV, I.; FISHBONE, L.; GOODEY, K.; LOOMIS, M.; CRAIN, B. JR.; LARSEN, R.

    2003-01-01

    The success of reducing the risk of nuclear proliferation through physical protection and material control/accounting systems depends upon the development of an effective design that includes consideration of the objectives of the systems and the resources available to implement the design. Included among the objectives of the design are facility characterization, definition of threat, and identification of targets. When considering resources, the designer must consider funds available, rapid low-cost elements, technology elements, human resources, and the availability of resources to sustain operation of the end system. The Siberian Chemical Combine (SCC) is a multi-function nuclear facility located in the Tomsk region of Siberia, Russia. Beginning in 1996, SCC joined with the United States Department of Energy (US/DOE) Material Protection, Control, and Accounting (MPC and A) Program to develop and implement MPC and A upgrades for the Radiochemical, Chemical Metallurgical, Conversion, Uranium Enrichment, and Reactor Plants of the SCC. At the Radiochemical Plant the MPC and A design and implementation process has been largely completed for the Plutonium Storage Facility and related areas of the Radiochemical Plant. Design and implementation of upgrades for the Radiochemical Plant include rapid physical protection upgrades such as bricking up of doors and windows, and installation of security-hardened doors. Rapid material control and accounting upgrades include installation of modern balances and bar code equipment. Comprehensive MPC and A upgrades include the installation of access controls to sensitive areas of the Plant, alarm communication and display (AC and D) systems to detect and annunciate alarm conditions, closed circuit (CCTV) systems to assess alarm conditions, central and secondary alarm station upgrades that enable security forces to assess and respond to alarm conditions, material control and accounting upgrades that include upgraded physical

  20. Determination of 14C age of inorganic and organic carbon in ancient Siberian permafrost

    Onstott, T. C.; Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Hodgins, G.; Rivkina, E.

    2017-12-01

    Permafrost represents a large reservoir of ancient carbon that could have an important impact on the global carbon budget during climate warming. Due to the low turnover rate of carbon by microorganisms at subzero temperatures, the persistence of ancient carbon in younger permafrost deposits could also pose challenges for radiocarbon dating of permafrost sediment. We utilized Accelerator Mass Spectrometry to determine the 14C age of inorganic carbon, labile and recalcitrant organic carbon in Siberian permafrost sediment sampled at various depths from 2.9 to 5.6m. The fraction of inorganic carbon (CO2) was collected after acidification using phosphoric acid. The labile (younger) and recalcitrant (old) organic carbon in the subsequent residues were collected after combustion at 400 ºC and 800 ºC, respectively. The percentages of inorganic carbon increased from the youngest (2.9m) to the oldest (5.6m), whereas the fractions for organic carbon varied significantly at different depths. The 14C age determined in the inorganic fraction in the top sample (2.9 m) was 21,760 yr BP and gradually increased to 33,900 yr BP in the relative deeper sediment (3.5 and 5.6 m). Surprisingly, the fraction of "younger" carbon liberated at 400 oC was older than the more recalcitrant and presumably older organic carbon liberated at 800 oC in all cases. Moreover, the 14C age of the younger and older organic carbon fractions did not increase with depth as observed in the carbonate fraction. In particular, the 14C age of the organic carbon in the top sample (38,590-41,700 yr BP) was much older than the deeper samples at depth of 3.5m (18,228-20,158 yr BP) and 5.6m (29,040-38,020 yr BP). It should be noticed that the metabolism of ancient carbon in frozen permafrost may vary at different depths due to the different proportion of necromass and metabolically active microbes. Therefore, additional knowledge about the carbon dynamics of permafrost and more investigation would be required to

  1. Features of Inner Structure of Placer Gold of the North-Eastern Part Siberian Platform

    Gerasimov, Boris; Zhuravlev, Anatolii; Ivanov, Alexey

    2017-12-01

    Mineral and raw material base of placer and ore gold is based on prognosis evaluation, which allows to define promising areas regarding gold-bearing deposit prospecting. But there are some difficulties in gold primary source predicting and prospecting at the North-east Siberian platform, because the studied area is overlapped by thick cover of the Cenozoic deposits, where traditional methods of gold deposit prospecting are ineffective. In this connection, detailed study of typomorphic features of placer gold is important, because it contains key genetic information, necessary for development of mineralogical criteria of prognosis evaluation of ore gold content. Authors studied mineralogical-geochemical features of placer gold of the Anabar placer area for 15 years, with a view to identify indicators of gold, typical for different formation types of primary sources. This article presents results of these works. In placer regions, where primary sources of gold are not identified, there is need to study typomorphic features of placer gold, because it contains important genetic information, necessary for the development of mineralogical criteria of prognosis evaluation of ore gold content. Inner structures of gold from the Anabar placer region are studied, as one of the diagnostic typomorphic criteria as described in prominent method, developed by N.V. Petrovskaya [1980]. Etching of gold was carried out using reagent: HCl + HNO3 + FeCl3 × 6H2O + CrO3 +thioureat + water. Identified inner structures wer studied in details by means of scanning electron microscope JEOL JSM-6480LV. Two types of gold are identified according to the features of inner structure of placer gold of the Anabar region. First type - medium-high karat fine, well processed gold with significantly changed inner structure. This gold is allochthonous, which was redeposited many times from ancient intermediate reservoirs to younger deposits. Second type - low-medium karat, poorly rounded gold with

  2. Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

    R. B. Sparkes

    2016-10-01

    Full Text Available Mobilisation of terrestrial organic carbon (terrOC from permafrost environments in eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport or deposited across the wide East Siberian Arctic Shelf (ESAS. Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis–gas chromatography–mass spectrometry (py-GCMS to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial phenols, aromatics and cyclopentenones to marine pyridines. There is good agreement between proportion phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p < 0.01, n = 24. Furfurals, thought to represent carbohydrates, show no offshore trend and are likely found in both marine and terrestrial organic matter. We have also collected new radiocarbon data for bulk OC (14COC which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the aromatics group of compounds is likely sourced from old, aged terrOC, in contrast to the phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of phenols and pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and it shows that multiple river–ocean transects of surface sediments transition from river-dominated to

  3. Variability in above- and belowground carbon stocks in a Siberian larch watershed

    E. E. Webb

    2017-09-01

    Full Text Available Permafrost soils store between 1330 and 1580 Pg carbon (C, which is 3 times the amount of C in global vegetation, almost twice the amount of C in the atmosphere, and half of the global soil organic C pool. Despite the massive amount of C in permafrost, estimates of soil C storage in the high-latitude permafrost region are highly uncertain, primarily due to undersampling at all spatial scales; circumpolar soil C estimates lack sufficient continental spatial diversity, regional intensity, and replication at the field-site level. Siberian forests are particularly undersampled, yet the larch forests that dominate this region may store more than twice as much soil C as all other boreal forest types in the continuous permafrost zone combined. Here we present above- and belowground C stocks from 20 sites representing a gradient of stand age and structure in a larch watershed of the Kolyma River, near Chersky, Sakha Republic, Russia. We found that the majority of C stored in the top 1 m of the watershed was stored belowground (92 %, with 19 % in the top 10 cm of soil and 40 % in the top 30 cm. Carbon was more variable in surface soils (10 cm; coefficient of variation (CV  =  0.35 between stands than in the top 30 cm (CV  =  0.14 or soil profile to 1 m (CV  =  0.20. Combined active-layer and deep frozen deposits (surface – 15 m contained 205 kg C m−2 (yedoma, non-ice wedge and 331 kg C m−2 (alas, which, even when accounting for landscape-level ice content, is an order of magnitude more C than that stored in the top meter of soil and 2 orders of magnitude more C than in aboveground biomass. Aboveground biomass was composed of primarily larch (53 % but also included understory vegetation (30 %, woody debris (11 % and snag (6 % biomass. While aboveground biomass contained relatively little (8 % of the C stocks in the watershed, aboveground processes were linked to thaw depth and

  4. Thaw pond dynamics and carbon emissions in a Siberian lowland tundra landscape

    van Huissteden, Ko; Heijmans, Monique; Dean, Josh; Meisel, Ove; Goovaerts, Arne; Parmentier, Frans-Jan; Schaepman-Strub, Gabriela; Belelli Marchesini, Luca; Kononov, Alexander; Maximov, Trofim; Borges, Alberto; Bouillon, Steven

    2017-04-01

    Arctic climate change induces drastic changes in permafrost surface wetness. As a result of thawing ground ice bodies, ice wedge troughs and thaw ponds are formed. Alternatively, ongoing thaw may enhance drainage as a result of increased interconnectedness of thawing ice wedge troughs, as inferred from a model study (Liljedahl et al., 2016, Nature Geoscience, DOI: 10.1038/NGEO2674). However, a recent review highlighted the limited predictability of consequences of thawing permafrost on hydrology (Walvoord and Kurylyk, 2016, Vadose Zone J., DOI:10.2136/vzj2016.01.0010). Overall, these changes in tundra wetness modify carbon cycling in the Arctic and in particular the emissions of CO2 and CH4 to the atmosphere, providing a possibly positive feedback on climate change. Here we present the results of a combined remote sensing, geomorphological, vegetation and biogechemical study of thaw ponds in Arctic Siberian tundra, at Kytalyk research station near Chokurdakh, Indigirka lowlands. The station is located in an area dominated by Pleistocene ice-rich 'yedoma' sediments and drained thaw lake bottoms of Holocene age. The development of three types of ponds in the Kytalyk area (polygon centre ponds, ice wedge troughs and thaw ponds) has been traced with high resolution satellite and aerial imagery. The remote sensing data show net areal expansion of all types of ponds. Next to formation of new ponds, local vegetation change from dry vegetation types to wet, sedge-dominated vegetation is common. Thawing ice wedges and thaw ponds show an increase in area and number at most studied locations. In particular the area of polygon centre ponds increased strongly between 2010 and 2015, but this is highly sensitive to antecedent precipitation conditions. Despite a nearly 60% increase of the area of thawing ice wedge troughs, there is no evidence of decreasing water surfaces by increasing drainage through connected ice wedge troughs. The number of thaw ponds shows an equilibrium

  5. Wildfire smoke in the Siberian Arctic in summer: source characterization and plume evolution from airborne measurements

    P. Ciais

    2009-12-01

    Full Text Available We present airborne measurements of carbon dioxide (CO2, carbon monoxide (CO, ozone (O3, equivalent black carbon (EBC and ultra fine particles over North-Eastern Siberia in July 2008 performed during the YAK-AEROSIB/POLARCAT experiment. During a "golden day" (11 July 2008 a number of biomass burning plumes were encountered with CO mixing ratio enhancements of up to 500 ppb relative to a background of 90 ppb. Number concentrations of aerosols in the size range 3.5–200 nm peaked at 4000 cm−3 and the EBC content reached 1.4 μg m−3. These high concentrations were caused by forest fires in the vicinity of the landing airport in Yakutsk where measurements in fresh smoke could be made during the descent. We estimate a combustion efficiency of 90 ± 3% based on CO and CO2 measurements and a CO emission factor of 65.5 ± 10.8 g CO per kilogram of dry matter burned. This suggests a potential increase in the average northern hemispheric CO mixing ratio of 3.0–7.2 ppb per million hectares of Siberian forest burned. For BC, we estimate an emission factor of 0.52 ± 0.07 g BC kg−1, comparable to values reported in the literature. The emission ratio of ultra-fine particles (3.5–200 nm was 26 cm−3 (ppb CO−1, consistent with other airborne studies.

    The transport of identified biomass burning plumes was investigated using the FLEXPART Lagrangian model. Based on sampling of wildfire plumes from the same source but with different atmospheric ages derived from FLEXPART, we estimate that the e-folding lifetimes of EBC and ultra fine particles (between 3.5 and 200 nm in size against removal and growth processes are 5.1 and 5.5 days respectively, supporting lifetime estimates used in various modelling studies.

  6. [Fleas community in introduced Siberian chipmunks (Tamias sibiricus Laxmann) in Forest of Sénart, France].

    Pisanu, B; Marmet, J; Beaucournu, J C; Chapuis, J L

    2008-03-01

    We examined the fleas community in an introduced population of Siberian chipmunks, Tamias sibiricus, between 2005 and 2007, in the Forest of Sénart (Essonne, France). We collected and identified 383 fleas on 463 chipmunks (total: 1,891 captures on 471 chipmunks). In 2005, 120 fleas were also collected on 65 bank voles, Clethrionomys glareolus, and on 25 wood mice, Apodemus sylvaticus, trapped within the same area. Ceratophyllus sciurorum sciurorum formed 73.6% of the chipmunks' flea community, with an annual prevalence (P) ranging between 8 and 13% and a mean intensity (I) ranging between 1.1 and 1.6 fleas per individual. Among the six other species infecting this Sciurid, Ctenophthalmus agyrtes impavidus constituted 17.2% (P: 1.6-2.2%; I: 1.1-2.6), and Megabothris turbidus 8.1% (P: 0.8-1.9%; I: 1.0-1.4) of the flea community, respectively. These last two species represented respectively 60.8% and 36.6% of the flea community on the bank vole and the wood mouse. Originated from Asia, chipmunks did not import any flea species to Sénart, probably because they were used as pets before their release in the wild. Abundance in C. s. sciurorum increased with adult chipmunk density and with juvenile density in summer. On adult chipmunks C. s. sciurorum tented to decrease with increasing abundance of red squirrels (Sciurus vulgaris]. Moreover, the two other flea species mainly infected young chipmunks during the fall, and their number was not related to chipmunk density. However, the distribution of species within the flea community became more balanced with increase juvenile chipmunk density. Overall, these results indicate that the close phyletic relationship between chipmunks and red squirrels contributed in the acquisition and the spread of fleas by chipmunks. Primary and secondary hosts densities, their habitat use, and more specifically burrowing activities and tree canopy use, also played a role in the spread of fleas on chipmunks.

  7. Defining poverty as distinctively human

    H.P.P. Lötter

    2007-05-01

    Full Text Available While it is relatively easy for most people to identify human beings suffering from poverty, it is rather more difficult to come to a proper understanding of poverty. In this article the author wants to deepen our understanding of poverty by interpreting the conventional definitions of poverty in a new light. The article starts with a defence of a claim that poverty is a concept uniquely applicable to humans. It then present a critical discussion of the distinction between absolute and relative poverty and it is then argued that a revision of this distinction can provide general standards applicable to humans everywhere.

  8. Effects of 60 Hz Magnetic Field Exposure on the Pineal and Hypothalamic-Pituitary-Gonadal Axis in the Siberian Hamster (Phodopus Sungorus)

    Wilson, Bary W.(BATTELLE (PACIFIC NW LAB)); Matt, Kathleen S.(Arizona State University); Morris, James E.(BATTELLE (PACIFIC NW LAB)); Sasser, Lyle B.(BATTELLE (PACIFIC NW LAB)); Miller, Douglas L.(BATTELLE (PACIFIC NW LAB)); Anderson, Larry E.(BATTELLE (PACIFIC NW LAB))

    1999-11-15

    Experiments using the dwarf Siberian hamster Phodopus sungorus were carried out to determine possible neuroendocrine consequences of one-time and repeated exposures to 60 Hz magnetic fields (MF). Animals were maintained in either a short-light (SL, 8 h light:16 h dar) or long-light (LL, 16 h light:8h dark) photoperiod.

  9. The Potential Impact of CO2 and Air Temperature Increases on Krummholz's Transformation into Arborescent Form in the Southern Siberian Mountains

    Kharuk, V. I.; Dvinskaya, M. L.; Im, S. T.; Ranson, K. J.

    2011-01-01

    Trees in the southern Siberian Mountains forest-tundra ecotone have considerably increased their radial and apical growth increments during the last few decades. This leads to the widespread vertical transformation of mat and prostrate krummholz forms of larch (Larix sibirica Ledeb) and Siberian pine (Pinus sibirica Du Tour). An analysis of the radial growth increments showed that these transformations began in the mid-1980s. Larch showed a greater resistance to the harsh alpine environment and attained a vertical growth form in areas where Siberian pine is still krummholz. Upper larch treeline is about 10 m higher than Siberian pine treeline. Observed apical and radial growth increment increases were correlated with CO2 concentration (r = 0.83-0.87), summer temperatures (r = 0.55-0.64), and "cold period" (i.e. September-May) air temperatures (r = 0.36-0.37). Positive correlation between growth increments and winter precipitation was attributed to snow cover protection for trees during wintertime.

  10. Ovarian matrix metalloproteinases are differentially regulated during the estrous cycle but not during short photoperiod induced regression in Siberian hamsters (Phodopus sungorus

    Vrooman Lisa A

    2010-06-01

    Full Text Available Abstract Background Matrix metalloproteinases (MMPs are implicated as mediators for ovarian remodeling events, and are involved with ovarian recrudescence during seasonal breeding cycles in Siberian hamsters. However, involvement of these proteases as the photoinhibited ovary undergoes atrophy and regression had not been assessed. We hypothesized that 1 MMPs and their tissue inhibitors, the TIMPs would be present and differentially regulated during the normal estrous cycle in Siberian hamsters, and that 2 MMP/TIMP mRNA and protein levels would increase as inhibitory photoperiod induced ovarian degeneration. Methods MMP-2, -9, -14 and TIMP-1 and -2 mRNA and protein were examined in the stages of estrous (proestrus [P], estrus [E], diestrus I [DI], and diestrus II [DII] in Siberian hamsters, as well as after exposure to 3, 6, 9, and 12 weeks of inhibitory short photoperiod (SD. Results MMP-9 exhibited a 1.6-1.8 fold decrease in mRNA expression in DII (p Conclusions Although MMPs appear to be involved in the normal ovarian estrus cycle at the protein level in hamsters, those examined in the present study are unlikely to be key players i