WorldWideScience

Sample records for program analyses revealed

  1. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  2. Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication.

    Directory of Open Access Journals (Sweden)

    James A Stahl

    2013-09-01

    Full Text Available Lytic gammaherpesvirus (GHV replication facilitates the establishment of lifelong latent infection, which places the infected host at risk for numerous cancers. As obligate intracellular parasites, GHVs must control and usurp cellular signaling pathways in order to successfully replicate, disseminate to stable latency reservoirs in the host, and prevent immune-mediated clearance. To facilitate a systems-level understanding of phosphorylation-dependent signaling events directed by GHVs during lytic replication, we utilized label-free quantitative mass spectrometry to interrogate the lytic replication cycle of murine gammaherpesvirus-68 (MHV68. Compared to controls, MHV68 infection regulated by 2-fold or greater ca. 86% of identified phosphopeptides - a regulatory scale not previously observed in phosphoproteomic evaluations of discrete signal-inducing stimuli. Network analyses demonstrated that the infection-associated induction or repression of specific cellular proteins globally altered the flow of information through the host phosphoprotein network, yielding major changes to functional protein clusters and ontologically associated proteins. A series of orthogonal bioinformatics analyses revealed that MAPK and CDK-related signaling events were overrepresented in the infection-associated phosphoproteome and identified 155 host proteins, such as the transcription factor c-Jun, as putative downstream targets. Importantly, functional tests of bioinformatics-based predictions confirmed ERK1/2 and CDK1/2 as kinases that facilitate MHV68 replication and also demonstrated the importance of c-Jun. Finally, a transposon-mutant virus screen identified the MHV68 cyclin D ortholog as a viral protein that contributes to the prominent MAPK/CDK signature of the infection-associated phosphoproteome. Together, these analyses enhance an understanding of how GHVs reorganize and usurp intracellular signaling networks to facilitate infection and replication.

  3. Automating Ultrasonic Vocalization Analyses: The WAAVES Program

    Science.gov (United States)

    Reno, James M.; Marker, Bryan; Cormack, Lawrence K.; Schallert, Timothy; Duvauchelle, Christine L.

    2014-01-01

    Background Human emotion is a crucial component of drug abuse and addiction. Ultrasonic vocalizations (USVs) elicited by rodents are a highly translational animal model of emotion in drug abuse studies. A major roadblock to comprehensive use of USV data is the overwhelming burden to attain accurate USV assessment in a timely manner. One of the most accurate methods of analyzing USVs, human auditory detection with simultaneous spectrogram inspection, requires USV sound files to be played back 4% normal speed. New Method WAAVES (WAV-file Automated Analysis of Vocalizations Environment Specific) is an automated USV assessment program utilizing MATLAB’s Signal and Image Processing Toolboxes in conjunction with a series of customized filters to separate USV calls from background noise, and accurately tabulate and categorize USVs as flat or frequency-modulated (FM) calls. In the current report, WAAVES functionality is demonstrated by USV analyses of cocaine self-administration data collected over 10 daily sessions. Results WAAVES counts are significantly correlated with human auditory counts (r(48)=0.9925; p<0.001). Statistical analyses used WAAVES output to examine individual differences in USV responses to cocaine, cocaine-associated cues and relationships between USVs, cocaine intake and locomotor activity. Comparison with Existing Method WAAVES output is highly accurate and provides tabulated data in approximately 0.4% of the time required when using human auditory detection methods. Conclusions The development of a customized USV analysis program, such as WAAVES streamlines USV assessment and enhances the ability to utilize USVs as a tool to advance drug abuse research and ultimately develop effective treatments. PMID:23832016

  4. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-01-01

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics).

  5. Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues

    DEFF Research Database (Denmark)

    Wagner, Sebastian A; Beli, Petra; Weinert, Brian T

    2012-01-01

    including proteasomal degradation of proteins, DNA damage repair and innateimmune responses. Here we combine high-resolution mass spectrometry with single-stepimmunoenrichment of di-glycine modified peptides for mapping of endogenous putativeubiquitylation sites in murine tissues. We identify more than 20......Posttranslational modifications of proteins increase the complexity of the cellular proteome andenable rapid regulation of protein functions in response to environmental changes. Proteinubiquitylation is a central regulatory posttranslational modification that controls numerousbiological processes......,000 unique ubiquitylation sites onproteins involved in diverse biological processes. Our data reveals that ubiquitylation regulates coresignaling pathways common for each of the studied tissues. In addition, we discover thatubiquitylation regulates tissue-specific signaling networks. Many tissue...

  6. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members.

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-01-05

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or 'hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). Graphical Abstract ᅟ.

  7. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations.

    Science.gov (United States)

    Angelone-Alasaad, Samer; Biebach, Iris; Pérez, Jesús M; Soriguer, Ramón C; Granados, José E

    2017-01-01

    Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.

  8. Genome size analyses of Pucciniales reveal the largest fungal genomes

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    Silvia eTavares

    2014-08-01

    Full Text Available Rust fungi (Basidiomycota, Pucciniales are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 151.5 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi. In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1,800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp. Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94 %. The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7,000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  9. Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information.

    Science.gov (United States)

    Siwek, M; Finocchiaro, R; Curik, I; Portolano, B

    2011-02-01

    Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amovaФ(ST) estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amovaФ(SC) estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  10. Systematic derivation of correct variability-aware program analyses

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Dimovski, Aleksandar S.; Brabrand, Claus

    2015-01-01

    A recent line of work lifts particular verification and analysis methods to Software Product Lines (SPL). In an effort to generalize such case-by-case approaches, we develop a systematic methodology for lifting single-program analyses to SPLs using abstract interpretation. Abstract interpretation...... for lifting analyses and Galois connections. We prove that for analyses developed using our method, the soundness of lifting follows by construction. The resulting variational abstract interpretation is a conceptual framework for understanding, deriving, and validating static analyses for SPLs. Then we show...... how to derive the corresponding variational dataflow equations for an example static analysis, a constant propagation analysis. We also describe how to approximate variability by applying variability-aware abstractions to SPL analysis. Finally, we discuss how to efficiently implement our method...

  11. SPSS and SAS programs for generalizability theory analyses.

    Science.gov (United States)

    Mushquash, Christopher; O'Connor, Brian P

    2006-08-01

    The identification and reduction of measurement errors is a major challenge in psychological testing. Most investigators rely solely on classical test theory for assessing reliability, whereas most experts have long recommended using generalizability theory instead. One reason for the common neglect of generalizability theory is the absence of analytic facilities for this purpose in popular statistical software packages. This article provides a brief introduction to generalizability theory, describes easy to use SPSS, SAS, and MATLAB programs for conducting the recommended analyses, and provides an illustrative example, using data (N = 329) for the Rosenberg Self-Esteem Scale. Program output includes variance components, relative and absolute errors and generalizability coefficients, coefficients for D studies, and graphs of D study results.

  12. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

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    Heidi G. Parker

    2017-04-01

    Full Text Available There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

  13. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development.

    Science.gov (United States)

    Parker, Heidi G; Dreger, Dayna L; Rimbault, Maud; Davis, Brian W; Mullen, Alexandra B; Carpintero-Ramirez, Gretchen; Ostrander, Elaine A

    2017-04-25

    There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  15. Analyse

    DEFF Research Database (Denmark)

    Greve, Bent

    2007-01-01

    Analyse i Politiken om frynsegoder med udgangspunkt i bogen Occupational Welfare - Winners and Losers publiceret på Edward Elgar......Analyse i Politiken om frynsegoder med udgangspunkt i bogen Occupational Welfare - Winners and Losers publiceret på Edward Elgar...

  16. Type-based associations in grapheme-color synaesthesia revealed by response time distribution analyses.

    Science.gov (United States)

    Saiki, Jun; Yoshioka, Ayako; Yamamoto, Hiroki

    2011-12-01

    Determining the nature of binding in grapheme-color synaesthesia has consequences for understanding the neural basis of synaesthesia and visual awareness in general. We evaluated type- and token-based letter-color binding using a synaesthetic version of the object-reviewing paradigm. Although mean response times failed to reveal any significant differences between synaesthetes and control participants, RT analyses with ex-Gaussian distributions revealed that the response facilitation in the synaesthesia group reflected type representations exclusively, while response facilitation in the control group, who learned letter-color associations, was dominated by token representations. Thus, letter-color associations in associator synaesthetes are type-based, and do not involve binding to object tokens, consistent with their subjective reports. Contrary to recent studies that failed to find differences between synaesthetes and non-synaesthetes with behavioral measures, response time distribution analyses indicate that color sensations in synaesthetes are not simply the extreme form of normal letter-color associations, and cannot be attributed to demand characteristics. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    Science.gov (United States)

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  18. Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa

    Science.gov (United States)

    Mohanta, Tapan K.; Bae, Hanhong

    2017-01-01

    Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNASer found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O. sativa and to our knowledge, this is the smallest gene of eukaryotic lineage reported so far. Analyses revealed the presence of several novel/pseudo tRNA genes in O. sativa which are reported for the first time. Multiple sequence alignment of tRNAs revealed the presence of family specific conserved consensus sequences. Functional study of these novel tRNA and family specific conserved consensus sequences will be crucial to decipher their importance in biological events. The rate of transition of O. sativa tRNA was found to be higher than the rate of transversion. Evolutionary study revealed, O. sativa tRNAs were evolved from the lineages of multiple common ancestors. Duplication and loss study of tRNAs genes revealed, majority of the O. sativa tRNA were duplicated and 17 of them were found to be undergone loss during the evolution. Orthology and paralogy study showed, the majority of O. sativa tRNA were paralogous and only a few of tRNASer were found to contain orthologous tRNAs. PMID:28713421

  19. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Science.gov (United States)

    Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

  20. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Directory of Open Access Journals (Sweden)

    Tod W Reeder

    Full Text Available Squamate reptiles (lizards and snakes are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa. Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia. These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses without considering the possible impact of molecular data on their placement.

  1. Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle.

    Directory of Open Access Journals (Sweden)

    Angela Cánovas

    Full Text Available Puberty is a complex physiological event by which animals mature into an adult capable of sexual reproduction. In order to enhance our understanding of the genes and regulatory pathways and networks involved in puberty, we characterized the transcriptome of five reproductive tissues (i.e. hypothalamus, pituitary gland, ovary, uterus, and endometrium as well as tissues known to be relevant to growth and metabolism needed to achieve puberty (i.e., longissimus dorsi muscle, adipose, and liver. These tissues were collected from pre- and post-pubertal Brangus heifers (3/8 Brahman; Bos indicus x 5/8 Angus; Bos taurus derived from a population of cattle used to identify quantitative trait loci associated with fertility traits (i.e., age of first observed corpus luteum (ACL, first service conception (FSC, and heifer pregnancy (HPG. In order to exploit the power of complementary omics analyses, pre- and post-puberty co-expression gene networks were constructed by combining the results from genome-wide association studies (GWAS, RNA-Seq, and bovine transcription factors. Eight tissues among pre-pubertal and post-pubertal Brangus heifers revealed 1,515 differentially expressed and 943 tissue-specific genes within the 17,832 genes confirmed by RNA-Seq analysis. The hypothalamus experienced the most notable up-regulation of genes via puberty (i.e., 204 out of 275 genes. Combining the results of GWAS and RNA-Seq, we identified 25 loci containing a single nucleotide polymorphism (SNP associated with ACL, FSC, and (or HPG. Seventeen of these SNP were within a gene and 13 of the genes were expressed in uterus or endometrium. Multi-tissue omics analyses revealed 2,450 co-expressed genes relative to puberty. The pre-pubertal network had 372,861 connections whereas the post-pubertal network had 328,357 connections. A sub-network from this process revealed key transcriptional regulators (i.e., PITX2, FOXA1, DACH2, PROP1, SIX6, etc.. Results from these multi

  2. Individual-based analyses reveal limited functional overlap in a coral reef fish community.

    Science.gov (United States)

    Brandl, Simon J; Bellwood, David R

    2014-05-01

    Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on

  3. Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development

    Science.gov (United States)

    Collins, James J.; Hou, Xiaowen; Romanova, Elena V.; Lambrus, Bramwell G.; Miller, Claire M.; Saberi, Amir; Sweedler, Jonathan V.; Newmark, Phillip A.

    2010-01-01

    Bioactive peptides (i.e., neuropeptides or peptide hormones) represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites. PMID:20967238

  4. Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

    Directory of Open Access Journals (Sweden)

    James J Collins

    Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

  5. Analysing Student Programs in the PHP Intelligent Tutoring System

    Science.gov (United States)

    Weragama, Dinesha; Reye, Jim

    2014-01-01

    Programming is a subject that many beginning students find difficult. The PHP Intelligent Tutoring System (PHP ITS) has been designed with the aim of making it easier for novices to learn the PHP language in order to develop dynamic web pages. Programming requires practice. This makes it necessary to include practical exercises in any ITS that…

  6. Exome Analyses of Long QT Syndrome Reveal Candidate Pathogenic Mutations in Calmodulin-Interacting Genes

    Science.gov (United States)

    Nakagawa, Hidewaki; Ozaki, Kouichi; Miya, Fuyuki; Satake, Wataru; Toda, Tatsushi; Miyamoto, Yoshihiro; Fujimoto, Akihiro; Suzuki, Yutaka; Kubo, Michiaki; Tsunoda, Tatsuhiko; Shimizu, Wataru; Tanaka, Toshihiro

    2015-01-01

    Long QT syndrome (LQTS) is an arrhythmogenic disorder that can lead to sudden death. To date, mutations in 15 LQTS-susceptibility genes have been implicated. However, the genetic cause for approximately 20% of LQTS patients remains elusive. Here, we performed whole-exome sequencing analyses on 59 LQTS and 61 unaffected individuals in 35 families and 138 unrelated LQTS cases, after genetic screening of known LQTS genes. Our systematic analysis of familial cases and subsequent verification by Sanger sequencing identified 92 candidate mutations in 88 genes for 23 of the 35 families (65.7%): these included eleven de novo, five recessive (two homozygous and three compound heterozygous) and seventy-three dominant mutations. Although no novel commonly mutated gene was identified other than known LQTS genes, protein-protein interaction (PPI) network analyses revealed ten new pathogenic candidates that directly or indirectly interact with proteins encoded by known LQTS genes. Furthermore, candidate gene based association studies using an independent set of 138 unrelated LQTS cases and 587 controls identified an additional novel candidate. Together, mutations in these new candidates and known genes explained 37.1% of the LQTS families (13 in 35). Moreover, half of the newly identified candidates directly interact with calmodulin (5 in 11; comparison with all genes; p=0.042). Subsequent variant analysis in the independent set of 138 cases identified 16 variants in the 11 genes, of which 14 were in calmodulin-interacting genes (87.5%). These results suggest an important role of calmodulin and its interacting proteins in the pathogenesis of LQTS. PMID:26132555

  7. Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum.

    Directory of Open Access Journals (Sweden)

    Natalie J Garton

    2008-04-01

    Full Text Available Tuberculous sputum provides a sample of bacilli that must be eliminated by chemotherapy and that may go on to transmit infection. A preliminary observation that Mycobacterium tuberculosis cells contain triacylglycerol lipid bodies in sputum, but not when growing in vitro, led us to investigate the extent of this phenomenon and its physiological basis.Microscopy-positive sputum samples from the UK and The Gambia were investigated for their content of lipid body-positive mycobacteria by combined Nile red and auramine staining. All samples contained a lipid body-positive population varying from 3% to 86% of the acid-fast bacilli present. The recent finding that triacylglycerol synthase is expressed by mycobacteria when they enter in vitro nonreplicating persistence led us to investigate whether this state was also associated with lipid body formation. We found that, when placed in laboratory conditions inducing nonreplicating persistence, two M. tuberculosis strains had lipid body levels comparable to those found in sputum. We investigated these physiological findings further by comparing the M. tuberculosis transcriptome of growing and nonreplicating persistence cultures with that obtained directly from sputum samples. Although sputum has traditionally been thought to contain actively growing tubercle bacilli, our transcript analyses refute the hypothesis that these cells predominate. Rather, they reinforce the results of the lipid body analyses by revealing transcriptional signatures that can be clearly attributed to slowly replicating or nonreplicating mycobacteria. Finally, the lipid body count was highly correlated (R(2 = 0.64, p < 0.03 with time to positivity in diagnostic liquid cultures, thereby establishing a direct link between this cytological feature and the size of a potential nonreplicating population.As nonreplicating tubercle bacilli are tolerant to the cidal action of antibiotics and resistant to multiple stresses, identification

  8. Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders.

    Science.gov (United States)

    Zhao, Huiying; Nyholt, Dale R

    2017-02-01

    Studies using genome-wide association (GWA) single nucleotide polymorphism (SNP) level data have indicated genetic overlap across the five major disorders in the Psychiatric Genomics Consortium (PGC): attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BPD), major depressive disorder (MDD), and schizophrenia (SCZ). However, such SNP-level analyses reveal little about the underlying biology and are reliant on correlated SNP effects across disorders. In contrast to SNPs, genes are more closely related to biology and gene-based tests can incorporate allelic heterogeneity. This study aimed to extend genetic overlap analysis across the five disorders from SNP level to gene level using a novel gene-based approach. Gene-based tests for association were performed using PGC GWA summary results for the five disorders in samples including 33,332 cases and 27,888 controls of European ancestry. After accounting for non-independence of gene-based test results, we determined whether the proportion of genes with association across multiple disorders was more than expected by chance. Similar to previous SNP-level analyses, we observed significant pairwise genetic overlap between ASD, BPD, MDD and SCZ. However, our approach also produced evidence for genetic overlap between ADHD and ASD, ADHD and BPD, and ADHD and MDD. Combining gene-based association results across disorders, 36 genes produced genome-wide significant P values (<3.2 × 10-6). Pathway analysis of genes with P values <1.0 × 10-3 highlighted magnesium ion binding and transport, as well as signal peptide processing, and provide insight into the biological mechanisms underlying these major psychiatric disorders.

  9. Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals.

    Science.gov (United States)

    Fortunato, Sofia A V; Adamski, Marcin; Adamska, Maja

    2015-12-01

    Developmental transcription factors (DTFs) control development of animals by affecting expression of target genes, some of which are transcription factors themselves. In bilaterians and cnidarians, conserved DTFs are involved in homologous processes such as gastrulation or specification of neurons. The genome of Amphimedon queenslandica, the first sponge to be sequenced, revealed that only a fraction of these conserved DTF families are present in demosponges. This finding was in line with the view that morphological complexity in the animal lineage correlates with developmental toolkit complexity. However, as the phylum Porifera is very diverse, Amphimedon's genome may not be representative of all sponges. The recently sequenced genomes of calcareous sponges Sycon ciliatum and Leucosolenia complicata allowed investigations of DTFs in a sponge lineage evolutionarily distant from demosponges. Surprisingly, the phylogenetic analyses of identified DTFs revealed striking differences between the calcareous sponges and Amphimedon. As these differences appear to be a result of independent gene loss events in the two sponge lineages, the last common ancestor of sponges had to possess a much more diverse repertoire of DTFs than extant sponges. Developmental expression of sponge homologs of genes involved in specification of the Bilaterian endomesoderm and the neurosensory cells suggests that roles of many DTFs date back to the last common ancestor of all animals. Strikingly, even DTFs displaying apparent pan-metazoan conservation of sequence and function are not immune to being lost from individual species genomes. The quest for a comprehensive picture of the developmental toolkit in the last common metazoan ancestor is thus greatly benefitting from the increasing accessibility of sequencing, allowing comparisons of multiple genomes within each phylum. Copyright © 2015. Published by Elsevier B.V.

  10. Multiparametric Analyses Reveal the pH-Dependence of Silicon Biomineralization in Diatoms

    Science.gov (United States)

    Hervé, Vincent; Derr, Julien; Douady, Stéphane; Quinet, Michelle; Moisan, Lionel; Lopez, Pascal Jean

    2012-01-01

    Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism. PMID:23144697

  11. Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum.

    Science.gov (United States)

    Hong, Yan; Tang, Xingjiao; Huang, He; Zhang, Yuan; Dai, Silan

    2015-03-17

    The flower colour of agricultural products is very important for their commercial value, which is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis. However, the deep molecular mechanism remains elusive, and many problems regarding the phenotypic change and the corresponding gene regulation are still unclear. In the present study, Chrysanthemum × morifolium 'Purple Reagan', a light-responding pigmentation cultivar, was selected to investigate the mechanism of light-induced anthocyanin biosynthesis using transcriptomic analyses. Only cyanidin derivatives were identified based on the analyses of the pigmentation in ray florets. Shading experiments revealed that the capitulum was the key organ and that its bud stage was the key phase responding to light. These results were used to design five libraries for transcriptomic analyses, including three capitulum developmental stages and two light conditions. RNA sequences were de novo assembled into 103,517 unigenes, of which 60,712 were annotated against four public protein databases. As many as 2,135 unigenes were differentially expressed between the light and dark libraries with 923 up-regulated and 1,212 down-regulated unigenes in response to shading. Next, interactive pathway analysis showed that the anthocyanin biosynthetic pathway was the only complete metabolic pathway both modulated in response to light and related to capitulum development. Following the shading treatment, nearly all structural genes involved in the anthocyanin biosynthetic pathway were down-regulated. Moreover, three CmMYB genes and one CmbHLH gene were identified as key transcription factors that might participate in the regulation of anthocyanin biosynthesis under light conditions based on clustering analysis and validation by RT-qPCR. Finally, a light-induced anthocyanin biosynthesis pathway in chrysanthemums was inferred. The pigmentation of the ray

  12. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake.

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, Jana; Knudsen, Rune; Kuhn, Jesper A; Henriksen, Eirik H; Siwertsson, Anna; Shaw, Jenny C; Kuris, Armand M; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D; Kostadinova, Aneta

    2017-05-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages) and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages. Copyright © 2017 Australian Society for Parasitology. All rights reserved.

  13. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

    Science.gov (United States)

    Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

    2017-09-01

    The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

  14. Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell-wall structure and assembly

    Science.gov (United States)

    Desmarais, Samantha M.; De Pedro, Miguel A.; Cava, Felipe; Huang, Kerwyn Casey

    2013-01-01

    The peptidoglycan (PG) cell wall is a unique macromolecule responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria. A quantitative understanding of the relationships between PG architecture, morphogenesis, immune system activation, and pathogenesis can provide molecular-scale insights into the function of proteins involved in cell-wall synthesis and cell growth. High Performance Liquid Chromatography (HPLC) has played an important role in our understanding of the structural and chemical complexity of the cell wall by providing an analytical method to quantify differences in chemical composition. Here, we present a primer on the basic chemical features of wall structure that can be revealed through HPLC, along with a description of the applications of HPLC PG analyses for interpreting the effects of genetic and chemical perturbations to a variety of bacterial species in different environments. We describe the physical consequences of different PG compositions on cell shape, and review complementary experimental and computational methodologies for PG analysis. Finally, we present a partial list of future targets of development for HPLC and related techniques. PMID:23679048

  15. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  16. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

    Science.gov (United States)

    Leliaert, Frederik; Tronholm, Ana; Lemieux, Claude; Turmel, Monique; DePriest, Michael S.; Bhattacharya, Debashish; Karol, Kenneth G.; Fredericq, Suzanne; Zechman, Frederick W.; Lopez-Bautista, Juan M.

    2016-01-01

    The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov. PMID:27157793

  17. Transcriptome and biochemical analyses revealed a detailed proanthocyanidin biosynthesis pathway in brown cotton fiber.

    Directory of Open Access Journals (Sweden)

    Yue-Hua Xiao

    Full Text Available Brown cotton fiber is the major raw material for colored cotton industry. Previous studies have showed that the brown pigments in cotton fiber belong to proanthocyanidins (PAs. To clarify the details of PA biosynthesis pathway in brown cotton fiber, gene expression profiles in developing brown and white fibers were compared via digital gene expression profiling and qRT-PCR. Compared to white cotton fiber, all steps from phenylalanine to PA monomers (flavan-3-ols were significantly up-regulated in brown fiber. Liquid chromatography mass spectrometry analyses showed that most of free flavan-3-ols in brown fiber were in 2, 3-trans form (gallocatechin and catechin, and the main units of polymeric PAs were trihydroxylated on B ring. Consistent with monomeric composition, the transcript levels of flavonoid 3', 5'-hydroxylase and leucoanthocyanidin reductase in cotton fiber were much higher than their competing enzymes acting on the same substrates (dihydroflavonol 4-reductase and anthocyanidin synthase, respectively. Taken together, our data revealed a detailed PA biosynthesis pathway wholly activated in brown cotton fiber, and demonstrated that flavonoid 3', 5'-hydroxylase and leucoanthocyanidin reductase represented the primary flow of PA biosynthesis in cotton fiber.

  18. Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis).

    Science.gov (United States)

    Li, Dejun; Wang, Xuncheng; Deng, Zhi; Liu, Hui; Yang, Hong; He, Guangming

    2016-03-23

    Tapping panel dryness (TPD) is a serious threat to natural rubber yields from rubber trees, but the molecular mechanisms underlying TPD remain poorly understood. To identify TPD-related genes and reveal these molecular mechanisms, we sequenced and compared the transcriptomes of bark between healthy and TPD trees. In total, 57,760 assembled genes were obtained and analyzed in details. In contrast to healthy rubber trees, 5652 and 2485 genes were up- or downregulated, respectively, in TPD trees. The TPD-related genes were significantly enriched in eight GO terms and five KEGG pathways and were closely associated with ROS metabolism, programmed cell death and rubber biosynthesis. Our results suggest that rubber tree TPD is a complex process involving many genes. The observed lower rubber yield from TPD trees might result from lower isopentenyl diphosphate (IPP) available for rubber biosynthesis and from downregulation of the genes in post-IPP steps of rubber biosynthesis pathway. Our results not only extend our understanding of the complex molecular events involved in TPD but also will be useful for developing effective measures to control TPD of rubber trees.

  19. Fecal genotyping and contaminant analyses reveal variation in individual river otter exposure to localized persistent contaminants.

    Science.gov (United States)

    Guertin, Daniel A; Harestad, Alton S; Ben-David, Merav; Drouillard, Ken G; Elliott, John E

    2010-02-01

    The present study investigated polyhalogenated aromatic hydrocarbon (PHAH) concentrations in feces of known river otters (Lontra canadensis) along the coast of southern Vancouver Island, British Columbia, Canada. Specifically, we combined microsatellite genotyping of DNA from feces for individual identification with fecal contaminant analyses to evaluate exposure of 23 wild otters to organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenylethers (PBDEs). Overall, feces collected from otters in urban/industrial Victoria Harbor had the greatest concentrations of nearly all compounds assessed. Fecal concentrations of OCPs and PBDEs were generally low throughout the region, whereas PCBs dominated in all locations. Re-sampling of known otters over space and time revealed that PCB exposure varied with movement and landscape use. Otters with the highest fecal PCB concentrations were those inhabiting the inner reaches of Victoria Harbor and adjacent Esquimalt Harbor, and those venturing into the harbor systems. Over 50% of samples collected from eight known otters in Victoria Harbor had total-PCB concentrations above the maximum allowable concentration as established for Eurasian otter (Lutra lutra) feces, with a geometric mean value (10.6 mg/kg lipid wt) that exceeded the reproductive toxicity threshold (9 mg/kg lipid wt). Those results are consistent with our findings from 1998 and 2004, and indicate that the harbors of southern Vancouver Island, particularly Victoria Harbor, are a chronic source of PCB exposure for otters. The present study further demonstrates the suitability of using otter feces as a noninvasive/destructive biomonitoring tool in contaminant studies, particularly when sampling of the same individuals at the local population-level is desired. Copyright 2009 SETAC.

  20. Geochemical analyses reveal the importance of environmental history for blue carbon sequestration

    Science.gov (United States)

    Kelleway, J. J.; Saintilan, N.; Macreadie, P. I.; Baldock, J. A.; Heijnis, H.; Zawadzki, A.; Gadd, P.; Jacobsen, G.; Ralph, P. J.

    2017-07-01

    Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands are known to respond to changes imposed by geomorphic evolution, climatic, sea level, and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores—two collected from marine-influenced saltmarshes (Wapengo marine site (WAP-M) and Port Stephens marine site (POR-M)) and two from fluvial influenced saltmarshes (Wapengo fluvial site (WAP-F) and Port Stephens fluvial site (POR-F))—highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13C nuclear magnetic resonance analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C; however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales.

  1. Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida

    Science.gov (United States)

    Cao, Peili; Guo, Dongchun; Liu, Jiasen; Jiang, Qian; Xu, Zhuofei; Qu, Liandong

    2017-01-01

    Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P. multocida genomes, evolutionary features were systematically analyzed in this study. Clustering of 70,565 protein-coding genes showed that the pangenome of 33 P. multocida strains was composed of 1,602 core genes, 1,364 dispensable genes, and 1,070 strain-specific genes. Of these, we identified a full spectrum of genes related to virulence factors and revealed genetic diversity of these potential virulence markers across P. multocida strains, e.g., bcbAB, fcbC, lipA, bexDCA, ctrCD, lgtA, lgtC, lic2A involved in biogenesis of surface polysaccharides, hsf encoding autotransporter adhesin, and fhaB encoding filamentous haemagglutinin. Furthermore, based on genome-wide positive selection scanning, a total of 35 genes were subject to strong selection pressure. Extensive analyses of protein subcellular location indicated that membrane-associated genes were highly abundant among all positively selected genes. The detected amino acid sites undergoing adaptive selection were preferably located in extracellular space, perhaps associated with bacterial evasion of host immune responses. Our findings shed more light on conservation and distribution of virulence-associated genes across P. multocida strains. Meanwhile, this study provides a genetic context for future researches on the mechanism of adaptive evolution in P. multocida. PMID:28611758

  2. Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida

    Directory of Open Access Journals (Sweden)

    Peili Cao

    2017-05-01

    Full Text Available Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P. multocida genomes, evolutionary features were systematically analyzed in this study. Clustering of 70,565 protein-coding genes showed that the pangenome of 33 P. multocida strains was composed of 1,602 core genes, 1,364 dispensable genes, and 1,070 strain-specific genes. Of these, we identified a full spectrum of genes related to virulence factors and revealed genetic diversity of these potential virulence markers across P. multocida strains, e.g., bcbAB, fcbC, lipA, bexDCA, ctrCD, lgtA, lgtC, lic2A involved in biogenesis of surface polysaccharides, hsf encoding autotransporter adhesin, and fhaB encoding filamentous haemagglutinin. Furthermore, based on genome-wide positive selection scanning, a total of 35 genes were subject to strong selection pressure. Extensive analyses of protein subcellular location indicated that membrane-associated genes were highly abundant among all positively selected genes. The detected amino acid sites undergoing adaptive selection were preferably located in extracellular space, perhaps associated with bacterial evasion of host immune responses. Our findings shed more light on conservation and distribution of virulence-associated genes across P. multocida strains. Meanwhile, this study provides a genetic context for future researches on the mechanism of adaptive evolution in P. multocida.

  3. Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida.

    Science.gov (United States)

    Cao, Peili; Guo, Dongchun; Liu, Jiasen; Jiang, Qian; Xu, Zhuofei; Qu, Liandong

    2017-01-01

    Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P. multocida genomes, evolutionary features were systematically analyzed in this study. Clustering of 70,565 protein-coding genes showed that the pangenome of 33 P. multocida strains was composed of 1,602 core genes, 1,364 dispensable genes, and 1,070 strain-specific genes. Of these, we identified a full spectrum of genes related to virulence factors and revealed genetic diversity of these potential virulence markers across P. multocida strains, e.g., bcbAB, fcbC, lipA, bexDCA, ctrCD, lgtA, lgtC, lic2A involved in biogenesis of surface polysaccharides, hsf encoding autotransporter adhesin, and fhaB encoding filamentous haemagglutinin. Furthermore, based on genome-wide positive selection scanning, a total of 35 genes were subject to strong selection pressure. Extensive analyses of protein subcellular location indicated that membrane-associated genes were highly abundant among all positively selected genes. The detected amino acid sites undergoing adaptive selection were preferably located in extracellular space, perhaps associated with bacterial evasion of host immune responses. Our findings shed more light on conservation and distribution of virulence-associated genes across P. multocida strains. Meanwhile, this study provides a genetic context for future researches on the mechanism of adaptive evolution in P. multocida.

  4. Object-oriented fault tree evaluation program for quantitative analyses

    Science.gov (United States)

    Patterson-Hine, F. A.; Koen, B. V.

    1988-01-01

    Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

  5. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodríguez, Jorge P.

    2017-03-02

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  6. Big data analyses reveal patterns and drivers of the movements of southern elephant seals.

    Science.gov (United States)

    Rodríguez, Jorge P; Fernández-Gracia, Juan; Thums, Michele; Hindell, Mark A; Sequeira, Ana M M; Meekan, Mark G; Costa, Daniel P; Guinet, Christophe; Harcourt, Robert G; McMahon, Clive R; Muelbert, Monica; Duarte, Carlos M; Eguíluz, Víctor M

    2017-03-08

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with "big data", that require no 'a priori' assumptions about the behaviour of the target agents, to analyse a pooled tracking dataset of 272 elephant seals (Mirounga leonina) in the Southern Ocean, that was comprised of >500,000 location estimates collected over more than a decade. Our analyses showed that the displacements of these seals were described by a truncated power law distribution across several spatial and temporal scales, with a clear signature of directed movement. This pattern was evident when analysing the aggregated tracks despite a wide diversity of individual trajectories. We also identified marine provinces that described the migratory and foraging habitats of these seals. Our analysis provides evidence for the presence of intrinsic drivers of movement, such as memory, that cannot be detected using common models of movement behaviour. These results highlight the potential for "big data" techniques to provide new insights into movement behaviour when applied to large datasets of animal tracking.

  7. Correlated mutation analyses on super-family alignments reveal functionally important residues.

    NARCIS (Netherlands)

    Kuipers, R.K.P.; Joosten, H.J.; Verwiel, E.; Paans, S.; Akerboom, J.; Oost, J. van der; Leferink, N.G.; Berkel, W.J. van; Vriend, G.; Schaap, P.J.

    2009-01-01

    Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the number of sequences, by their evolutionary distances, and by the quality of the alignments. These

  8. Correlated mutation analyses on super-family alignments reveal functionally important residues

    NARCIS (Netherlands)

    Kuipers, R.K.; Joosten, H.J.; Verwiel, E.; Paans, J.; Akerboom, J.; Oost, van der J.; Leferink, N.G.H.; Berkel, van W.J.H.; Vriend, G.; Schaap, P.J.

    2009-01-01

    Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the number of sequences, by their evolutionary distances, and by the quality of the alignments. These

  9. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

    Science.gov (United States)

    Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

  10. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery

    DEFF Research Database (Denmark)

    Poulsen, Michael; Oh, Dong-Chan; Clardy, Jon

    2011-01-01

    and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15...... and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding...

  11. Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility.

    Science.gov (United States)

    Rowe, Heather C; Rieseberg, Loren H

    2013-05-23

    Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession. While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions. While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species.

  12. Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis)

    OpenAIRE

    Dejun Li; Xuncheng Wang; Zhi Deng; Hui Liu; Hong Yang; Guangming He

    2016-01-01

    Tapping panel dryness (TPD) is a serious threat to natural rubber yields from rubber trees, but the molecular mechanisms underlying TPD remain poorly understood. To identify TPD-related genes and reveal these molecular mechanisms, we sequenced and compared the transcriptomes of bark between healthy and TPD trees. In total, 57,760 assembled genes were obtained and analyzed in details. In contrast to healthy rubber trees, 5652 and 2485 genes were up- or downregulated, respectively, in TPD trees...

  13. Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments.

    Science.gov (United States)

    de Vries, Maria; Schöler, Anne; Ertl, Julia; Xu, Zhuofei; Schloter, Michael

    2015-07-01

    Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil, and relies heavily on the activity of cellulose-degrading microorganisms. Here we address the question of how different tillage treatments affect soil microbial communities and their cellulose-degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as their microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT, and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3 and 94, auxiliary activity family 8 and carbohydrate-binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall, this study reveals the stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility

    Science.gov (United States)

    2013-01-01

    Background Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession. Results While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions. Conclusions While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species. PMID:23701699

  15. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    DEFF Research Database (Denmark)

    Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria

    2015-01-01

    of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide...

  16. Proteome Analyses Using iTRAQ Labeling Reveal Critical Mechanisms in Alternate Bearing Malus prunifolia.

    Science.gov (United States)

    Fan, Sheng; Zhang, Dong; Lei, Chao; Chen, Hongfei; Xing, Libo; Ma, Juanjuan; Zhao, Caiping; Han, Mingyu

    2016-10-07

    Alternate bearing (AB) trees, including Malus prunifolia, are characterized by alternating cycles of heavy (ON tree) and low (OFF tree) fruit loads. The mechanisms regulating the AB phenomenon have not been fully characterized. We completed an iTRAQ-based investigation of M. prunifolia to identify the proteome and metabolic differences between the leaves of ON and OFF trees. We identified 667 differentially expressed proteins, and they influenced multiple biochemical pathways, including photosynthesis, carbohydrate metabolism, glycolysis, protein processing, redox activities, and secondary metabolism. Bioinformatics analyses indicated photosynthesis was the most significant biological process affecting the AB. We observed that 47 photosynthetic proteins affecting photosystem I and II reaction centers, cytochrome b6/f complex, electron transport, and light-harvesting chlorophyll were less abundant in ON tree leaves than in OFF tree leaves. Additionally, physiological analyses validated the potential metabolic activities. Nitrogen and phosphorus contents were significantly higher in ON tree leaves, while potassium levels were lower. Starch content, ZR, GA4+7 levels, and flower control gene expression levels (i.e., MdFT1, MdLFY, MdAP1, and MdSPL9) were lower in ON tree leaves than in OFF tree leaves, suggesting they affected the AB phenotype. Our findings help further investigate on the photosynthesis as well as other processes in AB. Those identified DEPs and important biological processes can be useful theoretical basis and provide new insights into the molecular mechanisms regulating AB in perennial woody plants.

  17. Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

  18. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Directory of Open Access Journals (Sweden)

    Pengpeng Li

    Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  19. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  20. Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53

    Science.gov (United States)

    Cairns, Jonathan M.; Menon, Suraj; Pérez-Mancera, Pedro A.; Tomimatsu, Kosuke; Bermejo-Rodriguez, Camino; Ito, Yoko; Chandra, Tamir; Narita, Masako; Lyons, Scott K.; Lynch, Andy G.; Kimura, Hiroshi; Ohbayashi, Tetsuya; Tavaré, Simon; Narita, Masashi

    2015-01-01

    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. PMID:25790137

  1. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  2. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Shan Goh

    Full Text Available BACKGROUND: Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS: Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50. When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS: RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

  3. Distinct Particle Morphologies Revealed through Comparative Parallel Analyses of Retrovirus-Like Particles.

    Science.gov (United States)

    Martin, Jessica L; Cao, Sheng; Maldonado, Jose O; Zhang, Wei; Mansky, Louis M

    2016-09-15

    The Gag protein is the main retroviral structural protein, and its expression alone is usually sufficient for production of virus-like particles (VLPs). In this study, we sought to investigate-in parallel comparative analyses-Gag cellular distribution, VLP size, and basic morphological features using Gag expression constructs (Gag or Gag-YFP, where YFP is yellow fluorescent protein) created from all representative retroviral genera: Alpharetrovirus, Betaretrovirus, Deltaretrovirus, Epsilonretrovirus, Gammaretrovirus, Lentivirus, and Spumavirus. We analyzed Gag cellular distribution by confocal microscopy, VLP budding by thin-section transmission electron microscopy (TEM), and general morphological features of the VLPs by cryogenic transmission electron microscopy (cryo-TEM). Punctate Gag was observed near the plasma membrane for all Gag constructs tested except for the representative Beta- and Epsilonretrovirus Gag proteins. This is the first report of Epsilonretrovirus Gag localizing to the nucleus of HeLa cells. While VLPs were not produced by the representative Beta- and Epsilonretrovirus Gag proteins, the other Gag proteins produced VLPs as confirmed by TEM, and morphological differences were observed by cryo-TEM. In particular, we observed Deltaretrovirus-like particles with flat regions of electron density that did not follow viral membrane curvature, Lentivirus-like particles with a narrow range and consistent electron density, suggesting a tightly packed Gag lattice, and Spumavirus-like particles with large envelope protein spikes and no visible electron density associated with a Gag lattice. Taken together, these parallel comparative analyses demonstrate for the first time the distinct morphological features that exist among retrovirus-like particles. Investigation of these differences will provide greater insights into the retroviral assembly pathway. Comparative analysis among retroviruses has been critically important in enhancing our understanding of

  4. Underestimation of species richness in neotropical frogs revealed by mtDNA analyses.

    Directory of Open Access Journals (Sweden)

    Antoine Fouquet

    Full Text Available BACKGROUND: Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness. METHODOLOGY: Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. PRINCIPAL FINDINGS: In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. CONCLUSIONS: Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates

  5. Proteomic Analyses Reveal a Role of Cytoplasmic Droplets as an Energy Source during Epididymal Sperm Maturation

    Science.gov (United States)

    Yuan, Shuiqiao; Zheng, Huili; Zheng, Zhihong; Yan, Wei

    2013-01-01

    A small portion of cytoplasm is generally retained as the cytoplasmic droplet (CD) on the flagellum of spermatozoa after spermiation in mice. CDs are believed to play a role in osmoadaptation by allowing water entrance or exit. However, many lines of evidence suggest that CDs may have roles beyond osmoregulation. To gain more insights, we purified CDs from murine epididymal spermatozoa and conducted proteomic analyses on proteins highly enriched in CDs. Among 105 proteins identified, 71 (68%) were enzymes involved in energy metabolism. We also found that sperm mitochondria underwent a reactivation process and glycolytic enzymes were further distributed and incorporated into different regions of the flagellum during epididymal sperm maturation. Both processes appeared to require CDs. Our data suggest that the CD represents a transient organelle that serves as an energy source essential for epididymal sperm maturation. PMID:24155961

  6. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

    Directory of Open Access Journals (Sweden)

    Sun Qi

    2009-11-01

    Full Text Available Abstract Background The bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species. Some Salmonella serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium, two host restricted serotypes (Typhi [two genomes] and Paratyphi and one host adapted serotype (Choleraesuis were used to identify core genome genes that show evidence for recombination and positive selection. Results Overall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] ompC, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns. Conclusion Our data show that, among the four serotypes analyzed, (i less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii branch specific positive selection contributes to the evolution of host restricted Salmonella serotypes.

  7. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types

    Science.gov (United States)

    Li, Qiyuan; Stram, Alexander; Chen, Constance; Kar, Siddhartha; Gayther, Simon; Pharoah, Paul; Haiman, Christopher; Stranger, Barbara; Kraft, Peter; Freedman, Matthew L.

    2014-01-01

    The majority of trait-associated loci discovered through genome-wide association studies are located outside of known protein coding regions. Consequently, it is difficult to ascertain the mechanism underlying these variants and to pinpoint the causal alleles. Expression quantitative trait loci (eQTLs) provide an organizing principle to address both of these issues. eQTLs are genetic loci that correlate with RNA transcript levels. Large-scale data sets such as the Cancer Genome Atlas (TCGA) provide an ideal opportunity to systematically evaluate eQTLs as they have generated multiple data types on hundreds of samples. We evaluated the determinants of gene expression (germline variants and somatic copy number and methylation) and performed cis-eQTL analyses for mRNA expression and miRNA expression in five tumor types (breast, colon, kidney, lung and prostate). We next tested 149 known cancer risk loci for eQTL effects, and observed that 42 (28.2%) were significantly associated with at least one transcript. Lastly, we described a fine-mapping strategy for these 42 eQTL target–gene associations based on an integrated strategy that combines the eQTL level of significance and the regulatory potential as measured by DNaseI hypersensitivity. For each of the risk loci, our analyses suggested 1 to 81 candidate causal variants that may be prioritized for downstream functional analysis. In summary, our study provided a comprehensive landscape of the genetic determinants of gene expression in different tumor types and ranked the genes and loci for further functional assessment of known cancer risk loci. PMID:24907074

  8. Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling.

    Science.gov (United States)

    Schluttenhofer, Craig; Pattanaik, Sitakanta; Patra, Barunava; Yuan, Ling

    2014-06-20

    To combat infection to biotic stress plants elicit the biosynthesis of numerous natural products, many of which are valuable pharmaceutical compounds. Jasmonate is a central regulator of defense response to pathogens and accumulation of specialized metabolites. Catharanthus roseus produces a large number of terpenoid indole alkaloids (TIAs) and is an excellent model for understanding the regulation of this class of valuable compounds. Recent work illustrates a possible role for the Catharanthus WRKY transcription factors (TFs) in regulating TIA biosynthesis. In Arabidopsis and other plants, the WRKY TF family is also shown to play important role in controlling tolerance to biotic and abiotic stresses, as well as secondary metabolism. Here, we describe the WRKY TF families in response to jasmonate in Arabidopsis and Catharanthus. Publically available Arabidopsis microarrays revealed at least 30% (22 of 72) of WRKY TFs respond to jasmonate treatments. Microarray analysis identified at least six jasmonate responsive Arabidopsis WRKY genes (AtWRKY7, AtWRKY20, AtWRKY26, AtWRKY45, AtWRKY48, and AtWRKY72) that have not been previously reported. The Catharanthus WRKY TF family is comprised of at least 48 members. Phylogenetic clustering reveals 11 group I, 32 group II, and 5 group III WRKY TFs. Furthermore, we found that at least 25% (12 of 48) were jasmonate responsive, and 75% (9 of 12) of the jasmonate responsive CrWRKYs are orthologs of AtWRKYs known to be regulated by jasmonate. Overall, the CrWRKY family, ascertained from transcriptome sequences, contains approximately 75% of the number of WRKYs found in other sequenced asterid species (pepper, tomato, potato, and bladderwort). Microarray and transcriptomic data indicate that expression of WRKY TFs in Arabidopsis and Catharanthus are under tight spatio-temporal and developmental control, and potentially have a significant role in jasmonate signaling. Profiling of CrWRKY expression in response to jasmonate treatment

  9. Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

    DEFF Research Database (Denmark)

    Reis, Eduardo M; Ojopi, Elida P B; Alberto, Fernando L

    2005-01-01

    with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers......A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual...... curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including...

  10. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  11. Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

    Science.gov (United States)

    Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

    2017-01-01

    Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant

  12. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery.

    Directory of Open Access Journals (Sweden)

    Michael Poulsen

    2011-02-01

    Full Text Available Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15 of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest.

  13. Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus.

    Science.gov (United States)

    Fouquet, Antoine; Recoder, Renato; Teixeira, Mauro; Cassimiro, José; Amaro, Renata Cecília; Camacho, Agustín; Damasceno, Roberta; Carnaval, Ana Carolina; Moritz, Craig; Rodrigues, Miguel Trefaut

    2012-03-01

    Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization.

    Science.gov (United States)

    Leonardi, Michela; Barbujani, Guido; Manica, Andrea

    2017-06-14

    Archaeological evidence shows that, in the long run, Neolitization (the transition from foraging to food production) was associated with demographic growth. We used two methods (patterns of linkage disequilibrium from whole-genome SNPs and MSMC estimates on genomes) to reconstruct the demographic profiles for respectively 64 and 24 modern-day populations with contrasting lifestyles across the Old World (sub-Saharan Africa, south-eastern Asia, Siberia). Surprisingly, in all regions, food producers had larger effective population sizes (N e) than foragers already 20 k years ago, well before the Neolithic revolution. As expected, this difference further increased ~12-10 k years ago, around or just before the onset of food production. Using paleoclimate reconstructions, we show that the early difference in N e cannot be explained by food producers inhabiting more favorable regions. A number of mechanisms, including ancestral differences in census size, sedentism, exploitation of the natural resources, social stratification or connectivity between groups, might have led to the early differences in Ne detected in our analyses. Irrespective of the specific mechanisms involved, our results provide further evidence that long term cultural differences among populations of Palaeolithic hunter-gatherers are likely to have played an important role in the later Neolithization process.

  15. Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae, a Dominant Alpine Species in Taiwan.

    Directory of Open Access Journals (Sweden)

    Chi-Chun Huang

    Full Text Available Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

  16. Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan.

    Science.gov (United States)

    Huang, Chi-Chun; Hsu, Tsai-Wen; Wang, Hao-Ven; Liu, Zin-Huang; Chen, Yi-Yen; Chiu, Chi-Te; Huang, Chao-Li; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh

    2016-01-01

    Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

  17. Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi.

    Science.gov (United States)

    Zhang, Zhen-Na; Wu, Qin-Yi; Zhang, Gui-Zhi; Zhu, Yue-Yan; Murphy, Robert W; Liu, Zhen; Zou, Cheng-Gang

    2015-08-10

    CFEM domain commonly occurs in fungal extracellular membrane proteins. To provide insights for understanding putative functions of CFEM, we investigate the evolutionary dynamics of CFEM domains by systematic comparative genomic analyses among diverse animals, plants, and more than 100 fungal species, which are representative across the entire group of fungi. We here show that CFEM domain is unique to fungi. Experiments using tissue culture demonstrate that the CFEM-containing ESTs in some plants originate from endophytic fungi. We also find that CFEM domain does not occur in all fungi. Its single origin dates to the most recent common ancestors of Ascomycota and Basidiomycota, instead of multiple origins. Although the length and architecture of CFEM domains are relatively conserved, the domain-number varies significantly among different fungal species. In general, pathogenic fungi have a larger number of domains compared to other species. Domain-expansion across fungal genomes appears to be driven by domain duplication and gene duplication via recombination. These findings generate a clear evolutionary trajectory of CFEM domains and provide novel insights into the functional exchange of CFEM-containing proteins from cell-surface components to mediators in host-pathogen interactions.

  18. Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

    2012-05-25

    Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).

  19. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  20. Combined Metabolomic and Correlation Networks Analyses Reveal Fumarase Insufficiency Altered Amino Acids Metabolism.

    Science.gov (United States)

    Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

    2017-11-11

    Fumarase catalyzes the interconversion of fumarate and L-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased level of fumarate and decreased level of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles that induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient HUVEC cells and negative controls. A total of 24 altered metabolites involved in 7 metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, L-malic acid, L-aspartic acid, glycine and L-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. ALT and GDH activities increased significantly in fumarase deficiency HUVEC cells. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. This article is protected by copyright. All rights reserved.

  1. Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants

    Science.gov (United States)

    Olafsdottir, Thorunn A.; Lindqvist, Madelene; Nookaew, Intawat; Andersen, Peter; Maertzdorf, Jeroen; Persson, Josefine; Christensen, Dennis; Zhang, Yuan; Anderson, Jenna; Khoomrung, Sakda; Sen, Partho; Agger, Else Marie; Coler, Rhea; Carter, Darrick; Meinke, Andreas; Rappuoli, Rino; Kaufmann, Stefan H. E.; Reed, Steven G.; Harandi, Ali M.

    2016-12-01

    A better understanding of the mechanisms of action of human adjuvants could inform a rational development of next generation vaccines for human use. Here, we exploited a genome wide transcriptomics analysis combined with a systems biology approach to determine the molecular signatures induced by four clinically tested vaccine adjuvants, namely CAF01, IC31, GLA-SE and Alum in mice. We report signature molecules, pathways, gene modules and networks, which are shared by or otherwise exclusive to these clinical-grade adjuvants in whole blood and draining lymph nodes of mice. Intriguingly, co-expression analysis revealed blood gene modules highly enriched for molecules with documented roles in T follicular helper (TFH) and germinal center (GC) responses. We could show that all adjuvants enhanced, although with different magnitude and kinetics, TFH and GC B cell responses in draining lymph nodes. These results represent, to our knowledge, the first comparative systems analysis of clinically tested vaccine adjuvants that may provide new insights into the mechanisms of action of human adjuvants.

  2. Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians' skin.

    Science.gov (United States)

    Fan, Wenqiao; Jiang, Yusong; Zhang, Meixia; Yang, Donglin; Chen, Zhongzhu; Sun, Hanchang; Lan, Xuelian; Yan, Fan; Xu, Jingming; Yuan, Wanan

    2017-01-01

    Skin as the first barrier against external invasions plays an essential role for the survival of amphibians on land. Understanding the genetic basis of skin function is significant in revealing the mechanisms underlying immunity of amphibians. In this study, we de novo sequenced and comparatively analyzed skin transcriptomes from three different amphibian species, Andrias davidianus, Bufo gargarizans, and Rana nigromaculata Hallowell. Functional classification of unigenes in each amphibian showed high accordance, with the most represented GO terms and KEGG pathways related to basic biological processes, such as binding and metabolism and immune system. As for the unigenes, GO and KEGG distributions of conserved orthologs in each species were similar, with the predominantly enriched pathways including RNA polymerase, nucleotide metabolism, and defense. The positively selected orthologs in each amphibian were also similar, which were primarily involved in stimulus response, cell metabolic, membrane, and catalytic activity. Furthermore, a total of 50 antimicrobial peptides from 26 different categories were identified in the three amphibians, and one of these showed high efficiency in inhibiting the growth of different bacteria. Our understanding of innate immune function of amphibian skin has increased basis on the immune-related unigenes, pathways, and antimicrobial peptides in amphibians.

  3. Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians’ skin

    Science.gov (United States)

    Zhang, Meixia; Yang, Donglin; Chen, Zhongzhu; Lan, Xuelian; Yan, Fan; Xu, Jingming; Yuan, Wanan

    2017-01-01

    Skin as the first barrier against external invasions plays an essential role for the survival of amphibians on land. Understanding the genetic basis of skin function is significant in revealing the mechanisms underlying immunity of amphibians. In this study, we de novo sequenced and comparatively analyzed skin transcriptomes from three different amphibian species, Andrias davidianus, Bufo gargarizans, and Rana nigromaculata Hallowell. Functional classification of unigenes in each amphibian showed high accordance, with the most represented GO terms and KEGG pathways related to basic biological processes, such as binding and metabolism and immune system. As for the unigenes, GO and KEGG distributions of conserved orthologs in each species were similar, with the predominantly enriched pathways including RNA polymerase, nucleotide metabolism, and defense. The positively selected orthologs in each amphibian were also similar, which were primarily involved in stimulus response, cell metabolic, membrane, and catalytic activity. Furthermore, a total of 50 antimicrobial peptides from 26 different categories were identified in the three amphibians, and one of these showed high efficiency in inhibiting the growth of different bacteria. Our understanding of innate immune function of amphibian skin has increased basis on the immune-related unigenes, pathways, and antimicrobial peptides in amphibians. PMID:29267366

  4. Dynamic changes in brewing yeast cells in culture revealed by statistical analyses of yeast morphological data.

    Science.gov (United States)

    Ohnuki, Shinsuke; Enomoto, Kenichi; Yoshimoto, Hiroyuki; Ohya, Yoshikazu

    2014-03-01

    The vitality of brewing yeasts has been used to monitor their physiological state during fermentation. To investigate the fermentation process, we used the image processing software, CalMorph, which generates morphological data on yeast mother cells and bud shape, nuclear shape and location, and actin distribution. We found that 248 parameters changed significantly during fermentation. Successive use of principal component analysis (PCA) revealed several important features of yeast, providing insight into the dynamic changes in the yeast population. First, PCA indicated that much of the observed variability in the experiment was summarized in just two components: a change with a peak and a change over time. Second, PCA indicated the independent and important morphological features responsible for dynamic changes: budding ratio, nucleus position, neck position, and actin organization. Thus, the large amount of data provided by imaging analysis can be used to monitor the fermentation processes involved in beer and bioethanol production. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  5. Integrative analyses reveal novel strategies in HPV11,-16 and-45 early infection

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Rossing, Maria; Andersen, Ditte

    2012-01-01

    The interaction between human papillomavirus (HPV) and host cells is not well understood. We investigate the early stage of HPV infections by global expression profiling in a cell model, in which HaCaT cells were transfected with HPV11, HPV16 or HPV45 genomes. We report the differential expression...... of genes not previously implicated in HPV biology, such as the PSG family and ANKRD1, and of genes implicated in the biology of other viruses, e. g. MX1, IFI44 and DDX60. Carcinogenesis-related genes, e. g. ABL2, MGLL and CYR61, were upregulated by high-risk HPV16 and -45. The integrative analysis revealed...... the suppression of DNA repair by HPV11 and -16, and downregulation of cytoskeleton genes by all HPV types. Various signalling pathways were affected by the HPVs: IL-2 by HPV11; JAK-STAT by HPV16; and TGF-beta, NOTCH and tyrosine kinase signalling by HPV45. This study uncovered novel strategies employed by HPV...

  6. Clinical, cellular, and bioinformatic analyses reveal involvement of WRAP53 overexpression in carcinogenesis of lung adenocarcinoma.

    Science.gov (United States)

    Yuan, Xiao-Shuai; Cao, Long-Xiang; Hu, Ye-Ji; Bao, Fei-Chao; Wang, Zhi-Tian; Cao, Jin-Lin; Yuan, Ping; Lv, Wang; Hu, Jian

    2017-03-01

    Lung cancer, of which non-small cell lung cancer accounts for 80%, remains a leading cause of cancer-related mortality and morbidity worldwide. Our study revealed that the expression of WD repeat containing antisense to P53 (WRAP53) is higher in lung-adenocarcinoma specimens than in specimens from adjacent non-tumor tissues. The prevalence of WRAP53 overexpression was significantly higher in patients with tumor larger than 3.0 cm than in patients with tumor smaller than 3.0 cm. The depletion of WRAP53 inhibits the proliferation of lung-adenocarcinoma A549 and SPC-A-1 cells via G1/S cell-cycle arrest. Several proteins interacting with WRAP53 were identified through co-immunoprecipitation and liquid chromatography/mass spectrometry. These key proteins indicated previously undiscovered functions of WRAP53. These observations strongly suggested that WRAP53 should be considered a promising target in the prevention or treatment of lung adenocarcinoma.

  7. COMPARATIVE ANALYSES OF MORPHOLOGICAL CHARACTERS IN SPHAERODORIDAE AND ALLIES (ANNELIDA REVEALED BY AN INTEGRATIVE MICROSCOPICAL APPROACH

    Directory of Open Access Journals (Sweden)

    Conrad eHelm

    2015-01-01

    Full Text Available Sphaerodoridae is a group of benthic marine worms (Annelida characterized by the presence of spherical tubercles covering their whole surface. They are commonly considered as belonging to Phyllodocida although sistergroup relationships are still far from being understood. Primary homology assessment of their morphological features are lacking, hindering the appraisal of evolutionary relationships between taxa. Therefore, our detailed morphological investigation focuses on different Sphaerodoridae as well as on other members of Phyllodocida using an integrative approach combining scanning electron microscopy (SEM as well as immunohistochemistry with standard neuronal (anti-5-HT and muscular (phalloidin-rhodamine markers and subsequent CLSM analysis of whole mounts and sections. Furthermore, we provide histological (HES and light microscopical data to shed light on the structures and hypothetical function of sphaerodorid key morphological features. We provide fundamental details into the sphaerodorid morphology supporting a Phyllodocida ancestry of these enigmatic worms. However, the muscular arrangement and the presence of an axial muscular pharynx is similar to conditions observed in other members of the Errantia too. Furthermore, nervous system and muscle staining as well as SEM and histological observations of different types of tubercles indicate a homology of the so called microtubercles, present in the long-bodied sphaerodorids, to the dorsal cirri of other Errantia. The macrotubercles seem to represent a sphaerodorid autapomorphy based on our investigations. Therefore, our results allow comparisons concerning morphological patterns between Sphaerodoridae and other Phyllodocida and constitute a starting point for further comparative investigations to reveal the evolution of the remarkable Sphaerodoridae.

  8. Cost and cost threshold analyses for 12 innovative US HIV linkage and retention in care programs.

    Science.gov (United States)

    Jain, Kriti M; Maulsby, Catherine; Brantley, Meredith; Kim, Jeeyon Janet; Zulliger, Rose; Riordan, Maura; Charles, Vignetta; Holtgrave, David R

    2016-09-01

    Out of >1,000,000 people living with HIV in the USA, an estimated 60% were not adequately engaged in medical care in 2011. In response, AIDS United spearheaded 12 HIV linkage and retention in care programs. These programs were supported by the Social Innovation Fund, a White House initiative. Each program reflected the needs of its local population living with HIV. Economic analyses of such programs, such as cost and cost threshold analyses, provide important information for policy-makers and others allocating resources or planning programs. Implementation costs were examined from societal and payer perspectives. This paper presents the results of cost threshold analyses, which provide an estimated number of HIV transmissions that would have to be averted for each program to be considered cost-saving and cost-effective. The methods were adapted from the US Panel on Cost-effectiveness in Health and Medicine. Per client program costs ranged from $1109.45 to $7602.54 from a societal perspective. The cost-saving thresholds ranged from 0.32 to 1.19 infections averted, and the cost-effectiveness thresholds ranged from 0.11 to 0.43 infections averted by the programs. These results suggest that such programs are a sound and efficient investment towards supporting goals set by US HIV policy-makers. Cost-utility data are pending.

  9. Transcriptomic and hormone analyses reveal mechanisms underlying petal elongation in Chrysanthemum morifolium 'Jinba'.

    Science.gov (United States)

    Wang, Jingjing; Wang, Haibin; Ding, Lian; Song, Aiping; Shen, Feng; Jiang, Jiafu; Chen, Sumei; Chen, Fadi

    2017-04-01

    Auxin regulates chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate chrysanthemum petal elongation. As an ornamental species, Chrysanthemum morifolium has high ornamental and economic value. Petal size is the primary factor that influences the ornamental value of chrysanthemum, but the mechanism underlying the development of C. morifolium petals remains unclear. In our study, we tracked the growth of petals and found that the basal region of 'Jinba' petals showed a higher elongation rate, exhibiting rapid cell elongation during petal growth. During petal elongation growth, auxin was demonstrated to promote cell elongation and an increase in cell numbers in the petal basal region. To further study the molecular mechanisms underlying petal growth, the RNA-seq (high-throughput cDNA sequencing) technique was employed. Four cDNA libraries were assembled from petals in the budding, bud breaking, early blooming and full blooming stages of 'Jinba' flower development. Analysis of differentially expressed genes (DEGs) showed that auxin was the most important regulator in controlling petal growth. The TEOSINTEBRANCHED 1, CYCLOIDEA and PCF transcription factor genes (TCPs), basic helix-loop-helix-encoding gene (bHLH), glutaredoxin-C (GRXC) and other zinc finger protein genes exhibited obvious up-regulation and might have significant effects on the growth of 'Jinba' petals. Given the interaction between these genes in Arabidopsis thaliana, we speculated that auxin signal transduction might exhibit a close relationship with transcription factors through TCPs. In summary, we present the first comprehensive transcriptomic and hormone analyses of C. morifolium petals. The results offer direction in identifying the mechanism underlying the development of chrysanthemum petals in the elongated phase and have great significance in improving the

  10. Histopathology combined with transcriptome analyses reveals the mechanism of resistance to Meloidogyne incognita in Cucumis metuliferus.

    Science.gov (United States)

    Ye, De-You; Qi, Yong-Hong; Cao, Su-Fang; Wei, Bing-Qiang; Zhang, Hua-Sheng

    2017-05-01

    Root-knot nematodes (Meloidogyne spp.) cause serious threat to cucumber production. Cucumis metuliferus, a relative of cucumber, is reported to be resistant to Meloidogyne incognita, yet the underlying resistance mechanism remains unclear. In this study, the response of resistant C. metuliferus accession PI482443 following nematode infection was studied in comparison with susceptible C. sativus cv. Jinlv No.3. Roots of selected Cucumis seedings were analysed using histological and biochemical techniques. Transcriptome changes of the resistance reaction were investigated by RNA-seq. The results showed that penetration and development of the nematode in resistant plants were reduced when compared to susceptible plants. Infection of a resistant genotype with M. incognita resulted in a hypersensitive reaction. The induction of phenylalanine ammonia lyase and peroxidase activities after infection was greater in resistant than susceptible roots. Several of the most relevant genes for phenylpropanoid biosynthesis, plant hormone signal transduction, and the plant-pathogen interaction pathway that are involved in resistance to the nematode were significantly altered. The resistance in C. metuliferus PI482443 to M. incognita was associated with reduced nematode penetration, retardation of nematode development, and hypersensitive necrosis. The expression of genes resulting in the deposition of lignin, toxic compounds synthesis, cell wall reinforcement, suppression of nematode feeding and resistance protein accumulation, and activation of several transcription factors might all contribute to the resistance response to the pest. These results may lead to a better understanding of the resistance mechanism and aid in the identification of potential targets resistant to pests for cucumber improvement. Copyright © 2017 Elsevier GmbH. All rights reserved.

  11. Phosphorylation-mediated Regulatory Networks in Mycelia of Pyricularia oryzae Revealed by Phosphoproteomic Analyses.

    Science.gov (United States)

    Wang, Rui-Jin; Peng, Junbo; Li, Qing X; Peng, You-Liang

    2017-09-01

    Protein phosphorylation is known to regulate pathogenesis, mycelial growth, conidiation and stress response in Pyricularia oryzae However, phosphorylation mediated regulatory networks in the fungal pathogen remain largely to be uncovered. In this study, we identified 1621 phosphorylation sites of 799 proteins in mycelia of P. oryzae, including 899 new p-sites of 536 proteins and 47 new p-sites of 31 pathogenicity-related proteins. From the sequences flanking the phosphorylation sites, 19 conserved phosphorylation motifs were identified. Notably, phosphorylation was detected in 7 proteins that function upstream of Pmk1, but not in Pmk1 and its downstream Mst12 and Sfl1 that have been known to regulate appressorium formation and infection hyphal growth of P. oryzae Interestingly, phosphorylation was detected at the site Ser(240) of Pmp1, which is a putative protein phosphatase highly conserved in filamentous fungi but not characterized. We thus generated Δpmp1 deletion mutants and dominant allele PMP1(S240D) mutants. Phenotyping analyses indicated that Pmp1 is required for virulence, conidiation and mycelial growth. Further, we observed that phosphorylation level of Pmk1 in mycelia was significantly increased in the Δpmp1 mutant, but decreased in the PMP1(S240D) mutant in comparison with the wild type, demonstrating that Pmp1 phosphorylated at Ser(240) is important for regulating phosphorylation of Pmk1. To our surprise, phosphorylation of Mps1, another MAP kinase required for cell wall integrity and appressorium formation of P. oryzae, was also significantly enhanced in the Δpmp1 mutant, but decreased in the PMP1(S240D) mutant. In addition, we found that Pmp1 directly interacts with Mps1 and the region AA180-230 of Pmp1 is required for the interaction. In summary, this study sheds new lights on the protein phosphorylation mediated regulatory networks in P. oryzae. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Hemoglobin analyses in the Netherlands reveal more than 80 different variants including six novel ones.

    Science.gov (United States)

    van Zwieten, Rob; Veldthuis, Martijn; Delzenne, Barend; Berghuis, Jeffrey; Groen, Joke; Ait Ichou, Fatima; Clifford, Els; Harteveld, Cornelis L; Stroobants, An K

    2014-01-01

    More than 20,000 blood samples of individuals living in The Netherlands and suspected of hemolytic anemia or diabetes were analyzed by high resolution cation exchange high performance liquid chromatography (HPLC). Besides common disease-related hemoglobins (Hbs), rare variants were also detected. The variant Hbs were retrospectively analyzed by capillary zone electrophoresis (CZE) and by isoelectric focusing (IEF). For unambiguous identification, the globin genes were sequenced. Most of the 80 Hb variants detected by initial screening on HPLC were also separated by capillary electrophoresis (CE), but a few variants were only detectable with one of these methods. Some variants were unstable, had thalassemic properties or increased oxygen affinity, and some interfered with Hb A2 measurement, detection of sickle cell Hb or Hb A1c quantification. Two of the six novel variants, Hb Enschede (HBA2: c.308G  > A, p.Ser103Asn) and Hb Weesp (HBA1: c.301C > T, p.Leu101Phe), had no clinical consequences. In contrast, two others appeared clinically significant: Hb Ede (HBB: c.53A > T, p.Lys18Met) caused thalassemia and Hb Waterland (HBB: c.428C > T, pAla143Val) was related to mild polycytemia. Hb A2-Venlo (HBD: c.193G > A, p.Gly65Ser) and Hb A2-Rotterdam (HBD: c.38A > C, p.Asn13Thr) interfered with Hb A2 quantification. This survey shows that HPLC analysis followed by globin gene sequencing of rare variants is an effective method to reveal Hb variants.

  13. Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms1

    Science.gov (United States)

    Yang, Tianquan; Dong, Xue; Li, De-Zhu

    2016-01-01

    Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm. PMID:27208275

  14. Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird.

    Science.gov (United States)

    Khimoun, Aurélie; Peterman, William; Eraud, Cyril; Faivre, Bruno; Navarro, Nicolas; Garnier, Stéphane

    2017-10-01

    Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order (i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then (ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea). We detected a small-scale reduction of gene flow mainly driven by land cover, with a negative impact of the nonforest matrix on landscape functional connectivity. However, matrix components did not equally constrain gene flow, as their conductivity increased with increasing structural similarity with forest habitat: urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. Our results revealed a higher performance of IBR compared to LCP in explaining gene flow, reflecting suboptimal movements across this human-modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results emphasize the need for an objective definition of landscape scales (landscape extent and thematic resolution) and highlight potential pitfalls associated with parameterization of resistance surfaces. © 2017 John Wiley & Sons Ltd.

  15. Network analyses reveal pervasive functional regulation between proteases in the human protease web.

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    Nikolaus Fortelny

    2014-05-01

    Full Text Available Proteolytic processing is an irreversible posttranslational modification affecting a large portion of the proteome. Protease-cleaved mediators frequently exhibit altered activity, and biological pathways are often regulated by proteolytic processing. Many of these mechanisms have not been appreciated as being protease-dependent, and the potential in unraveling a complex new dimension of biological control is increasingly recognized. Proteases are currently believed to act individually or in isolated cascades. However, conclusive but scattered biochemical evidence indicates broader regulation of proteases by protease and inhibitor interactions. Therefore, to systematically study such interactions, we assembled curated protease cleavage and inhibition data into a global, computational representation, termed the protease web. This revealed that proteases pervasively influence the activity of other proteases directly or by cleaving intermediate proteases or protease inhibitors. The protease web spans four classes of proteases and inhibitors and so links both recently and classically described protease groups and cascades, which can no longer be viewed as operating in isolation in vivo. We demonstrated that this observation, termed reachability, is robust to alterations in the data and will only increase in the future as additional data are added. We further show how subnetworks of the web are operational in 23 different tissues reflecting different phenotypes. We applied our network to develop novel insights into biologically relevant protease interactions using cell-specific proteases of the polymorphonuclear leukocyte as a system. Predictions from the protease web on the activity of matrix metalloproteinase 8 (MMP8 and neutrophil elastase being linked by an inactivating cleavage of serpinA1 by MMP8 were validated and explain perplexing Mmp8-/- versus wild-type polymorphonuclear chemokine cleavages in vivo. Our findings supply systematically

  16. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

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    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  17. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    Science.gov (United States)

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama-Jr, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA2s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not efficiently

  18. Comparative analyses reveal discrepancies among results of commonly used methods for Anopheles gambiaemolecular form identification

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    Pinto João

    2011-08-01

    Full Text Available Abstract Background Anopheles gambiae M and S molecular forms, the major malaria vectors in the Afro-tropical region, are ongoing a process of ecological diversification and adaptive lineage splitting, which is affecting malaria transmission and vector control strategies in West Africa. These two incipient species are defined on the basis of single nucleotide differences in the IGS and ITS regions of multicopy rDNA located on the X-chromosome. A number of PCR and PCR-RFLP approaches based on form-specific SNPs in the IGS region are used for M and S identification. Moreover, a PCR-method to detect the M-specific insertion of a short interspersed transposable element (SINE200 has recently been introduced as an alternative identification approach. However, a large-scale comparative analysis of four widely used PCR or PCR-RFLP genotyping methods for M and S identification was never carried out to evaluate whether they could be used interchangeably, as commonly assumed. Results The genotyping of more than 400 A. gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, highlighted discrepancies among results obtained by the different approaches due to different kinds of biases, which may result in an overestimation of MS putative hybrids, as follows: i incorrect match of M and S specific primers used in the allele specific-PCR approach; ii presence of polymorphisms in the recognition sequence of restriction enzymes used in the PCR-RFLP approaches; iii incomplete cleavage during the restriction reactions; iv presence of different copy numbers of M and S-specific IGS-arrays in single individuals in areas of secondary contact between the two forms. Conclusions The results reveal that the PCR and PCR-RFLP approaches most commonly utilized to identify A. gambiae M and S forms are not fully interchangeable as usually assumed, and highlight limits of the actual definition of the two molecular forms, which might

  19. Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in 'Anji Baicha' (Camellia sinensis).

    Science.gov (United States)

    Li, Chun-Fang; Xu, Yan-Xia; Ma, Jian-Qiang; Jin, Ji-Qiang; Huang, Dan-Juan; Yao, Ming-Zhe; Ma, Chun-Lei; Chen, Liang

    2016-09-08

    The new shoots of the albino tea cultivar 'Anji Baicha' are yellow or white at low temperatures and turn green as the environmental temperatures increase during the early spring. 'Anji Baicha' metabolite profiles exhibit considerable variability over three color and developmental stages, especially regarding the carotenoid, chlorophyll, and theanine concentrations. Previous studies focused on physiological characteristics, gene expression differences, and variations in metabolite abundances in albino tea plant leaves at specific growth stages. However, the molecular mechanisms regulating metabolite biosynthesis in various color and developmental stages in albino tea leaves have not been fully characterized. We used RNA-sequencing to analyze 'Anji Baicha' leaves at the yellow-green, albescent, and re-greening stages. The leaf transcriptomes differed considerably among the three stages. Functional classifications based on Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that differentially expressed unigenes were mainly related to metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and carbon fixation in photosynthetic organisms. Chemical analyses revealed higher β-carotene and theanine levels, but lower chlorophyll a levels, in the albescent stage than in the green stage. Furthermore, unigenes involved in carotenoid, chlorophyll, and theanine biosyntheses were identified, and the expression patterns of the differentially expressed unigenes in these biosynthesis pathways were characterized. Through co-expression analyses, we identified the key genes in these pathways. These genes may be responsible for the metabolite biosynthesis differences among the different leaf color and developmental stages of 'Anji Baicha' tea plants. Our study presents the results of transcriptomic and biochemical analyses of 'Anji Baicha' tea plants at various stages. The distinct transcriptome profiles

  20. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

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    Stéphane Uroz

    Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

  1. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

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    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  2. Metagenomics and in situ analyses reveal Propionivibrio spp. to be abundant GAO in biological wastewater treatment systems

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Albertsen, Mads; Stokholm-Bjerregaard, Mikkel

    Enhanced biological phosphorus removal (EBPR) is widely applied for phosphorus removal from wastewater. The process relies on polyphosphate-accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth. However, glycogen-accumulating organisms (GAOs) may...... and genome annotation supported that the “Ca. Accumulibacter” and Propionivibrio were behaving as PAO and GAO, respectively. FISH analyses of full-scale EBPR systems revealed that Propionivibrio spp. can be abundant. The discovery of Propionivibrio, a putative GAO closely related to “Ca. Accumulibacter...

  3. Secondary Data Analyses of Conclusions Drawn by the Program Implementers of a Positive Youth Development Program in Hong Kong

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    Andrew M. H. Siu

    2010-01-01

    Full Text Available The Tier 2 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes is designed for adolescents with significant psychosocial needs, and its various programs are designed and implemented by social workers (program implementers for specific student groups in different schools. Using subjective outcome evaluation data collected from the program participants (Form C at 207 schools, the program implementers were asked to aggregate data and write down five conclusions (n = 1,035 in their evaluation reports. The conclusions stated in the evaluation reports were further analyzed via secondary data analyses in this study. Results showed that the participants regarded the Tier 2 Program as a success, and was effective in enhancing self-understanding, interpersonal skills, and self-management. They liked the experiential learning approach and activities that are novel, interesting, diversified, adventure-based, and outdoor in nature. They also liked instructors who were friendly, supportive, well-prepared, and able to bring challenges and give positive recognition. Most of the difficulties encountered in running the programs were related to time constraints, clashes with other activities, and motivation of participants. Consistent with the previous evaluation findings, the present study suggests that the Tier 2 Program was well received by the participants and that it was beneficial to the development of the program participants.

  4. Secondary data analyses of conclusions drawn by the program implementers of a positive youth development program in Hong Kong.

    Science.gov (United States)

    Siu, Andrew M H; Shek, Daniel T L

    2010-02-12

    The Tier 2 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes) is designed for adolescents with significant psychosocial needs, and its various programs are designed and implemented by social workers (program implementers) for specific student groups in different schools. Using subjective outcome evaluation data collected from the program participants (Form C) at 207 schools, the program implementers were asked to aggregate data and write down five conclusions (n = 1,035) in their evaluation reports. The conclusions stated in the evaluation reports were further analyzed via secondary data analyses in this study. Results showed that the participants regarded the Tier 2 Program as a success, and was effective in enhancing self-understanding, interpersonal skills, and self-management. They liked the experiential learning approach and activities that are novel, interesting, diversified, adventure-based, and outdoor in nature. They also liked instructors who were friendly, supportive, well-prepared, and able to bring challenges and give positive recognition. Most of the difficulties encountered in running the programs were related to time constraints, clashes with other activities, and motivation of participants. Consistent with the previous evaluation findings, the present study suggests that the Tier 2 Program was well received by the participants and that it was beneficial to the development of the program participants.

  5. Targeted metabolomic analyses of cellular models of pelizaeus-merzbacher disease reveal plasmalogen and myo-inositol solute carrier dysfunction

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    Pelzer Lindsay

    2011-06-01

    Full Text Available Abstract Background Leukodystrophies are devastating diseases characterized by dys- and hypo-myelination. While there are a number of histological and imaging studies of these disorders, there are limited biochemical data available. We undertook targeted lipidomic analyses of Pelizaeus-Merzbacher disease (PMD fibroblasts, PMD lymphocytes, and 158JP oligodendrocytes, a murine model of PMD, to define the lipid changes in these cell models. Further targeted metabolomics analyses were conducted to obtain a preliminary evaluation of the metabolic consequences of lipid changes and gene mutations in these cell models. Results In both PMD fibroblasts and lymphocytes, and 158JP oligodendrocytes, ethanolamine plasmalogens were significantly decreased. Labeling studies with 158JP oligodendrocytes further demonstrated a decreased rate of lipid remodeling at sn-2. Targeted metabolomics analyses of these cells revealed dramatic increases in cellular levels of myo-inositol. Further uptake studies demonstrated increased rates of myo-inositol uptake by PMD lymphocytes. Conclusions Our data demonstrating PlsEtn decrements, support previous studies indicating leukodystrophy cells possess significant peroxisomal deficits. Our data for the first time also demonstrate that decrements in peroxisomal function coupled with the PLP1 gene defects of PMD, result in changes in the function of membrane myo-inositol solute carriers resulting in dramatic increases in cellular myo-inositol levels.

  6. Global Geometric Morphometric Analyses of the Human Pelvis Reveal Substantial Neutral Population History Effects, Even across Sexes

    Science.gov (United States)

    Betti, Lia; von Cramon-Taubadel, Noreen; Manica, Andrea; Lycett, Stephen J.

    2013-01-01

    Recent applications of population genetic models to human craniodental traits have revealed a strong neutral component to patterns of global variation. However, little work has been undertaken to determine whether neutral processes might also be influencing the postcranium, perhaps due to substantial evidence for selection and plastic environmental responses in these regions. Recent work has provided evidence for neutral effects in the pelvis, but has been limited in regard to shape data (small numbers of linear measurements) and restricted only to males. Here, we use geometric morphometric methods to examine population variation in the human os coxae (pelvic bone) in both males and females. Neutrality is examined via apportionment of variance patterns and fit to an Out-of-Africa serial founder effect model, which is known to structure neutral genetic patterns. Moreover, we compare males and females directly, and the true versus false pelvis, in order to examine potential obstetrical effects. Our results indicate evidence for substantial neutral population history effects on pelvic shape variation. They also reveal evidence for the effect of obstetrical constraints, but these affect males and females to equivalent extents. Our results do not deny an important role for selection in regard to specific aspects of human pelvic variation, especially in terms of features associated with body size and proportions. However, our analyses demonstrate that at a global level, the shape of the os coxae reveals substantial evidence for neutral variation. Our analyses thus indicate that population variation in the human pelvis might be used to address important questions concerning population history, just as the human cranium has done. PMID:23409086

  7. Effectiveness of a selective alcohol prevention program targeting personality risk factors: Results of interaction analyses.

    Science.gov (United States)

    Lammers, Jeroen; Goossens, Ferry; Conrod, Patricia; Engels, Rutger; Wiers, Reinout W; Kleinjan, Marloes

    2017-08-01

    To explore whether specific groups of adolescents (i.e., scoring high on personality risk traits, having a lower education level, or being male) benefit more from the Preventure intervention with regard to curbing their drinking behaviour. A clustered randomized controlled trial, with participants randomly assigned to a 2-session coping skills intervention or a control no-intervention condition. Fifteen secondary schools throughout The Netherlands; 7 schools in the intervention and 8 schools in the control condition. 699 adolescents aged 13-15; 343 allocated to the intervention and 356 to the control condition; with drinking experience and elevated scores in either negative thinking, anxiety sensitivity, impulsivity or sensation seeking. Differential effectiveness of the Preventure program was examined for the personality traits group, education level and gender on past-month binge drinking (main outcome), binge frequency, alcohol use, alcohol frequency and problem drinking, at 12months post-intervention. Preventure is a selective school-based alcohol prevention programme targeting personality risk factors. The comparator was a no-intervention control. Intervention effects were moderated by the personality traits group and by education level. More specifically, significant intervention effects were found on reducing alcohol use within the anxiety sensitivity group (OR=2.14, CI=1.40, 3.29) and reducing binge drinking (OR=1.76, CI=1.38, 2.24) and binge drinking frequency (β=0.24, p=0.04) within the sensation seeking group at 12months post-intervention. Also, lower educated young adolescents reduced binge drinking (OR=1.47, CI=1.14, 1.88), binge drinking frequency (β=0.25, p=0.04), alcohol use (OR=1.32, CI=1.06, 1.65) and alcohol use frequency (β=0.47, p=0.01), but not those in the higher education group. Post hoc latent-growth analyses revealed significant effects on the development of binge drinking (β=-0.19, p=0.02) and binge drinking frequency (β=-0.10, p=0

  8. TMT-based quantitative proteomics analyses reveal novel defense mechanisms of Brassica napus against the devastating necrotrophic pathogen Sclerotinia sclerotiorum.

    Science.gov (United States)

    Cao, Jia-Yi; Xu, You-Ping; Cai, Xin-Zhong

    2016-06-30

    The white mould disease, caused by Sclerotinia sclerotiorum, is one of the most important diseases in the vital oil crop Brassica napus. Nevertheless, the defense mechanisms of B. napus against S. sclerotiorum are poorly understood. In this study, we performed comparative quantitative proteomics analyses to reveal B. napus defense mechanisms against S. sclerotiorum. The proteomes of B. napus leaves inoculated with S. sclerotiorum wild-type strain 1980 and nonpathogenic mutant strain Ep-1PB as well as empty agar plug as the control were analyzed using TMT label-based quantitative analysis technique. A total of 79, 299 and 173 proteins consistently differentially expressed between Ep-1PB- and mock-inoculated leaves, 1980- and mock-inoculated leaves, as well as 1980- and Ep-1PB-inoculated leaves, respectively, were identified. The differential expression of 12 selected proteins was confirmed by qRT-PCR analyses. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction prediction analyses revealed that redox homeostasis, lipid signaling, calcium signaling, histone and DNA methylation-mediated transcription regulation and defense-related proteins such as defensin and defensin-like proteins and cyanate lyase, contribute to defense against S. sclerotiorum. Our results provide new insights into molecular mechanisms that may be involved in defense responses of B. napus to S. sclerotiorum. The Sclerotinia white mould disease is one of the most important diseases in the significant oil crop Brassica napus. Nevertheless, the defense mechanisms of B. napus against S. sclerotiorum are still largely unknown to date. In this study, we addressed this issue by performing TMT label-based comparative quantitative analyses of the proteomes of B. napus leaves inoculated with S. sclerotiorum wild-type strain 1980 and nonpathogenic mutant strain Ep-1PB as well as empty agar plug as the control. Through comparative analyses on 79, 299, and 173

  9. Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae reveal concordant genetic structure across the Hawaiian Archipelago.

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    Kimberly R Andrews

    Full Text Available The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787 and E. "marshi" (formerly E. carbunculus; N = 770 with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus and a submesophotic grouper (Hyporthodus quernus. Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management

  10. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.

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    Bo Yuan

    2015-12-01

    Full Text Available Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100 is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles.

  11. Morphological and biochemical analyses of original and regenerated lizard tails reveal variation in protein and lipid composition.

    Science.gov (United States)

    Boozalis, Ted S; LaSalle, Landon T; Davis, Jon R

    2012-01-01

    Caudal autotomy, or voluntary self-amputation of the tail, is a common and effective predator evasion mechanism used by most lizard species. The tail contributes to a multitude of biological functions such as locomotion, energetics, and social interactions, and thus there are often costs associated with autotomy. Notably, relatively little is known regarding bioenergetic costs of caudal autotomy in lizards, though key morphological differences exist between the original and regenerated tail that could alter the biochemistry and energetics. Therefore, we investigated lizard caudal biochemical content before and after regeneration in three gecko and one skink species. Specifically, we integrated biochemical and morphological analyses to quantify protein and lipid content in original and regenerated tails. All lizards lost significant body mass, mostly protein, due to autotomy and biochemical results indicated that original tails of all species contained a greater proportion of protein than lipid. Morphological analyses of two gecko species revealed interspecific differences in protein and lipid content of regenerated lizard tails. Results of this study contribute to our understanding of the biochemical consequences of a widespread predator evasion mechanism. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.

    Science.gov (United States)

    Garg, Rohini; Shankar, Rama; Thakkar, Bijal; Kudapa, Himabindu; Krishnamurthy, Lakshmanan; Mantri, Nitin; Varshney, Rajeev K; Bhatia, Sabhyata; Jain, Mukesh

    2016-01-13

    Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.

  13. Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters.

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    Guillaume Sapriel

    2009-10-01

    Full Text Available Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH(4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles.Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations.Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level to genomic (organization in clusters, dosage compensation by gene duplication, and by post-transcriptional regulation and spatial distribution of SIT proteins.

  14. Differential MicroRNA Analyses of Burkholderia pseudomallei- and Francisella tularensis-Exposed hPBMCs Reveal Potential Biomarkers

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    Regina Z. Cer

    2017-01-01

    Full Text Available Increasing evidence that microRNAs (miRNAs play important roles in the immune response against infectious agents suggests that miRNA might be exploitable as signatures of exposure to specific infectious agents. In order to identify potential early miRNA biomarkers of bacterial infections, human peripheral blood mononuclear cells (hPBMCs were exposed to two select agents, Burkholderia pseudomallei K96243 and Francisella tularensis SHU S4, as well as to the nonpathogenic control Escherichia coli DH5α. RNA samples were harvested at three early time points, 30, 60, and 120 minutes postexposure, then sequenced. RNAseq analyses identified 87 miRNAs to be differentially expressed (DE in a linear fashion. Of these, 31 miRNAs were tested using the miScript miRNA qPCR assay. Through RNAseq identification and qPCR validation, we identified differentially expressed miRNA species that may be involved in the early response to bacterial infections. Based upon its upregulation at early time points postexposure in two different individuals, hsa-mir-30c-5p is a miRNA species that could be studied further as a potential biomarker for exposure to these gram-negative intracellular pathogens. Gene ontology functional analyses demonstrated that programmed cell death is the first ranking biological process associated with miRNAs that are upregulated in F. tularensis-exposed hPBMCs.

  15. Structural and biochemical analyses of Microcystis aeruginosa O-acetylserine sulfhydrylases reveal a negative feedback regulation of cysteine biosynthesis.

    Science.gov (United States)

    Lu, Mo; Xu, Bo-Ying; Zhou, Kang; Cheng, Wang; Jiang, Yong-Liang; Chen, Yuxing; Zhou, Cong-Zhao

    2014-02-01

    O-acetylserine sulfhydrylase (OASS) catalyzes the final step of cysteine biosynthesis from O-acetylserine (OAS) and inorganic sulfide in plants and bacteria. Bioinformatics analyses combined with activity assays enabled us to annotate the two putative genes of Microcystis aeruginosa PCC 7806 to CysK1 and CysK2, which encode the two 75% sequence-identical OASS paralogs. Moreover, we solved the crystal structures of CysK1 at 2.30Ǻ and cystine-complexed CysK2 at 1.91Ǻ, revealing a quite similar overall structure that belongs to the family of fold-type II PLP-dependent enzymes. Structural comparison indicated a significant induced fit upon binding to the cystine, which occupies the binding site for the substrate OAS and blocks the product release tunnel. Subsequent enzymatic assays further confirmed that cystine is a competitive inhibitor of the substrate OAS. Moreover, multiple-sequence alignment revealed that the cystine-binding residues are highly conserved in all OASS proteins, suggesting that this auto-inhibition of cystine might be a universal mechanism of cysteine biosynthesis pathway. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus.

    Science.gov (United States)

    Lu, Kun; Peng, Liu; Zhang, Chao; Lu, Junhua; Yang, Bo; Xiao, Zhongchun; Liang, Ying; Xu, Xingfu; Qu, Cunmin; Zhang, Kai; Liu, Liezhao; Zhu, Qinlong; Fu, Minglian; Yuan, Xiaoyan; Li, Jiana

    2017-01-01

    Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties.

  17. Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola.

    Science.gov (United States)

    Raman, H; Raman, R; Coombes, N; Song, J; Prangnell, R; Bandaranayake, C; Tahira, R; Sundaramoorthi, V; Killian, A; Meng, J; Dennis, E S; Balasubramanian, S

    2016-06-01

    Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes. ©2015 The Authors. Plant, Cell & Environment published by JohnWiley & Sons Ltd.

  18. Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells.

    Science.gov (United States)

    Ross, Sarah H; Rollings, Christina; Anderson, Karen E; Hawkins, Phillip T; Stephens, Len R; Cantrell, Doreen A

    2016-09-20

    Interleukin-2 (IL-2) is a fundamental cytokine that controls proliferation and differentiation of T cells. Here, we used high-resolution mass spectrometry to generate a comprehensive and detailed map of IL-2 protein phosphorylations in cytotoxic T cells (CTL). The data revealed that Janus kinases (JAKs) couple IL-2 receptors to the coordinated phosphorylation of transcription factors, regulators of chromatin, mRNA translation, GTPases, vesicle trafficking, and the actin and microtubule cytoskeleton. We identified an IL-2-JAK-independent SRC family Tyr-kinase-controlled signaling network that regulates ∼10% of the CTL phosphoproteome, the production of phosphatidylinositol (3,4,5)-trisphosphate (PIP3), and the activity of the serine/threonine kinase AKT. These data reveal a signaling framework wherein IL-2-JAK-controlled pathways coordinate with IL-2-independent networks of kinase activity and provide a resource toward the further understanding of the networks of protein phosphorylation that program CTL fate. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Application of the ASP3D Computer Program to Unsteady Aerodynamic and Aeroelastic Analyses

    Science.gov (United States)

    Batina, John T.

    2006-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation - 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The paper presents unsteady aerodynamic and aeroelastic applications of ASP3D to assess the time dependent capability and demonstrate various features of the code.

  20. Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

    Science.gov (United States)

    Lieblein-Boff, Jacqueline C; Johnson, Elizabeth J; Kennedy, Adam D; Lai, Chron-Si; Kuchan, Matthew J

    2015-01-01

    Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510) were excluded. In addition, moderate correlations with xenobiotic relationships (2) or those driven by single outliers (3) were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

  1. Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

    Directory of Open Access Journals (Sweden)

    Jacqueline C Lieblein-Boff

    Full Text Available Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510 were excluded. In addition, moderate correlations with xenobiotic relationships (2 or those driven by single outliers (3 were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

  2. Introduction of the ASP3D Computer Program for Unsteady Aerodynamic and Aeroelastic Analyses

    Science.gov (United States)

    Batina, John T.

    2005-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The new ASP3D code is the result of a decade of developmental work on improvements to the small perturbation formulation, performed while the author was employed as a Senior Research Scientist in the Configuration Aerodynamics Branch at the NASA Langley Research Center. The ASP3D code is a significant improvement to the state-of-the-art for transonic aeroelastic analyses over the CAP-TSD code (Computational Aeroelasticity Program Transonic Small Disturbance), which was developed principally by the author in the mid-1980s. The author is in a unique position as the developer of both computer programs to compare, contrast, and ultimately make conclusions regarding the underlying formulations and utility of each code. The paper describes the salient features of the ASP3D code including the rationale for improvements in comparison with CAP-TSD. Numerous results are presented to demonstrate the ASP3D capability. The general conclusion is that the new ASP3D capability is superior to the older CAP-TSD code because of the myriad improvements developed and incorporated.

  3. Louisiana Barrier Island Comprehensive Monitoring (BICM) Program Summary Report: Data and Analyses 2006 through 2010

    Science.gov (United States)

    Kindinger, Jack G.; Buster, Noreen A.; Flocks, James G.; Bernier, Julie C.; Kulp, Mark A.

    2013-01-01

    The Barrier Island Comprehensive Monitoring (BICM) program was implemented under the Louisiana Coastal Area Science and Technology (LCA S&T) office as a component of the System Wide Assessment and Monitoring (SWAMP) program. The BICM project was developed by the State of Louisiana (Coastal Protection Restoration Authority [CPRA], formerly Department of Natural Resources [DNR]) to complement other Louisiana coastal monitoring programs such as the Coastwide Reference Monitoring System-Wetlands (CRMS-Wetlands) and was a collaborative research effort by CPRA, University of New Orleans (UNO), and the U.S. Geological Survey (USGS). The goal of the BICM program was to provide long-term data on the barrier islands of Louisiana that could be used to plan, design, evaluate, and maintain current and future barrier-island restoration projects. The BICM program used both historical and newly acquired (2006 to 2010) data to assess and monitor changes in the aerial and subaqueous extent of islands, habitat types, sediment texture and geotechnical properties, environmental processes, and vegetation composition. BICM datasets included aerial still and video photography (multiple time series) for shoreline positions, habitat mapping, and land loss; light detection and ranging (lidar) surveys for topographic elevations; single-beam and swath bathymetry; and sediment grab samples. Products produced using BICM data and analyses included (but were not limited to) storm-impact assessments, rate of shoreline and bathymetric change, shoreline-erosion and accretion maps, high-resolution elevation maps, coastal-shoreline and barrier-island habitat-classification maps, and coastal surficial-sediment characterization maps. Discussions in this report summarize the extensive data-collection efforts and present brief interpretive analyses for four coastal Louisiana geographic regions. In addition, several coastal-wide and topical themes were selected that integrate the data and analyses within a

  4. Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis

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    Couturier Marie

    2012-02-01

    Full Text Available Abstract Background Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemicellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation. Results In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases. Conclusion This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.

  5. Combination of transcriptomic and metabolomic analyses reveals a JAZ repressor in the jasmonate signaling pathway of Salvia miltiorrhiza

    Science.gov (United States)

    Ge, Qian; Zhang, Yuan; Hua, Wen-Ping; Wu, Yu-Cui; Jin, Xin-Xin; Song, Shuang-Hong; Wang, Zhe-Zhi

    2015-01-01

    Jasmonates (JAs) are plant-specific key signaling molecules that respond to various stimuli and are involved in the synthesis of secondary metabolites. However, little is known about the JA signal pathway, especially in economically significant medicinal plants. To determine the functions of novel genes that participate in the JA-mediated accumulation of secondary metabolites, we examined the metabolomic and transcriptomic signatures from Salvia miltiorrhiza. For the metabolome, 35 representative metabolites showing significant changes in rates of accumulation were extracted and identified. We also screened out 2131 differentially expressed unigenes, of which 30 were involeved in the phenolic secondary metabolic pathway, while 25 were in the JA biosynthesis and signal pathways. Among several MeJA-induced novel genes, SmJAZ8 was selected for detailed functional analysis. Transgenic plants over-expressing SmJAZ8 exhibited a JA-insensitive phenotype, suggesting that the gene is a transcriptional regulator in the JA signal pathway of S. miltiorrhiza. Furthermore, this transgenic tool revealed that JAZ genes have novel function in the constitutive accumulation of secondary metabolites. Based on these findings, we propose that the combined strategy of transcriptomic and metabolomic analyses is valuable for efficient discovery of novel genes in plants. PMID:26388160

  6. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

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    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  7. Boston children's hospital community asthma initiative: Five-year cost analyses of a home visiting program.

    Science.gov (United States)

    Bhaumik, Urmi; Sommer, Susan J; Giller-Leinwohl, Judith; Norris, Kerri; Tsopelas, Lindsay; Nethersole, Shari; Woods, Elizabeth R

    2017-03-01

    To evaluate the costs and benefits of the Boston Children's Hospital Community Asthma Initiative (CAI) through reduction of Emergency Department (ED) visits and hospitalizations for the full pilot-phase program participants. A cost-benefit analyses was conducted using hospital administrative data to determine an adjusted Return on Investment (ROI): on all 268 patients enrolled in the CAI program during the 33-month pilot program phase of CAI intervention between October 1, 2005 and June 30, 2008 using a comparison group of 818 patients from a similar cohort in neighboring ZIP codes without CAI intervention. Cost data through June 30, 2013 were used to examine cost changes and calculate an adjusted ROI over a 5-year post-intervention period. CAI patients had a cost reduction greater than the comparison group of $1,216 in Year 1 (P = 0.001), $1,320 in Year 2 (P management programs can decrease the incidence of costly hospitalizations and ED visits from asthma. An ROI of greater than one, as found in this cost analysis, supports the business case for the provision of community-based asthma services as part of patient-centered medical homes and Accountable Care Organizations.

  8. Molecular analyses reveal two geographic and genetic lineages for tapeworms, Taenia solium and Taenia saginata, from Ecuador using mitochondrial DNA.

    Science.gov (United States)

    Solano, Danilo; Navarro, Juan Carlos; León-Reyes, Antonio; Benítez-Ortiz, Washington; Rodríguez-Hidalgo, Richar

    2016-12-01

    Tapeworms Taenia solium and Taenia saginata are the causative agents of taeniasis/cysticercosis. These are diseases with high medical and veterinary importance due to their impact on public health and rural economy in tropical countries. The re-emergence of T. solium as a result of human migration, the economic burden affecting livestock industry, and the large variability of symptoms in several human cysticercosis, encourage studies on genetic diversity, and the identification of these parasites with molecular phylogenetic tools. Samples collected from the Ecuadorian provinces: Loja, Guayas, Manabí, Tungurahua (South), and Imbabura, Pichincha (North) from 2000 to 2012 were performed under Maximum Parsimony analyses and haplotype networks using partial sequences of mitochondrial DNA, cytochrome oxidase subunit I (COI) and NADH subunit I (NDI), from Genbank and own sequences of Taenia solium and Taenia saginata from Ecuador. Both species have shown reciprocal monophyly, which confirms its molecular taxonomic identity. The COI and NDI genes results suggest phylogenetic structure for both parasite species from south and north of Ecuador. In T. solium, both genes gene revealed greater geographic structure, whereas in T. saginata, the variability for both genes was low. In conclusion, COI haplotype networks of T. solium suggest two geographical events in the introduction of this species in Ecuador (African and Asian lineages) and occurring sympatric, probably through the most common routes of maritime trade between the XV-XIX centuries. Moreover, the evidence of two NDI geographical lineages in T. solium from the north (province of Imbabura) and the south (province of Loja) of Ecuador derivate from a common Indian ancestor open new approaches for studies on genetic populations and eco-epidemiology. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

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    Ana Carolina Vieira Araujo

    2016-10-01

    Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

  10. Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.

    Science.gov (United States)

    Ulaganathan, ThirumalaiSelvi; Helbert, William; Kopel, Moran; Banin, Ehud; Cygler, Miroslaw

    2018-01-30

    Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

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    Jason Carnes

    2015-01-01

    Full Text Available Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA. In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  12. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

    Science.gov (United States)

    Carnes, Jason; Anupama, Atashi; Balmer, Oliver; Jackson, Andrew; Lewis, Michael; Brown, Rob; Cestari, Igor; Desquesnes, Marc; Gendrin, Claire; Hertz-Fowler, Christiane; Imamura, Hideo; Ivens, Alasdair; Kořený, Luděk; Lai, De-Hua; MacLeod, Annette; McDermott, Suzanne M; Merritt, Chris; Monnerat, Severine; Moon, Wonjong; Myler, Peter; Phan, Isabelle; Ramasamy, Gowthaman; Sivam, Dhileep; Lun, Zhao-Rong; Lukeš, Julius; Stuart, Ken; Schnaufer, Achim

    2015-01-01

    Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

  13. Correlation analyses revealed global microRNA-mRNA expression associations in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Wang, Lan; Zhu, Jiang; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Xiao-Wei; Xia, Wei; Xie, Fang-Fei; He, Pei; Bing, Peng-Fei; Qiu, Ying-Hua; Lin, Xiang; Lu, Xin; Zhang, Lei; Yi, Neng-Jun; Zhang, Yong-Hong; Lei, Shu-Feng

    2017-09-06

    MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study. We predicted and achieved 861 miRNA-mRNA pairs (65 miRNAs, 412 mRNAs) using multiple bioinformatics programs, and found global negative miRNA-mRNA correlations in PBMC from all 46 study subjects. Among the 861 pairs of correlations, 19.5% were significant (P correlation network was complex and highlighted key miRNAs/genes in PBMC. Some miRNAs, such as hsa-miR-29a, hsa-miR-148a, regulate a cluster of target genes. Some genes, e.g., TNRC6A, are regulated by multiple miRNAs. The identified genes tend to be enriched in molecular functions of DNA and RNA binding, and biological processes such as protein transport, regulation of translation and chromatin modification. The results provided a global view of the miRNA-mRNA expression correlation profile in human PBMCs, which would facilitate in-depth investigation of biological functions of key miRNAs/mRNAs and better understanding of the pathogenesis underlying PBMC-related diseases.

  14. Trophic relationships on a fucoid shore in south-western Iceland as revealed by stable isotope analyses, laboratory experiments, field observations and gut analyses

    Science.gov (United States)

    Steinarsdóttir, M. B.; Ingólfsson, A.; Ólafsson, E.

    2009-04-01

    Rocky shores in the North Atlantic are known for their zonation patterns of both algae and animals, which can be expected to greatly affect food availability to consumers at different height levels on the shore. We tested the hypothesis that consumers would feed on the most abundant suitable food source in their surroundings. In total 36 species/taxa of common primary producers and consumers were sampled for stable isotope analyses from a sheltered fucoid shore at Hvassahraun in south-western Iceland. A selection of these species was also collected seasonally and from different height levels. Feeding experiments, field observations and gut analyses were also conducted. Our results were in good overall agreement with pre-existing knowledge of trophic relationships in the rocky intertidal. Consumers often appeared to be assimilating carbon and nitrogen from the most common diet in their immediate surroundings. The predator Nucella lapillus was thus feeding on different prey at different height levels in accordance with different densities of prey species. When tested in the laboratory, individuals taken from low on the shore would ignore the gastropod Littorina obtusata, uncommon at that height level, even when starved, while individuals from mid-shore readily ate the gastropod. This indicated that some kind of learned behaviour was involved. There were, however, important exceptions, most noteworthy the relatively small contribution to herbivores, both slow moving (the gastropod L. obtusata) and fast moving (the isopod Idotea granulosa and the amphipod Gammarus obtusatus) of the dominant alga at this site, Ascophyllum nodosum. The recent colonizer Fucus serratus seemed to be favoured. Selective feeding was indicated both by isotope signatures as well as by results of feeding experiments. Seasonal migrations of both slow and fast moving species could partly explain patterns observed.

  15. Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.

    Directory of Open Access Journals (Sweden)

    Marianna Niemi

    Full Text Available Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies.Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples, Medieval (14, and Post-Medieval (26 periods were investigated by sequencing 667 base pairs (bp from the mitochondrial DNA (mtDNA and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes genetic diversity in ancient cattle (45 samples with modern cattle populations in Europe and Asia (2094 samples revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples.The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.

  16. Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

    DEFF Research Database (Denmark)

    Brok, Jesper; Thorlund, Kristian; Gluud, Christian

    2008-01-01

    To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries analogous...

  17. Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

    DEFF Research Database (Denmark)

    Brok, J.; Thorlund, K.; Gluud, C.

    2008-01-01

    OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA......(30%)), 15% (TSA(15%)), or a risk reduction suggested by low-bias risk trials of the meta-analysis corrected for heterogeneity (TSA(LBHIS)). RESULTS: A total of 174 meta-analyses were eligible; 79 out of 174 (45%) meta-analyses were statistically significant (P

  18. Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

    National Research Council Canada - National Science Library

    da Silva, Danielle Costenaro; da Silveira Falavigna, Vítor; Fasoli, Marianna; Buffon, Vanessa; Porto, Diogo Denardi; Pappas, Jr, Georgios Joannis; Pezzotti, Mario; Pasquali, Giancarlo; Revers, Luís Fernando

    2016-01-01

    .... Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses...

  19. TITAN: a computer program for accident occurrence frequency analyses by component Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Nomura, Yasushi [Department of Fuel Cycle Safety Research, Nuclear Safety Research Center, Tokai Research Establishment, Japan Atomic Energy Research Institute, Tokai, Ibaraki (Japan); Tamaki, Hitoshi [Department of Safety Research Technical Support, Tokai Research Establishment, Japan Atomic Energy Research Institute, Tokai, Ibaraki (Japan); Kanai, Shigeru [Fuji Research Institute Corporation, Tokyo (Japan)

    2000-04-01

    In a plant system consisting of complex equipments and components for a reprocessing facility, there might be grace time between an initiating event and a resultant serious accident, allowing operating personnel to take remedial actions, thus, terminating the ongoing accident sequence. A component Monte Carlo simulation computer program TITAN has been developed to analyze such a complex reliability model including the grace time without any difficulty to obtain an accident occurrence frequency. Firstly, basic methods for the component Monte Carlo simulation is introduced to obtain an accident occurrence frequency, and then, the basic performance such as precision, convergence, and parallelization of calculation, is shown through calculation of a prototype accident sequence model. As an example to illustrate applicability to a real scale plant model, a red oil explosion in a German reprocessing plant model is simulated to show that TITAN can give an accident occurrence frequency with relatively good accuracy. Moreover, results of uncertainty analyses by TITAN are rendered to show another performance, and a proposal is made for introducing of a new input-data format to adapt the component Monte Carlo simulation. The present paper describes the calculational method, performance, applicability to a real scale, and new proposal for the TITAN code. In the Appendixes, a conventional analytical method is shown to avoid complex and laborious calculation to obtain a strict solution of accident occurrence frequency, compared with Monte Carlo method. The user's manual and the list/structure of program are also contained in the Appendixes to facilitate TITAN computer program usage. (author)

  20. Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells

    National Research Council Canada - National Science Library

    Ross, Sarah H; Rollings, Christina; Anderson, Karen E; Hawkins, Phillip T; Stephens, Len R; Cantrell, Doreen A

    2016-01-01

    ...). The data revealed that Janus kinases (JAKs) couple IL-2 receptors to the coordinated phosphorylation of transcription factors, regulators of chromatin, mRNA translation, GTPases, vesicle trafficking, and the actin and microtubule cytoskeleton...

  1. Novel autism subtype-dependent genetic variants are revealed by quantitative trait and subphenotype association analyses of published GWAS data.

    Science.gov (United States)

    Hu, Valerie W; Addington, Anjene; Hyman, Alexander

    2011-04-27

    The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders.

  2. Novel autism subtype-dependent genetic variants are revealed by quantitative trait and subphenotype association analyses of published GWAS data.

    Directory of Open Access Journals (Sweden)

    Valerie W Hu

    Full Text Available The heterogeneity of symptoms associated with autism spectrum disorders (ASDs has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs. The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL, were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders.

  3. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    , Foster City, CA, USA). Representative sequences have been deposited in GenBank, with accession numbers JN398671- JN399010. Data analyses DNA sequences were edited with the program BioEdit (version 7.0.1, Hall 1999) and aligned using the Clustal.... Molecular diversity indices, such as transitions, transversions, substitutions, and indels were obtained using program Arlequin version 3.11 (Excoffier et al. 2005). The aligned sequences were used to analyze the population structure and genetic variation...

  4. High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle

    Science.gov (United States)

    Selection Signatures (SS) assessed through analysis of genomic data are being widely studied to discover population specific regions selected via artificial or natural selection. Different methodologies have been proposed for these analyses, each having specific limitations as to the age of the sele...

  5. Complementary transcriptomic and proteomic analyses of a chlorophyll-deficient tea plant cultivar reveal multiple metabolic pathway changes.

    Science.gov (United States)

    Wang, Lu; Cao, Hongli; Chen, Changsong; Yue, Chuan; Hao, Xinyuan; Yang, Yajun; Wang, Xinchao

    2016-01-01

    To uncover the mechanisms that underlie the chlorina phenotype of the tea plant, this study employs morphological, biochemical, transcriptomic, and iTRAQ-based proteomic analyses to compare the green tea cultivar LJ43 and the yellow-leaf tea cultivar ZH1. ZH1 exhibited the chlorina phenotype, with significantly decreased chlorophyll content and abnormal chloroplast development compared with LJ43. ZH1 also displayed higher theanine and free amino acid content and lower carotenoid and catechin content. Microarray and iTRAQ analyses indicated that the differentially expressed genes and proteins could be mapped to the following pathways: 'phenylpropanoid biosynthesis,' 'glutathione metabolism,' 'phenylalanine metabolism,' 'photosynthesis,' and 'flavonoid biosynthesis.' Altered gene and protein levels in these pathways may account for the increased amino acid content and reduced chlorophyll and flavonoid content of ZH1. Altogether, this study combines transcriptomic and proteomic approaches to better understand the mechanisms responsible for the chlorina phenotype. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

    OpenAIRE

    Ray, Jessica L.; Althammer, Julia; Skaar, Katrine S; Simonelli, Paolo; Larsen, Aud; Stoecker, Diane; Sazhin, Andrey; Umer Z. Ijaz; Quince, Christopher; Nejstgaard, Jens C.; Frischer, Marc; Pohnert, Georg; Troedsson, Christofer

    2016-01-01

    In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (

  7. Longitudinal Analyses of Expressive Language Development Reveal Two Distinct Language Profiles among Young Children with Autism Spectrum Disorders

    OpenAIRE

    Tek, Saime; Mesite, Laura; Fein, Deborah; Naigles, Letitia

    2014-01-01

    Although children with ASD show significant variation in language skills, research on what type(s) of language profiles they demonstrate has been limited. Using growth-curve analyses, we investigated how different groups of young children with ASD show increases in the size of their lexicon, morpho-syntactic production as measured by Brown’s 14 grammatical morphemes, and wh-question complexity, compared to TD children, across six time points. Children with ASD who had higher verbal skills wer...

  8. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

    Directory of Open Access Journals (Sweden)

    Frederick H. Sheldon

    2013-03-01

    Full Text Available Insertion/deletion (indel mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP and a simple maximum likelihood (ML framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

  9. Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

    Directory of Open Access Journals (Sweden)

    Clémentine Delan-Forino

    2014-01-01

    Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

  10. Culture-independent analyses reveal novel Anaerolineaceae as abundant primary fermenters in anaerobic digesters treating waste activated sludge

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; Dueholm, Morten Simonsen

    2017-01-01

    primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms...... to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within...

  11. Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

    Science.gov (United States)

    Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

    2017-08-31

    The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

  12. Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression.

    Science.gov (United States)

    Xu, Fan; Yang, Jing; Chen, Jin; Wu, Qingyuan; Gong, Wei; Zhang, Jianguo; Shao, Weihua; Mu, Jun; Yang, Deyu; Yang, Yongtao; Li, Zhiwei; Xie, Peng

    2015-04-03

    Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more responsive to current pharmacological treatment and aid in separating out depressed patients in which current antidepressants are not particularly effective. Differential co-expression analysis (DCEA) and differential regulation analysis (DRA) were applied to compare the transcriptomic profiles of peripheral blood lymphocytes from patients with two depressive subtypes: major depressive disorder (MDD) and subsyndromal symptomatic depression (SSD). Six differentially regulated genes (DRGs) (FOSL1, SRF, JUN, TFAP4, SOX9, and HLF) and 16 transcription factor-to-target differentially co-expressed gene links or pairs (TF2target DCLs) appear to be the key differential factors in MDD; in contrast, one DRG (PATZ1) and eight TF2target DCLs appear to be the key differential factors in SSD. There was no overlap between the MDD target genes and SSD target genes. Venlafaxine (Efexor™, Effexor™) appears to have a significant effect on the gene expression profile of MDD patients but no significant effect on the gene expression profile of SSD patients. DCEA and DRA revealed no apparent similarities between the differential regulatory processes underlying MDD and SSD. This bioinformatic analysis may provide novel insights that can support future antidepressant R&D efforts.

  13. Multivariate analyses reveal a new assemblage of diverse and small archosauriforms (Reptilia, Diapsida) from the Upper Triassic of India

    Science.gov (United States)

    Shafi Bhat, Mohd; Ray, Sanghamitra; Mohan Datta, Pradipendra

    2017-04-01

    The study is based on a large collection of vertebrate microfossils collected from the Upper Triassic Tiki Formation of the Rewa Gondwana basin of India, which is a mud-dominated fluvial succession. About 8600 kg of mudrocks from the Tiki Formation were screen washed to yield 1865 vertebrate microfossils, of which 67% are isolated teeth. Of these, there are about 450 well-preserved teeth, which are leaf-shaped, slightly recurved and have subtriangular crowns with expanded and asymmetric bases, and distinct denticles both on the posterior or anterior carinae. The morphology of these teeth suggests that these belong to Archosauriformes (Heckert, 2004; Irmis et al., 2007). Since the teeth were found isolated, without being associated with any other skeletal elements, it is not possible to ascertain their taxonomic position up to the generic and species level. However, based on their distinct dental attributes, twelve morphotypes are identified, of which five show similarity with the teeth of the basal saurischian dinosaurs. Principal Component and Canonical Variate analyses (PCA and CVA) are performed on these isolated teeth to evaluate the differentiation of the specimens based on the variance of their variables and to assess the consistency of identification by qualitative and quantitative methods (Hammer and Harper, 2006). PCA and CVA are applied to the variance-covariance matrix of the logarithmically transformed variables, the latter including six measured dimensions characterizing the different crown proportions. Since the first three principal components (PCs) account for more than 98% of the total variance, PC4 is discarded. Principal component scores are plotted on PC 1 and PC 2, and PC 2 and PC 3 to show the scatter of the archosauriform teeth examined. Although distinct clustering of specimens belonging to the different morphotypes is seen, there is considerable overlapping as represented by the convex hull polygons. The quantitative analyses show that many

  14. Structural features of helical secondary structures and leucine-rich repeat superhelix in proteins as revealed by HELFIT analyses

    Science.gov (United States)

    Matsushima, Norio; Enkhbayar, Purevjav

    2012-09-01

    The HELFIT program determines the helical parameters - pitch, residues per turn (n), radius, and handedness - and p = rmsd / (N - 1)1/2 estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix or superhelix and "N" is helix/superhelix length. Helical secondary structures - α-helix and 310-helix - and solenoid structures of leucine rich repeats (LRRs) in The Protein Data Bank (PDB) were analyzed by the HELFIT program. The results indicate that the definition of 310-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 310-helix. The 310-helices observed in proteins are better referred to parahelices. A modification of the α-helix, termed the ω-helix, that has four residues in one turn of a helix, has been identified only in synthetic polypeptides. The results also demonstrate that the right-handed ω-helix occur really in proteins. The solenoid structures of LRR domains in brasinosteroid insensitive 1 (BRI1), internalin J (InlJ), and internalin A (InlA) are well represented by a superhelix rather than by a circular arc.

  15. Longitudinal analyses of expressive language development reveal two distinct language profiles among young children with autism spectrum disorders.

    Science.gov (United States)

    Tek, Saime; Mesite, Laura; Fein, Deborah; Naigles, Letitia

    2014-01-01

    Although children with autism spectrum disorders (ASD) show significant variation in language skills, research on what type(s) of language profiles they demonstrate has been limited. Using growth-curve analyses, we investigated how different groups of young children with ASD show increases in the size of their lexicon, morpho-syntactic production as measured by Brown's 14 grammatical morphemes, and wh-question complexity, compared to TD children, across six time points. Children with ASD who had higher verbal skills were comparable to TD children on most language measures, whereas the children with ASD who had low verbal skills had flatter trajectories in most language measures. Thus, two distinct language profiles emerged for children with ASD.

  16. Novel evolutionary lineages revealed in the Chaetothyriales (fungi based on multigene phylogenetic analyses and comparison of its secondary structure.

    Directory of Open Access Journals (Sweden)

    Martina Réblová

    Full Text Available Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS, large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA, β-tubulin, DNA replication licensing factor (mcm7 and second largest subunit of RNA polymerase II (rpb2. Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.

  17. Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Yanlong Wang

    Full Text Available We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli, Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology and KEGG (Kyoto encyclopedia of genes and genomes enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species scavenging, membrane proteins and ABC (ATP binding cassette transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

  18. Association analyses of porcine SERPINE1 reveal sex-specific effects on muscling, growth, fat accretion and meat quality.

    Science.gov (United States)

    Weisz, F; Bartenschlager, H; Knoll, A; Mileham, A; Deeb, N; Geldermann, H; Cepica, S

    2012-10-01

    The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM_213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F(2) population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

  19. Phylogenetic and morphologic analyses of a coastal fish reveals a marine biogeographic break of terrestrial origin in the southern Caribbean.

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    Ricardo Betancur-R

    Full Text Available BACKGROUND: Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world. METHODOLOGY/PRINCIPAL FINDINGS: Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a approximately 2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by approximately 150 km at the Santa Marta Massif (SMM in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated approximately 0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at approximately 0.78 my. MAIN CONCLUSIONS/SIGNIFICANCE: Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of

  20. Phylogenetic and Morphologic Analyses of a Coastal Fish Reveals a Marine Biogeographic Break of Terrestrial Origin in the Southern Caribbean

    Science.gov (United States)

    Betancur-R, Ricardo; Acero P., Arturo; Duque-Caro, Hermann; Santos, Scott R.

    2010-01-01

    Background Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world. Methodology/Principal Findings Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a ∼2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by ∼150 km at the Santa Marta Massif (SMM) in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated ∼0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at ∼0.78 my. Main Conclusions/Significance Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of additional Southern Caribbean taxa, particularly those with

  1. Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

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    Rémy Nicolle

    2017-11-01

    Full Text Available Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively. Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.

  2. Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling

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    Sylvestre Chea

    2016-02-01

    Full Text Available T and innate lymphoid cells (ILCs share some aspects of their developmental programs. However, although Notch signaling is strictly required for T cell development, it is dispensable for fetal ILC development. Constitutive activation of Notch signaling, at the common lymphoid progenitor stage, drives T cell development and abrogates ILC development by preventing Id2 expression. By combining single-cell transcriptomics and clonal culture strategies, we characterize two heterogeneous α4β7-expressing lymphoid progenitor compartments. αLP1 (Flt3+ still retains T cell potential and comprises the global ILC progenitor, while αLP2 (Flt3− consists of ILC precursors that are primed toward the different ILC lineages. Only a subset of αLP2 precursors is sensitive to Notch signaling required for their proliferation. Our study identifies, in a refined manner, the diversity of transitional stages of ILC development, their transcriptional signatures, and their differential dependence on Notch signaling.

  3. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses.

    Science.gov (United States)

    Magyari, Eniko K; Major, Agnes; Bálint, Miklós; Nédli, Judit; Braun, Mihály; Rácz, István; Parducci, Laura

    2011-03-10

    Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci.Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient

  4. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

    Directory of Open Access Journals (Sweden)

    Braun Mihály

    2011-03-01

    Full Text Available Abstract Background Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR record for spruce that helped us to infer changes in population size at this site. Results We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP and three bottlenecks (around 9180, 7200 and 2200 cal yr BP, likely triggered by climatic change and human impact. Conclusion Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher

  5. Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

    Science.gov (United States)

    McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

    2017-01-01

    Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

  6. Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development.

    Science.gov (United States)

    da Silva, Danielle Costenaro; da Silveira Falavigna, Vítor; Fasoli, Marianna; Buffon, Vanessa; Porto, Diogo Denardi; Pappas, Georgios Joannis; Pezzotti, Mario; Pasquali, Giancarlo; Revers, Luís Fernando

    2016-01-01

    The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.

  7. Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

    Science.gov (United States)

    Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Razafsky, David S.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

    2012-01-01

    Cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. However, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. Here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus Neurospora crassa, in which dynein is nonessential. Interestingly, our studies show that these mutations segregate into five different classes based on the in vivo localization of the mutated dynein motors. Furthermore, we have determined that the different classes of dynein mutations alter vesicle trafficking, microtubule organization, and nuclear distribution in distinct ways and require dynactin to different extents. In addition, biochemical analyses of dynein from one mutant strain show a strong correlation between its in vitro biochemical properties and the aberrant intracellular function of that altered dynein. When the mutations were mapped to the published dynein crystal structure, we found that the three-dimensional structural locations of the heavy chain mutations were linked to particular classes of altered dynein functions observed in cells. Together, our data indicate that the five classes of dynein mutations represent the entrapment of dynein at five separate points in the dynein mechanochemical and transport cycles. We have developed N. crassa as a model system where we can dissect the complexities of dynein structure, function, and interaction with other proteins with genetic, biochemical, and cell biological studies. PMID:22649085

  8. Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

    Science.gov (United States)

    Lee, Hong-Won; Kyung, Taeyoon; Yoo, Janghyun; Kim, Tackhoon; Chung, Chaeuk; Ryu, Ji Young; Lee, Hanki; Park, Kihyun; Lee, Sangkyu; Jones, Walton D.; Lim, Dae-Sik; Hyeon, Changbong; Do Heo, Won; Yoon, Tae-Young

    2013-01-01

    Co-immunoprecipitation (co-IP) has become a standard technique, but its protein-band output provides only static, qualitative information about protein–protein interactions. Here we demonstrate a real-time single-molecule co-IP technique that generates real-time videos of individual protein–protein interactions as they occur in unpurified cell extracts. By analysing single Ras–Raf interactions with a 50-ms time resolution, we have observed transient intermediates of the protein–protein interaction and determined all the essential kinetic rates. Using this technique, we have quantified the active fraction of native Ras proteins in xenograft tumours, normal tissue and cancer cell lines. We demonstrate that the oncogenic Ras mutations selectively increase the active-Ras fraction by one order of magnitude, without affecting total Ras levels or single-molecule signalling kinetics. Our approach allows us to probe the previously hidden, dynamic aspects of weak protein–protein interactions. It also suggests a path forward towards precision molecular diagnostics at the protein–protein interaction level. PMID:23422673

  9. Multilocus sequence analyses reveal extensive diversity and multiple origins of fluconazole resistance in Candida tropicalis from tropical China.

    Science.gov (United States)

    Wu, Jin-Yan; Guo, Hong; Wang, Hua-Min; Yi, Guo-Hui; Zhou, Li-Min; He, Xiao-Wen; Zhang, Ying; Xu, Jianping

    2017-02-10

    Candida tropicalis is among the most prevalent human pathogenic yeast species, second only to C. albicans in certain geographic regions such as East Asia and Brazil. However, compared to C. albicans, relatively little is known about the patterns of genetic variation in C. tropicalis. This study analyzed the genetic diversity and relationships among isolates of C. tropicalis from the southern Chinese island of Hainan. A total of 116 isolates were obtained from seven geographic regions located across the Island. For each isolate, a total of 2677 bp from six gene loci were sequenced and 79 (2.96%) polymorphic nucleotide sites were found in our sample. Comparisons with strains reported from other parts of the world identified significant novel diversities in Hainan, including an average of six novel sequences (with a range 1 to 14) per locus and 80 novel diploid sequence types. Most of the genetic variation was found within individual strains and there was abundant evidence for gene flow among the seven geographic locations within Hainan. Interestingly, our analyses identified no significant correlation between the diploid sequence types at the six loci and fluconazole susceptibility, consistent with multiple origins of fluconazole resistance in the Hainan population of C. tropicalis.

  10. Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China

    KAUST Repository

    Abd El Ghany, Moataz

    2016-05-25

    Human infections with Salmonella enterica subspecies enterica serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14 Salmonella Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of S. Senftenberg, designated SC1 and SC2, harboring variations in Salmonella pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures. Although the two variants shared the same serotype, the SC2 isolates of sequence type 14 (ST14) harbored intact SPI-1 and -2 and hence were characterized by possessing efficient invasion capabilities. In contrast, the SC1 isolates had structural deletion patterns in both SPI-1 and -2 that correlated with an impaired capacity to invade cultured human cells and also the year of their isolation. These atypical SC1 isolates also lacked the capacity to produce hydrogen sulfide. These findings highlight the emergence of atypical Salmonella Senftenberg variants in China and provide genetic validation that variants lacking SPI-1 and regions of SPI-2, which leads to impaired invasion capacity, can still cause clinical disease. These data have identified an emerging public health concern and highlight the need to strengthen surveillance to detect the prevalence and transmission of nontyphoidal Salmonella species.

  11. Folivory elicits a strong defense reaction in Catharanthus roseus: metabolomic and transcriptomic analyses reveal distinct local and systemic responses

    Science.gov (United States)

    Dugé de Bernonville, Thomas; Carqueijeiro, Inês; Lanoue, Arnaud; Lafontaine, Florent; Sánchez Bel, Paloma; Liesecke, Franziska; Musset, Karine; Oudin, Audrey; Glévarec, Gaëlle; Pichon, Olivier; Besseau, Sébastien; Clastre, Marc; St-Pierre, Benoit; Flors, Victor; Maury, Stéphane; Huguet, Elisabeth; O’Connor, Sarah E.; Courdavault, Vincent

    2017-01-01

    Plants deploy distinct secondary metabolisms to cope with environment pressure and to face bio-aggressors notably through the production of biologically active alkaloids. This metabolism-type is particularly elaborated in Catharanthus roseus that synthesizes more than a hundred different monoterpene indole alkaloids (MIAs). While the characterization of their biosynthetic pathway now reaches completion, still little is known about the role of MIAs during biotic attacks. As a consequence, we developed a new plant/herbivore interaction system by challenging C. roseus leaves with Manduca sexta larvae. Transcriptomic and metabolic analyses demonstrated that C. roseus respond to folivory by both local and systemic processes relying on the activation of specific gene sets and biosynthesis of distinct MIAs following jasmonate production. While a huge local accumulation of strictosidine was monitored in attacked leaves that could repel caterpillars through its protein reticulation properties, newly developed leaves displayed an increased biosynthesis of the toxic strictosidine-derived MIAs, vindoline and catharanthine, produced by up-regulation of MIA biosynthetic genes. In this context, leaf consumption resulted in a rapid death of caterpillars that could be linked to the MIA dimerization observed in intestinal tracts. Furthermore, this study also highlights the overall transcriptomic control of the plant defense processes occurring during herbivory. PMID:28094274

  12. Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis).

    Science.gov (United States)

    Ali, Mohammed; Li, Penghui; She, Guangbiao; Chen, Daofu; Wan, Xiaochun; Zhao, Jian

    2017-11-22

    A large number of terpenoid compounds have been extracted from different tissues of S. officinalis. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 6.6 Gb of raw data were generated from the transcriptome of S. officinalis leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 21 million, comprising 98 million of high-quality nucleotide bases. 48,671 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis. We identified 135 unigenes that are putatively involved in terpenoid metabolism, including 70 mevalonate and methyl-erythritol phosphate pathways, terpenoid backbone biosynthesis genes, and 65 terpene synthase genes. Moreover, five terpene synthase genes were studied for their functions in terpenoid biosynthesis by using transgenic tobacco; most transgenic tobacco plants expressing these terpene synthetic genes produced increased amounts of terpenoids compared with wild-type control. The combined data analyses from the transcriptome and metabolome provide new insights into our understanding of the complex metabolic genes in terpenoid-rich sage, and our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. officinalis.

  13. Transcriptome and proteome analyses reveal complex mechanisms of reproductive diapause in the two-spotted spider mite, Tetranychus urticae.

    Science.gov (United States)

    Zhao, J-Y; Zhao, X-T; Sun, J-T; Zou, L-F; Yang, S-X; Han, X; Zhu, W-C; Yin, Q; Hong, X-Y

    2017-04-01

    Although a variety of factors underlying diapause have been identified in arthropods and other organisms, the molecular mechanisms regulating diapause are still largely unknown. Here, to better understand this process, we examined diapause-associated genes in the two-spotted spider mite, Tetranychus urticae, by comparing the transcriptomes and proteomes of early diapausing and reproductive adult females. Amongst genes underlying diapause revealed by the transcriptomic and proteomic data sets, we described the noticeable change in Ca2+ -associated genes, including 65 Ca2+ -binding protein genes and 23 Ca2+ transporter genes, indicating that Ca2+ signalling has a substantial role in diapause regulation. Other interesting changes in diapause included up-regulation of (1) glutamate receptors that may be involved in synaptic plasticity changes, (2) genes involved in cytoskeletal reorganization including genes encoding each of the components of thick and thin filaments, tubulin and members of integrin signalling and (3) genes involved in anaerobic energy metabolism, which reflects a shift to anaerobic energy metabolism in early diapausing mites. © 2016 The Royal Entomological Society.

  14. Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations

    Directory of Open Access Journals (Sweden)

    Beena Mary Kadakkuzha

    2015-03-01

    Full Text Available Despite the importance of the long noncoding RNAs (lncRNAs in regulating biological functions, the expression profiles of lncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and prefrontal cortex (PFC, the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2,759 lncRNAs and 17,859 mRNAs in the hippocampus and 2561 lncRNAs and 17,464 mRNAs expressed in the PFC. The lncRNAs identified correspond to ~14% of the transcriptome of the hippocampus and PFC and ~70% of the lncRNAs annotated in the mouse genome (NCBIM37 and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that few of the tested lncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic lncRNA expression signatures. These results reveal an unexpected complexity of the lncRNA expression in the mouse brain.

  15. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection

    Directory of Open Access Journals (Sweden)

    Dongxu Xing

    2017-02-01

    Full Text Available The silkworm Bombyx mori is an economically important species. White muscardine caused by Beauveria bassiana is the main fungal disease in sericulture, and understanding the silkworm responses to B. bassiana infection is of particular interest. Herein, we investigated the molecular mechanisms underlying these responses in two silkworm strains Haoyue (HY, sensitive to B. bassiana and Kang 8 (K8, resistant to B. bassiana using an RNA-seq approach. For each strain, three biological replicates for immersion treatment, two replicates for injection treatment and three untreated controls were collected to generate 16 libraries for sequencing. Differentially expressed genes (DEGs between treated samples and untreated controls, and between the two silkworm strains, were identified. DEGs and the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG pathways of the two strains exhibited an obvious difference. Several genes encoding cuticle proteins, serine proteinase inhibitors (SPI and antimicrobial peptides (AMP and the drug metabolism pathway involved in toxin detoxification were considered to be related to the resistance of K8 to B. bassiana. These results revealed insight into the resistance and susceptibility of two silkworm strains against B. bassiana infection and provided a roadmap for silkworm molecular breeding to enhance its resistance to B. bassiana.

  16. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection.

    Science.gov (United States)

    Xing, Dongxu; Yang, Qiong; Jiang, Liang; Li, Qingrong; Xiao, Yang; Ye, Mingqiang; Xia, Qingyou

    2017-02-10

    The silkworm Bombyx mori is an economically important species. White muscardine caused by Beauveria bassiana is the main fungal disease in sericulture, and understanding the silkworm responses to B. bassiana infection is of particular interest. Herein, we investigated the molecular mechanisms underlying these responses in two silkworm strains Haoyue (HY, sensitive to B. bassiana) and Kang 8 (K8, resistant to B. bassiana) using an RNA-seq approach. For each strain, three biological replicates for immersion treatment, two replicates for injection treatment and three untreated controls were collected to generate 16 libraries for sequencing. Differentially expressed genes (DEGs) between treated samples and untreated controls, and between the two silkworm strains, were identified. DEGs and the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the two strains exhibited an obvious difference. Several genes encoding cuticle proteins, serine proteinase inhibitors (SPI) and antimicrobial peptides (AMP) and the drug metabolism pathway involved in toxin detoxification were considered to be related to the resistance of K8 to B. bassiana. These results revealed insight into the resistance and susceptibility of two silkworm strains against B. bassiana infection and provided a roadmap for silkworm molecular breeding to enhance its resistance to B. bassiana.

  17. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Directory of Open Access Journals (Sweden)

    Ayaka Yamamuro

    Full Text Available Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2 (based on the projected area of the anode. In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  18. Combined transcriptome and metabolome analyses of metformin effects reveal novel links between metabolic networks in steroidogenic systems.

    Science.gov (United States)

    Udhane, Sameer S; Legeza, Balazs; Marti, Nesa; Hertig, Damian; Diserens, Gaëlle; Nuoffer, Jean-Marc; Vermathen, Peter; Flück, Christa E

    2017-08-17

    Metformin is an antidiabetic drug, which inhibits mitochondrial respiratory-chain-complex I and thereby seems to affect the cellular metabolism in many ways. It is also used for the treatment of the polycystic ovary syndrome (PCOS), the most common endocrine disorder in women. In addition, metformin possesses antineoplastic properties. Although metformin promotes insulin-sensitivity and ameliorates reproductive abnormalities in PCOS, its exact mechanisms of action remain elusive. Therefore, we studied the transcriptome and the metabolome of metformin in human adrenal H295R cells. Microarray analysis revealed changes in 693 genes after metformin treatment. Using high resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS-NMR), we determined 38 intracellular metabolites. With bioinformatic tools we created an integrated pathway analysis to understand different intracellular processes targeted by metformin. Combined metabolomics and transcriptomics data analysis showed that metformin affects a broad range of cellular processes centered on the mitochondrium. Data confirmed several known effects of metformin on glucose and androgen metabolism, which had been identified in clinical and basic studies previously. But more importantly, novel links between the energy metabolism, sex steroid biosynthesis, the cell cycle and the immune system were identified. These omics studies shed light on a complex interplay between metabolic pathways in steroidogenic systems.

  19. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Science.gov (United States)

    Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2014-01-01

    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  20. Paleogenetic Analyses Reveal Unsuspected Phylogenetic Affinities between Mice and the Extinct Malpaisomys insularis, an Endemic Rodent of the Canaries

    Science.gov (United States)

    Gros-Balthazard, Muriel; Hughes, Sandrine; Alcover, Josep Antoni; Hutterer, Rainer; Rando, Juan Carlos; Michaux, Jacques; Hänni, Catherine

    2012-01-01

    Background The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. Methodology/Principal Findings In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse. PMID:22363563

  1. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

    Directory of Open Access Journals (Sweden)

    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  2. Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

    Directory of Open Access Journals (Sweden)

    Simon J. McIlroy

    2017-06-01

    Full Text Available Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.

  3. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp.) and a recently extinct lineage of spotted kiwi.

    Science.gov (United States)

    Shepherd, Lara D; Worthy, Trevor H; Tennyson, Alan J D; Scofield, R Paul; Ramstad, Kristina M; Lambert, David M

    2012-01-01

    The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.

  4. Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

    Science.gov (United States)

    Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2014-01-01

    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m−2 (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors. PMID:24852573

  5. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.

    Science.gov (United States)

    Kapeli, Katannya; Pratt, Gabriel A; Vu, Anthony Q; Hutt, Kasey R; Martinez, Fernando J; Sundararaman, Balaji; Batra, Ranjan; Freese, Peter; Lambert, Nicole J; Huelga, Stephanie C; Chun, Seung J; Liang, Tiffany Y; Chang, Jeremy; Donohue, John P; Shiue, Lily; Zhang, Jiayu; Zhu, Haining; Cambi, Franca; Kasarskis, Edward; Hoon, Shawn; Ares, Manuel; Burge, Christopher B; Ravits, John; Rigo, Frank; Yeo, Gene W

    2016-07-05

    The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3' untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism.

  6. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity

    Directory of Open Access Journals (Sweden)

    Larance Ronsard

    2017-08-01

    Full Text Available HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.

  7. Multigenic control of pod shattering resistance in Chinese rapeseed germplasm revealed by genome-wide association and linkage analyses

    Directory of Open Access Journals (Sweden)

    Jia Liu

    2016-07-01

    Full Text Available Majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL for resistance to pod shatter in unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH and inter-mated (IF2 crosses derived from R1 (resistant to pod shattering and R2 (prone to pod shattering accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02 and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09 and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06 could be repeatedly detected across environments in diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.

  8. Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species

    Directory of Open Access Journals (Sweden)

    Kaakoush Nadeem O

    2011-10-01

    Full Text Available Abstract Background Several studies have shown that significant genotypic heterogeneity exists among Campylobacter concisus strains. Recently, the genome of C. concisus UNSWCD, isolated from a patient with Crohn's disease, was sequenced. Results In this study, comparative analyses were performed between strain UNSWCD and BAA-1457, isolated from a patient with acute gastroenteritis. Searches between C. concisus UNSWCD and BAA-1457 showed that 76% of genes were homologues, whereas those between C. jejuni strains showed 90-91% to be homologues, indicating substantial variation exists within these two C. concisus genomes. More specific bidirectional homology searches identified 1593 genes that are shared between these strains, and 115 and 281 genes unique to UNSWCD and BAA-1457, respectively. Significantly, differences in the type of flagellin glycosylation pathways between the two strains were identified and confirmed by PCR. The protein profiles of UNSWCD, BAA-1457 and a further six strains of C. concisus were compared and analyzed bioinformatically, and this differentiated the strains into four clades. BAA-1457 was found to be highly divergent (average similarity: 56.8% from the other seven strains (mean average similarity ± standard deviation: 64.7 ± 1.7%. Furthermore, searches for homologues of the 1593 proteins found to be common between UNSWCD and BAA-1457 were conducted against all available bacterial genomes, and 18 proteins were found to be unique to C. concisus, of which 6 were predicted to be secreted, and may represent good markers for detection of this species. Conclusions This study has elucidated several features that may be responsible for the heterogeneity that exists among C. concisus strains, and has determined that the strain BAA-1457 is genetically atypical to other C. concisus strains and is not a good candidate reference strain.

  9. Biochemical and histochemical analyses revealing endophytic Alcaligenes faecalis mediated suppression of oxidative stress in Abelmoschus esculentus challenged with Sclerotium rolfsii.

    Science.gov (United States)

    Ray, Shatrupa; Singh, Vivek; Singh, Surendra; Sarma, Birinchi Kumar; Singh, Harikesh Bahadur

    2016-12-01

    Sclerotium rolfsii is a highly aggressive pathogen that causes huge economic losses, especially in temperate climates. Alcaligenes faecalis, particularly in endophytic form, has rarely been used to control this fungus. In this study, endophytic Alcaligenes sp. strain BHU 12, BHU 16 (isolated from Abelmoschus esculentus leaf) and BHU M7 (isolated from Andrographis paniculata leaf) were reported to trigger a wide range of host defenses in Okra plant against the collar-rot pathogen S. rolfsii. Endophytic colonization of the strains in ten days old plants was assessed through re-isolation of the rif-tagged strains on rifampicin augmented nutrient agar media. The ability of the endophytic strains to induce systemic defense responses in above-ground organs was assessed by collecting leaf tissues of the Okra plants grown under non-gnotobiotic conditions at different time intervals post seedling bacterization with the endophytic biocontrol agents. The pathogen challenged unprimed plants exhibited flaccidity of the stem and leaves at 48 h post infection (hpi) in contrast to the bioprimed and challenged plants. Biochemical and histochemical analyses explained the above phenomenon as activation of phyto-peroxidases leading to an increased metabolism of the reactive oxygen species (ROS), accompanied by activation of the phenylpropanoid network and a subsequent enhancement in plant phenolics. Interestingly, though the maximum increase in the defense pathways was observed in treatments with native endophytes of Okra plant, yet the enhancement in antioxidant pathway due to A. paniculata borne endophytes was also quite significant. Thus, this work clearly demonstrates how Okra plants respond to the "non-hostile" colonization of bacterial endophytes and how induced defense response can contribute to the biocontrol activity of the endophytic strains. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  10. Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

    2017-07-22

    DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4 > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

  11. Kinetic analyses reveal potent and early blockade of hepatitis C virus assembly by NS5A inhibitors.

    Science.gov (United States)

    McGivern, David R; Masaki, Takahiro; Williford, Sara; Ingravallo, Paul; Feng, Zongdi; Lahser, Frederick; Asante-Appiah, Ernest; Neddermann, Petra; De Francesco, Raffaele; Howe, Anita Y; Lemon, Stanley M

    2014-08-01

    All-oral regimens combining different classes of direct-acting antivirals (DAA) are highly effective for treatment of patients with chronic hepatitis C. NS5A inhibitors will likely form a component of future interferon-sparing treatment regimens. However, despite their potential, the detailed mechanism of action of NS5A inhibitors is unclear. To study their mechanisms, we compared their kinetics of antiviral suppression with those of other classes of DAA, using the hepatitis C virus genotype 1a cell culture-infectious virus H77S.3. We performed detailed kinetic analyses of specific steps in the hepatitis C virus life cycle using cell cultures incubated with protease inhibitors, polymerase inhibitors, or NS5A inhibitors. Assays were designed to measure active viral RNA synthesis and steady-state RNA abundance, polyprotein synthesis, virion assembly, and infectious virus production. Despite their high potency, NS5A inhibitors were slow to inhibit viral RNA synthesis compared with protease or polymerase inhibitors. By 24 hours after addition of an NS5A inhibitor, polyprotein synthesis was reduced <50%, even at micromolar concentrations. In contrast, inhibition of virus release by NS5A inhibitors was potent and rapid, with onset of inhibition as early as 2 hours. Cells incubated with NS5A inhibitors were rapidly depleted of intracellular infectious virus and RNA-containing hepatitis C virus particles, indicating a block in virus assembly. DAAs that target NS5A rapidly inhibit intracellular assembly of genotype 1a virions. They also inhibit formation of functional replicase complexes, but have no activity against preformed replicase, thereby resulting in slow shut-off of viral RNA synthesis. Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

  12. Structure-Function Analyses of a Staphylococcus epidermidis Autoinducing Peptide Reveals Motifs Critical for AgrC-type Receptor Modulation.

    Science.gov (United States)

    Yang, Tian; Tal-Gan, Yftah; Paharik, Alexandra E; Horswill, Alexander R; Blackwell, Helen E

    2016-07-15

    Staphylococcus epidermidis is frequently implicated in human infections associated with indwelling medical devices due to its ubiquity in the skin flora and formation of robust biofilms. The accessory gene regulator (agr) quorum sensing (QS) system plays a prominent role in the establishment of biofilms and infection by this bacterium. Agr activation is mediated by the binding of a peptide signal (or autoinducing peptide, AIP) to its cognate AgrC receptor. Many questions remain about the role of QS in S. epidermidis infections, as well as in mixed-microbial populations on a host, and chemical modulators of its agr system could provide novel insights into this signaling network. The AIP ligand provides an initial scaffold for the development of such probes; however, the structure-activity relationships (SARs) for activation of S. epidermidis AgrC receptors by AIPs are largely unknown. Herein, we report the first SAR analyses of an S. epidermidis AIP by performing systematic alanine and d-amino acid scans of the S. epidermidis AIP-I. On the basis of these results, we designed and identified potent, pan-group inhibitors of the AgrC receptors in the three S. epidermidis agr groups, as well as a set of AIP-I analogs capable of selective AgrC inhibition in either specific S. epidermidis agr groups or in another common staphylococcal species, S. aureus. In addition, we uncovered a non-native peptide agonist of AgrC-I that can strongly inhibit S. epidermidis biofilm growth. Together, these synthetic analogs represent new and readily accessible probes for investigating the roles of QS in S. epidermidis colonization and infections.

  13. Spliced leader-based analyses reveal the effects of polycyclic aromatic hydrocarbons on gene expression in the copepod Pseudodiaptomus poplesia.

    Science.gov (United States)

    Zhuang, Yunyun; Yang, Feifei; Xu, Donghui; Chen, Hongju; Zhang, Huan; Liu, Guangxing

    2017-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are a group of toxic and carcinogenic pollutants that can adversely affect the development, growth and reproduction of marine organisms including copepods. However, knowledge on the molecular mechanisms regulating the response to PAH exposure in marine planktonic copepods is limited. In this study, we investigated the survival and gene expression of the calanoid copepod Pseudodiaptomus poplesia upon exposure to two PAHs, 1, 2-dimethylnaphthalene (1, 2-NAPH) and pyrene. Acute toxicity responses resulted in 96-h LC50 of 788.98μgL-1 and 54.68μgL-1 for 1, 2-NAPH and pyrene, respectively. Using the recently discovered copepod spliced leader as a primer, we constructed full-length cDNA libraries from copepods exposed to sublethal concentrations and revealed 289 unique genes of diverse functions, including stress response genes and novel genes previously undocumented for this species. Eighty-three gene families were specifically expressed in PAH exposure libraries. We further analyzed the expression of seven target genes by reverse transcription-quantitative PCR in a time-course test with three sublethal concentrations. These target genes have primary roles in detoxification, oxidative defense, and signal transduction, and include different forms of glutathione S-transferase (GST), glutathione peroxidases (GPX), peroxiredoxin (PRDX), methylmalonate-semialdehyde dehydrogenase (MSDH) and ras-related C3 botulinum toxin substrate (RAC1). Expression stability of seven candidate reference genes were evaluated and the two most stable ones (RPL15 and RPS20 for 1, 2-NAPH exposure, RPL15 and EF1D for pyrene exposure) were used to normalize the expression levels of the target genes. Significant upregulation was detected in GST-T, GST-DE, GPX4, PRDX6 and RAC1 upon 1, 2-NAPH exposure, and GST-DE and MSDH upon pyrene exposure. These results indicated that the oxidative stress was induced and that signal transduction might be affected by PAH

  14. New Mycobacterium tuberculosis LAM sublineage with geographical specificity for the Old World revealed by phylogenetical and Bayesian analyses.

    Science.gov (United States)

    Reynaud, Yann; Rastogi, Nalin

    2016-12-01

    We recently showed that the Mycobacterium tuberculosis sublineage LAM9 could be subdivided as two distinct subpopulations - each reflecting its unique biogeographical structure and evolutionary history. We subsequently attempted to verify if this genetic structuration could be traced in an enlarged global sample. For this purpose, we analyzed global evolutionary relationships of LAM strains in a large dataset (n = 1923 isolates from 35 countries worldwide) with concomitant spoligotyping and MIRU-VNTR data, followed by a deeper analysis of LAM9 sublineage (n = 851 isolates). Based on a combination of phylogenetical analysis and Bayesian statistics, a total of three different clusters, tentatively named LAM9C1, C2 and C3 were described in this dataset. Closer inspection of the phylogenetic tree with concomitant data on origin of isolates with genetic clusterization revealed LAM9C3 being the most tightly knit group exclusively found in the Old World as opposed to LAM9C2 being a loosely-knit group without any phylogeographical specificity; while LAM9C1 appeared with a majority of strains being well-clustered despite some isolates that intermixed with unrelated LAM clusters. Subsequently, we hereby describe a new M. tuberculosis LAM sublineage named LAM9C3 with phylogeographical specificity for the Old World. These findings open new perspectives to study respective migration histories and adaptation to human hosts of specific M. tuberculosis clones during the exploration and conquest of the New World. We therefore plan to reevaluate the nomenclature and evolutionary history of various LAM sublineages using Whole Genome Sequencing (WGS). Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Analyses of N-linked glycans of PrPSc revealed predominantly 2,6-linked sialic acid residues.

    Science.gov (United States)

    Katorcha, Elizaveta; Baskakov, Ilia V

    2017-11-01

    Mammalian prions (PrPSc ) consist of misfolded, conformationally altered, self-replicating states of the sialoglycoprotein called prion protein or PrPC . Recent studies revealed that the sialylation status of PrPSc plays a major role in evading innate immunity and infecting a host. Establishing the type of linkage by which sialic acid residues are attached to galactose is important, as it helps to identify the sialyltransferases responsible for sialylating PrPC and outline strategies for manipulating the sialyation status of PrPSc . Using enzymatic treatment with sialidases and lectin blots, this study demonstrated that in N-linked glycans of PrPSc , the sialic acid residues are predominantly alpha 2,6-linked. High percentages of alpha 2,6-linked sialic acids were observed in PrPSc of three prion strains 22L, RML, and ME7, as well as PrPSc from brain, spleen, or N2a cells cultured in vitro. Moreover, the variation in the percentage of alpha 2,3- versus 2,6-linked sialic acid was found to be relatively minor between brain-, spleen-, or cell-derived PrPSc , suggesting that the type of linkage is independent of tissue type. Based on the current results, we propose that sialyltransferases of St6Gal family, which is responsible for attaching sialic acids via alpha 2,6-linkages to N-linked glycans, controls sialylation of PrPC and PrPSc . © 2017 Federation of European Biochemical Societies.

  16. Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2017-10-01

    Full Text Available Cymbidium, one of the most important orchid genera in horticulture, can be classified into epiphytic and terrestrial species. Generally, epiphytic Cymbidium seedlings can be easily propagated by tissue culture, but terrestrial seedlings are difficult to propagate. To date, the molecular mechanisms underlying the differences in the ease with which terrestrial and epiphytic cymbidiums can be propagated are largely unknown. Using RNA-sequencing, quantitative reverse transcription PCR and enzyme-linked immunosorbent assay, Cymbidium ‘Xiaofeng’ (CXF, which can be efficiently micropropagated, and terrestrial Cymbidium sinense ‘Qijianbaimo’ (CSQ, which has a low regeneration ability, were used to explore the molecular mechanisms underlying the micropropagation ability of Cymbidium species. To this end, 447 million clean short reads were generated, and 31,264 annotated unigenes were obtained from 10 cDNA libraries. A total of 1,290 differentially expressed genes (DEGs were identified between CXF and CSQ during shoot induction. Gene ontology (GO enrichment analysis indicated that the DEGs were significantly enriched in auxin pathway-related GO terms. Further analysis demonstrated that YUC and GH3 family genes, which play crucial roles in the regulation of auxin/IAA (indole-3-acetic acid metabolism, acted quickly in response to shoot induction culture in vitro and were closely correlated with variation in shoot regeneration between CXF and CSQ. In addition, the study showed that IAA accumulated rapidly and significantly during shoot induction in CXF compared to that in CSQ; in contrast, no significant changes in other hormones were observed between CXF and CSQ. Furthermore, shoot regeneration in CXF was inhibited by a yucasin-auxin biosynthesis inhibitor, indicating that increased IAA level is required for high-frequency shoot regeneration in CXF. In conclusion, our study revealed that YUC-mediated auxin biogenesis is involved in shoot

  17. Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance.

    Science.gov (United States)

    Sapeta, Helena; Lourenço, Tiago; Lorenz, Stefan; Grumaz, Christian; Kirstahler, Philipp; Barros, Pedro M; Costa, Joaquim Miguel; Sohn, Kai; Oliveira, M Margarida

    2016-02-01

    Jatropha curcas, a multipurpose plant attracting a great deal of attention due to its high oil content and quality for biofuel, is recognized as a drought-tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, using a combined approach of transcriptional profiling and morphophysiological characterization during a period of water-withholding (49 d) followed by rewatering (7 d). Morphophysiological measurements showed that J. curcas plants present different adaptation strategies to withstand moderate and severe drought. Therefore, RNA sequencing was performed for samples collected under moderate and severe stress followed by rewatering, for both roots and leaves. Jatropha curcas transcriptomic analysis revealed shoot- and root-specific adaptations across all investigated conditions, except under severe stress, when the dramatic transcriptomic reorganization at the root and shoot level surpassed organ specificity. These changes in gene expression were clearly shown by the down-regulation of genes involved in growth and water uptake, and up-regulation of genes related to osmotic adjustments and cellular homeostasis. However, organ-specific gene variations were also detected, such as strong up-regulation of abscisic acid synthesis in roots under moderate stress and of chlorophyll metabolism in leaves under severe stress. Functional validation further corroborated the differential expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  18. Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Lior Lobel

    2016-02-01

    Full Text Available Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen Listeria monocytogenes revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (e.g., metabolic genes and functions as a direct activator of the master virulence regulator gene, prfA. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY's regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (i.e., binds DNA under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., sigB, arg, his, actA, glpF, gadG, gdhA, poxB, glnR and fla genes, integrating metabolism, stress responses, motility and virulence in L. monocytogenes. This study establishes CodY as a multifaceted factor regulating L. monocytogenes physiology in a highly versatile manner.

  19. Evaluation of the Tier 1 Program of Project P.A.T.H.S.: Secondary Data Analyses of Conclusions Drawn by the Program Implementers

    Directory of Open Access Journals (Sweden)

    Daniel T. L. Shek

    2008-01-01

    Full Text Available The Tier 1 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes is a curricula-based positive youth development program. In the experimental implementation phase, 52 schools participated in the program. Based on subjective outcome evaluation data collected from the program participants (Form A and program implementers (Form B in each school, the program implementers were invited to write down five conclusions based on an integration of the evaluation findings (N = 52. The conclusions stated in the 52 evaluation reports were further analyzed via secondary data analyses in this paper. Results showed that most of the conclusions concerning perceptions of the Tier 1 Program, instructors, and effectiveness of the programs were positive in nature. There were also conclusions reflecting the respondents’ appreciation of the program. Finally, responses on the difficulties encountered and suggestions for improvements were observed. In conjunction with the previous evaluation findings, the present study suggests that the Tier 1 Program was well received by the stakeholders and the program was beneficial to the development of the program participants.

  20. Comparative Genomic, MicroRNA, and Tissue Analyses Reveal Subtle Differences between Non-Diabetic and Diabetic Foot Skin.

    Directory of Open Access Journals (Sweden)

    Horacio A Ramirez

    Full Text Available Diabetes Mellitus (DM is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches, we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS and healthy non-diabetic foot skin (NFS. MicroRNA (miR profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05. Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy

  1. Classification and regression tree and spatial analyses reveal geographic heterogeneity in genome wide linkage study of Indian visceral leishmaniasis.

    Directory of Open Access Journals (Sweden)

    Michaela Fakiola

    Full Text Available BACKGROUND: Genome wide linkage studies (GWLS have provided evidence for loci controlling visceral leishmaniasis on Chromosomes 1p22, 6q27, 22q12 in Sudan and 6q27, 9p21, 17q11-q21 in Brazil. Genome wide studies from the major focus of disease in India have not previously been reported. METHODS AND FINDINGS: We undertook a GWLS in India in which a primary ∼10 cM (515 microsatellites scan was carried out in 58 multicase pedigrees (74 nuclear families; 176 affected, 353 total individuals and replication sought in 79 pedigrees (102 nuclear families; 218 affected, 473 total individuals. The primary scan provided evidence (≥2 adjacent markers allele-sharing LOD≥0.59; nominal P≤0.05 for linkage on Chromosomes 2, 5, 6, 7, 8, 10, 11, 20 and X, with peaks at 6p25.3-p24.3 and 8p23.1-p21.3 contributed to largely by 31 Hindu families and at Xq21.1-q26.1 by 27 Muslim families. Refined mapping confirmed linkage across all primary scan families at 2q12.2-q14.1 and 11q13.2-q23.3, but only 11q13.2-q23.3 replicated (combined LOD = 1.59; P = 0.0034. Linkage at 6p25.3-p24.3 and 8p23.1-p21.3, and at Xq21.1-q26.1, was confirmed by refined mapping for primary Hindu and Muslim families, respectively, but only Xq21.1-q26.1 replicated across all Muslim families (combined LOD 1.49; P = 0.0045. STRUCTURE and SMARTPCA did not identify population genetic substructure related to religious group. Classification and regression tree, and spatial interpolation, analyses confirm geographical heterogeneity for linkages at 6p25.3-p24.3, 8p23.1-p21.3 and Xq21.1-q26.1, with specific clusters of families contributing LOD scores of 2.13 (P = 0.0009, 1.75 (P = 0.002 and 1.84 (P = 0.001, respectively. CONCLUSIONS: GWLS has identified novel loci that show geographical heterogeneity in their influence on susceptibility to VL in India.

  2. Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

    Directory of Open Access Journals (Sweden)

    Amemiya Chris T

    2010-11-01

    Full Text Available Abstract Background The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation in limb types, as is the case in amphibians, can probably not only be attributed to variation in Hox genes, but is likely to be the product of differences in gene regulation. With a collection of vertebrate genome sequences available today, we used a comparative genomics approach to study the posterior HoxD cluster of amphibians. A frog and a caecilian were included in the study to compare coding sequences as well as to determine the gain and loss of putative regulatory sequences. Results We sequenced the posterior end of the HoxD cluster of a caecilian and performed comparative analyses of this region using HoxD clusters of other vertebrates. We determined the presence of conserved non-coding sequences and traced gains and losses of these footprints during vertebrate evolution, with particular focus on amphibians. We found that the caecilian HoxD cluster is almost three times larger than its mammalian counterpart. This enlargement is accompanied with the loss of one gene and the accumulation of repeats in that area. A similar phenomenon was observed in the coelacanth, where a different gene was lost and expansion of the area where the gene was lost has occurred. At least one phylogenetic footprint present in all vertebrates was lost in amphibians. This conserved region is a known regulatory element and functions as a boundary element in neural tissue to prevent expression of Hoxd genes. Conclusion The posterior part of the HoxD cluster of Typhlonectes natans is among the largest known today. The loss of Hoxd-12 and the expansion of the intergenic region may exert an influence on the limb enhancer, by having to bypass a distance seven times that of regular HoxD clusters. Whether or not there is a correlation with the

  3. Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures

    Directory of Open Access Journals (Sweden)

    Schriemer David C

    2010-11-01

    Full Text Available Abstract Background Papaver somniferum (opium poppy is the source for several pharmaceutical benzylisoquinoline alkaloids including morphine, the codeine and sanguinarine. In response to treatment with a fungal elicitor, the biosynthesis and accumulation of sanguinarine is induced along with other plant defense responses in opium poppy cell cultures. The transcriptional induction of alkaloid metabolism in cultured cells provides an opportunity to identify components of this process via the integration of deep transcriptome and proteome databases generated using next-generation technologies. Results A cDNA library was prepared for opium poppy cell cultures treated with a fungal elicitor for 10 h. Using 454 GS-FLX Titanium pyrosequencing, 427,369 expressed sequence tags (ESTs with an average length of 462 bp were generated. Assembly of these sequences yielded 93,723 unigenes, of which 23,753 were assigned Gene Ontology annotations. Transcripts encoding all known sanguinarine biosynthetic enzymes were identified in the EST database, 5 of which were represented among the 50 most abundant transcripts. Liquid chromatography-tandem mass spectrometry (LC-MS/MS of total protein extracts from cell cultures treated with a fungal elicitor for 50 h facilitated the identification of 1,004 proteins. Proteins were fractionated by one-dimensional SDS-PAGE and digested with trypsin prior to LC-MS/MS analysis. Query of an opium poppy-specific EST database substantially enhanced peptide identification. Eight out of 10 known sanguinarine biosynthetic enzymes and many relevant primary metabolic enzymes were represented in the peptide database. Conclusions The integration of deep transcriptome and proteome analyses provides an effective platform to catalogue the components of secondary metabolism, and to identify genes encoding uncharacterized enzymes. The establishment of corresponding transcript and protein databases generated by next-generation technologies in a

  4. Magnetic and Sedimentological Analyses of Sediment Cores from Otsego Lake Reveal Climate and Possible Delta Dynamics Throughout the Holocene

    Science.gov (United States)

    Geiss, C. E.; Hasbargen, L. E.

    2015-12-01

    Otsego Lake (42°43'N, -74°54'W) is a large oligotrophic, monomictic lake in upstate New York that occupies a narrow, N-S trending basin (approx. 13 km length, 2 km width) and has a maximum water depth of approx. 50 m. We collected two sediment cores from a shallow (4 m water depth) bench near the SW shore of the lake. The cores were collected approximately 200 m off-shore from a small stream delta. Age control was established through five 14C AMS-dates obtained from terrestrial plant macrofossils. We analyzed sediments for their magnetic properties (magnetic susceptibility, anhysteretic- and isothermal remanent magnetization, hysteresis properties and coercivity distributions) and performed loss-on-ignition and X-ray analyses to determine the relative abundance of organic matter, quartz and calcite. The watershed of Otsego Lake rests in glacial debris and Devonian shale and limestone. The base of the core (> 9 ka) consists mostly of silt-sized, massive to weakly laminated siliceous and strongly magnetic sediments. Between 8-9 ka the climate warmed sufficiently to allow for the formation of calcareous sediments. Between 8 - 6 ka magnetic minerals are characterized by low abundance and small grainsize, while organic and inorganic carbon increase. Sedimentation rates decrease significantly between 6-2 ka (from ~100 cm/ka to 12-15 cm/ka). During this time interval the relative abundance of quartz increases, sediment becomes slightly more magnetic, and the magnetic grain-size increases as well. We interpret this time period as a low-stand, when lower lake levels allow for the redeposition and possible loss of sediment into the deeper part of the lake, as well as increased terrigenous input from the nearby lakeshore. This lowstand is clearly identified as a strong, continuous reflector in GPR profiles. Sediments younger than 2 ka are characterized by variable abundances of magnetic minerals, with magnetic remanence peaks appearing semi-periodically approximately every

  5. Transcriptome Analysis of Sexually Dimorphic Chinese White Wax Scale Insects Reveals Key Differences in Developmental Programs and Transcription Factor Expression

    Science.gov (United States)

    Yang, Pu; Chen, Xiao-Ming; Liu, Wei-Wei; Feng, Ying; Sun, Tao

    2015-01-01

    The Chinese white wax scale insect, Ericerus pela, represents one of the most dramatic examples of sexual dimorphism in any insect species. In this study, we showed that although E. pela males display complete metamorphosis similar to holometabolous insects, the species forms the sister group to Acyrthosiphon pisum and cluster with hemimetabolous insects. The gene expression profile and Gene Ontology (GO) analyses revealed that the two sexes engaged in distinct developmental programs. In particular, female development appeared to prioritize the expression of genes related to cellular, metabolic, and developmental processes and to anatomical structure formation in nymphs. By contrast, male nymphal development is characterized by the significant down-regulation of genes involved in chitin, the respiratory system, and neurons. The wing and appendage morphogenesis, anatomical and tissue structure morphogenesis programs activated after male nymphal development. Transcription factors (that convey juvenile hormone or ecdysone signals, and Hox genes) and DNA methyltransferase were also differentially expressed between females and males. These results may indicate the roles that these differentially expressed genes play in regulating sexual dimorphism through orchestrating complex genetic programs. This differential expression was particularly prominent for processes linked to female development and wing development in males. PMID:25634031

  6. Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

    Science.gov (United States)

    Zhang, Qiang; Rahim, Mir Munir A; Allan, David S J; Tu, Megan M; Belanger, Simon; Abou-Samra, Elias; Ma, Jaehun; Sekhon, Harman S; Fairhead, Todd; Zein, Haggag S; Carlyle, James R; Anderson, Stephen K; Makrigiannis, Andrew P

    2012-01-01

    The Nkrp1 (Klrb1)-Clr (Clec2) genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b), Nkrp1c (Klrb1c), and Clr-c (Clec2f) genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d) and Clr-g (Clec2i) showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells), as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

  7. Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

  8. Hanford Environmental Monitoring Program schedule for samples, analyses, and measurements for calendar year 1985

    Energy Technology Data Exchange (ETDEWEB)

    Blumer, P.J.; Price, K.R.; Eddy, P.A.; Carlile, J.M.V.

    1984-12-01

    This report provides the CY 1985 schedule of data collection for the routine Hanford Surface Environmental Monitoring and Ground-Water Monitoring Programs at the Hanford Site. The purpose is to evaluate and report the levels of radioactive and nonradioactive pollutants in the Hanford environs, as required in DOE Order 5484.1. The routine sampling schedule provided herein does not include samples scheduled to be collected during FY 1985 in support of special studies, special contractor support programs, or for quality control purposes. In addition, the routine program outlined in this schedule is subject to modification during the year in response to changes in site operations, program requirements, or unusual sample results.

  9. Initial Analyses of Change Detection Capabilities and Data Redundancies in the Long Term Resource Monitoring Program

    National Research Council Canada - National Science Library

    Lubinski, Kenneth

    2001-01-01

    Evaluations of Long Term Resource Monitoring Program sampling designs for water quality, fish, aquatic vegetation, and macroinvertebrates were initiated in 1999 by analyzing data collected since 1992...

  10. Provenance of eastern Magallanes foreland basin sediments: Mineralogical and geochemical analyses reveal Paleogene tectonic unroofing of the Fuegian Andes

    Science.gov (United States)

    Zahid, Khandaker

    practice in the determination of sedimentary provenance. This study describes a Microsoft Excel-based method of constructing sandstone provenance and classification related ternary diagrams. The technique demonstrated in this chapter stores sandstone point-count data, generate ternary diagrams with provenance and classification related internal fields, and generate publication-quality scientific diagrams, all in a single step only requiring widely available programs such as Microsoft Excel.

  11. Meta-Analyses and Review of Research on Pull-Out Programs in Gifted Education.

    Science.gov (United States)

    Vaughn, Vicki L.; And Others

    1991-01-01

    A meta-analysis was conducted on nine experimental studies dealing with pull-out programs for gifted students in grades one through nine. Results indicate that pull-out programs in gifted education have significant positive effects on achievement, critical thinking, and creativity, but not on student self-concept. (Author/JDD)

  12. Marine Ecosystems Analysis (MESA) Program, New York Bight Surficial Sediment Analyses

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Marine Ecosystems Analysis (MESA) Program, New York Bight Study was funded by NOAA and the Bureau of Land Management (BLM). The Atlas was a historical...

  13. Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus.

    Science.gov (United States)

    von der Heyden, Sophie; Lipinski, Marek R; Matthee, Conrad A

    2007-02-01

    The Cape hake species, Merluccius capensis and Merluccius paradoxus are the most important resource of the South African and Namibian demersal fishery, but it is unclear whether there is a single population of each shared by both countries. We analysed the population structure and evolutionary history of these two species using the variable 5' region of the mtDNA control region for 311 specimens of M. capensis and 333 specimens of M. paradoxus sampled between Lüderitz (southern Namibia) to south of Cape Point (South Africa). 107 haplotypes for M. capensis and eight haplotypes for M. paradoxus were recovered. AMOVA and pairwise Phi(st) analyses revealed no structure in M. capensis, however significant genetic differentiation between Namibian and South African 'populations' was detected for M. paradoxus. This was only restricted to mature fish older than 3 and 4 years and not for juvenile fish younger than 3 years. Analyses reveal that M. capensis has undergone population expansion (Fu's Fs=-26.65, Phistory of sympatric species, as well as addressing management issues within regions where commercially valuable fish stocks are shared between nations.

  14. Non-Constant Learning Rates in Retrospective Experience Curve Analyses and their Correlation to Deployment Programs

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Smith, Sarah J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sohn, Michael D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-07-16

    A key challenge for policy-makers and technology market forecasters is to estimate future technology costs and in particular the rate of cost reduction versus production volume. A related, critical question is what role should state and federal governments have in advancing energy efficient and renewable energy technologies? This work provides retrospective experience curves and learning rates for several energy-related technologies, each of which have a known history of federal and state deployment programs. We derive learning rates for eight technologies including energy efficient lighting technologies, stationary fuel cell systems, and residential solar photovoltaics, and provide an overview and timeline of historical deployment programs such as state and federal standards and state and national incentive programs for each technology. Piecewise linear regimes are observed in a range of technology experience curves, and public investments or deployment programs are found to be strongly correlated to an increase in learning rate across multiple technologies. A downward bend in the experience curve is found in 5 out of the 8 energy-related technologies presented here (electronic ballasts, magnetic ballasts, compact fluorescent lighting, general service fluorescent lighting, and the installed cost of solar PV). In each of the five downward-bending experience curves, we believe that an increase in the learning rate can be linked to deployment programs to some degree. This work sheds light on the endogenous versus exogenous contributions to technological innovation and highlights the impact of exogenous government sponsored deployment programs. This work can inform future policy investment direction and can shed light on market transformation and technology learning behavior.

  15. Light Water Reactor Sustainability Program Industry Application External Hazard Analyses Problem Statement

    Energy Technology Data Exchange (ETDEWEB)

    Szilard, Ronaldo Henriques [Idaho National Lab. (INL), Idaho Falls, ID (United States); Coleman, Justin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Smith, Curtis L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Prescott, Steven [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kammerer, Annie [Annie Kammerer Consulting, Rye, NH (United States); Youngblood, Robert [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pope, Chad [Idaho State Univ., Pocatello, ID (United States)

    2015-07-01

    Risk-Informed Margin Management Industry Application on External Events. More specifically, combined events, seismically induced external flooding analyses for a generic nuclear power plant with a generic site soil, and generic power plant system and structure. The focus of this report is to define the problem above, set up the analysis, describe the methods to be used, tools to be applied to each problem, and data analysis and validation associated with the above.

  16. A simple program to measure and analyse tree rings using Excel, R and SigmaScan

    Science.gov (United States)

    Hietz, Peter

    2011-01-01

    I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood–earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code. PMID:26109835

  17. A simple program to measure and analyse tree rings using Excel, R and SigmaScan.

    Science.gov (United States)

    Hietz, Peter

    I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood-earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code.

  18. IMPROVEMENTS IN HANFORD TRANSURANIC (TRU) PROGRAM UTILIZING SYSTEMS MODELING AND ANALYSES

    Energy Technology Data Exchange (ETDEWEB)

    UYTIOCO EM

    2007-11-12

    Hanford's Transuranic (TRU) Program is responsible for certifying contact-handled (CH) TRU waste and shipping the certified waste to the Waste Isolation Pilot Plant (WIPP). Hanford's CH TRU waste includes material that is in retrievable storage as well as above ground storage, and newly generated waste. Certifying a typical container entails retrieving and then characterizing it (Real-Time Radiography, Non-Destructive Assay, and Head Space Gas Sampling), validating records (data review and reconciliation), and designating the container for a payload. The certified payload is then shipped to WIPP. Systems modeling and analysis techniques were applied to Hanford's TRU Program to help streamline the certification process and increase shipping rates.

  19. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis).

    Science.gov (United States)

    Dohms, Kimberly M; Graham, Brendan A; Burg, Theresa M

    2017-12-01

    An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.

  20. Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Mark H.; Qian, Weijun; Wang, Haixing; Petyuk, Vladislav A.; Bloom, Joshua S.; Sforza, Daniel M.; Lacan, Goran; Liu, Dahai; Khan, Arshad H.; Cantor, Rita M.; Bigelow, Diana J.; Melega, William P.; Camp, David G.; Smith, Richard D.; Smith, Desmond J.

    2008-02-10

    The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson disease (PD) are not completely understood. Here we use mass spectrometry and microarrays to study the proteomic and transcriptomic changes in the striatum of two mouse models of PD, induced by the distinct neurotoxins 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Proteomic analyses resulted in the identification and relative quantification of 912 proteins with two or more unique peptides and 85 proteins with significant abundance changes following neurotoxin treatment. Similarly, microarray analyses revealed 181 genes with significant changes in mRNA following neurotoxin treatment. The combined protein and gene list provides a clearer picture of the potential mechanisms underlying neurodegeneration observed in PD. Functional analysis of this combined list revealed a number of significant categories, including mitochondrial dysfunction, oxidative stress response and apoptosis. Additionally, codon usage and miRNAs may play an important role in translational control in the striatum. These results constitute one of the largest datasets integrating protein and transcript changes for these neurotoxin models with many similar endpoint phenotypes but distinct mechanisms.

  1. Complete genomic sequence analyses of the first group A giraffe rotavirus reveals close evolutionary relationship with rotaviruses infecting other members of the Artiodactyla.

    Science.gov (United States)

    O'Shea, Helen; Mulherin, Emily; Matthijnssens, Jelle; McCusker, Matthew P; Collins, P J; Cashman, Olivia; Gunn, Lynda; Beltman, Marijke E; Fanning, Séamus

    2014-05-14

    Group A Rotaviruses (RVA) have been established as significant contributory agents of acute gastroenteritis in young children and many animal species. In 2008, we described the first RVA strain detected in a giraffe calf (RVA/Giraffe-wt/IRL/GirRV/2008/G10P[11]), presenting with acute diarrhoea. Molecular characterisation of the VP7 and VP4 genes revealed the bovine-like genotypes G10 and P[11], respectively. To further investigate the origin of this giraffe RVA strain, the 9 remaining gene segments were sequenced and analysed, revealing the following genotype constellation: G10-P[11]-I2-R2-C2-M2-A3-N2-T6-E2-H3. This genotype constellation is very similar to RVA strains isolated from cattle or other members of the artiodactyls. Phylogenetic analyses confirmed the close relationship between GirRV and RVA strains with a bovine-like genotype constellation detected from several host species, including humans. These results suggest that RVA strain GirRV was the result of an interspecies transmission from a bovine host to the giraffe calf. However, we cannot rule out completely that this bovine-like RVA genotype constellation may be enzootic in giraffes. Future RVA surveillance in giraffes may answer this intriguing question. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Scanning electron microscopic analyses of Ferrocyanide tank wastes for the Ferrocyanide safety program

    Energy Technology Data Exchange (ETDEWEB)

    Callaway, W.S.

    1995-09-01

    This is Fiscal Year 1995 Annual Report on the progress of activities relating to the application of scanning electron microscopy in addressing the Ferrocyanide Safety Issue associated with Hanford Site high-level radioactive waste tanks. The status of the FY 1995 activities directed towards establishing facilities capable of providing SEM based micro-characterization of ferrocyanide tank wastes is described. A summary of key events in the SEM task over FY 1995 and target activities in FY 1996 are presented. A brief overview of the potential applications of computer controlled SEM analytical data in light of analyses of ferrocyanide simulants performed by an independent contractor is also presented

  3. Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

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    Kai-Chun Chang

    2012-01-01

    Full Text Available Programmed ribosomal frameshifting (PRF serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.

  4. SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer.

    Science.gov (United States)

    Standfuss, Christoph; Pospisil, Heike; Klein, Andreas

    2012-08-31

    Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs). We analyzed DNA from mouse mammary gland epithelial cells using the Affymetrix Mouse Diversity Genotyping array (MOUSEDIVm520650) and calculated the CNAs. Segmental copy number alterations were computed based on the probeset CNAs using the circular binary segmentation algorithm. Motif search was performed in breakpoint regions (inter-segment regions) with the MEME suite to identify common motif sequences. Here we present a four stage mouse model addressing copy number alterations in tumorigenesis. No considerable changes in CNA were identified for non-transgenic mice, but a stepwise increase in CNA was found during tumor development. The segmental copy number alteration revealed informative chromosomal fragmentation patterns. In inter-segment regions (hypothetical breakpoint sides) unique motifs were found. Our analyses suggest genome reorganization as a stepwise process that involves amplifications and deletions of chromosomal regions. We conclude from distinctive fragmentation patterns that conserved as well as individual breakpoints exist which promote tumorigenesis.

  5. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

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    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  6. Case Study Analyses of the Impact of Flipped Learning in Teaching Programming Robots

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    Majlinda Fetaji

    2016-11-01

    Full Text Available The focus of the research study was to investigate and find out the benefits of the flipped learning pedagogy on the student learning in teaching programming Robotics classes. Also, the assessment of whether it has any advantages over the traditional teaching methods in computer sciences. Assessment of learners on their attitudes, motivation, and effectiveness when using flipped classroom compared with traditional classroom has been realized. The research questions investigated are: “What kind of problems can we face when we have robotics classes in the traditional methods?”, “If we applied flipped learning method, can we solve these problems?”. In order to analyze all this, a case study experiment was realized and insights as well as recommendations are presented.

  7. SUBCHANFLOW: a thermal hydraulic sub-channel program to analyse fuel rod bundles and reactor cores

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, V.; Imke, U.; Ivanov, A. [Karlsruhe Institute of Technology, Institute of Neutron Physics and Reactor Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen (Germany); Gomez, R., E-mail: Victor.Sanchez@kit.ed [University of Applied Sciences Offenburg, Badstr. 24, 77652 Offenburg (Germany)

    2010-10-15

    The improvement of numerical analysis tools for the design and safety evaluation of reactor cores in a continuous effort in the nuclear community not only to improve the plant efficiency but also to demonstrate high degree of safety. Investigations at the Institute of Neutron Physics and Reactor Technology of the Karlsruhe Institute of Technology (KIT) are focused on the further development and qualification of subchannel and system codes using experimental data. The majority of sub-channel codes in use likes Thesis, Bacchus, Cobra and Matra, were developed in the seventies and eighties. The programming style is rather obsolete and most of these codes are working internally with British Units instead of Si-Units. In the case of water, outdated steam tables are used. Both the trends to improve the efficiency of light water reactors (LWR) and the involvement of KIT in European projects related to the study of the technical feasibility of different fast reactors systems reinforced the need for the development and improvement of sub-channel codes, since they will play a key role in performing better designs as stand-alone tools or coupled to neutron physical codes (deterministic or stochastic). Hence, KIT started the development of a new sub-channel code SUBCHANFLOW based on the Cobra-family. SUBCHANFLOW is a modular code programmed in Fortran-95 with dynamic memory allocation using Si-units. Different fluids like liquid metals and water are available as coolant. In addition some models were improved or replaced by new ones. In this paper the structure, the physical models and the current validation status will be presented and discussed. (Author)

  8. Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis.

    Science.gov (United States)

    Rahman, Syed Asad; Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z; Tyagi, Anil K; Hasnain, Seyed E

    2014-11-04

    Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size--their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. The complete sequence analysis of Mycobacterium indicus pranii, a novel species of Mycobacterium shown earlier to have strong immunomodulatory properties and currently in use for

  9. Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.

    Science.gov (United States)

    Zhou, Yang; Utsunomiya, Yuri T; Xu, Lingyang; Hay, El Hamidi Abdel; Bickhart, Derek M; Sonstegard, Tad S; Van Tassell, Curtis P; Garcia, Jose Fernando; Liu, George E

    2016-07-06

    We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.

  10. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855 (Mollusca, Ommastrephidae in the eastern tropical Atlantic.

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    Véronique Merten

    Full Text Available In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855 (Cephalopoda, Ommastrephidae is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding were combined with stable isotope data (∂15N and ∂13C of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp., but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae, crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and

  11. DNA Radiation Environments Program - Spring 1990 2-meter box experiments and analyses

    Energy Technology Data Exchange (ETDEWEB)

    Santoro, R.T (Oak Ridge National Lab., TN (United States)); Whitaker, S.Y. (Clark Atlanta Univ., GA (United States))

    1992-09-01

    This report summarizes the Spring 1990 2-m Box Experiments performed at the Army Pulse Radiation Facility (APRF) at Aberdeen Proving Ground, Maryland. These studies were sponsored by the Defense Nuclear Agency (DNA) under the Radiation Environments Program to obtain measured data for benchmarking the Adjoint Monte Carlo Code System, MASH, Version 1.0. MASH was developed as the Department of Defense and NATO code system for calculating neutron and gamma-ray radiation fields and shielding protection factors for armored vehicles and military structures against nuclear weapon radiation. In the experiments, neutron and gamma-ray dose and reduction factors were measured in the free-field and as a function of position on an anthropomorphic phantom that was placed outside and inside the steel-walled 2-m box. The data were acquired at a distance of 400-m from the APRF reactor. The measurements were performed by APRF, Bubble Technology Industries, the Defence Research Establishment Ottawa, Establishment Technique Central de l'Armement, and Harry Diamond Laboratory. Calculations were carried out by the Oak Ridge National Laboratory and Science Applications International Corporation. The purpose of these experiments was to measure the neutron and gamma-ray dose as a function of detector location on the phantom for cases when the phantom was standing in the free-field and inside of the box. Neutron measurements were made using a BD-IOOR bubble detector and gamma-ray measurements were made using thermoluminescent detectors (TLD). Calculated and measured data were compared in terms of the C/M ratio. DNA mandated that C/M values of {plus minus}20% define the acceptable limits for the comparison of the dose and reduction factor data and for qualifying the MASH code in replicating integral parameters.

  12. DNA Radiation Environments Program Spring 1991 2-meter box experiments and analyses

    Energy Technology Data Exchange (ETDEWEB)

    Santoro, R.T. [Oak Ridge National Lab., TN (United States); Whitaker, S.Y. [Clark Atlanta Univ., GA (United States)

    1993-03-01

    This report summarizes the Spring 1991 2-m Box experiments that were performed at the Army Pulse Radiation Facility (APRF) at Aberdeen Proving Ground. These studies were sponsored by the Defense Nuclear Agency (DNA) under the Radiation Environments Program to obtain measured data for benchmarking the Adjoint Monte Carlo Code System, MASH, Version 1.0. The MASH code system was developed for the Department of Defense and NATO for calculating neutron and gamma-ray radiation fields and shielding protection factors for armored vehicles and military structures against nuclear weapon radiation. In the 2-m Box experiments, neutron and gamma-ray dose rates and reduction factors were measured in the free-field and as a function of position on an anthropomorphic phantom that was placed outside and inside a borated polyethylene lined steel-walled 2-m box. The data were acquired at a distance of 400-m from the APRF reactor. The purpose of these experiments was to measure the neutron and gamma-ray dose rates as a function of detector location on the phantom for cases when the phantom was in the free-field and inside of the box. Neutron measurements were made using a BD-100R bubble detector and gamma-ray measurements were made using thermoluminescent detectors (TLD). Calculated and measured data were compared in terms of the C/M ratio. The calculated and measured neutron and gamma-ray dose rates and reduction factors agreed on the average within the {plus_minus}20% limits mandated by DNA and demonstrate the capability of the MASH code system in reproducing measured data in nominally shielded assemblies.

  13. DNA Radiation Environments Program Spring 1991 2-meter box experiments and analyses. [DEfense Nuclear Agency (DNA)

    Energy Technology Data Exchange (ETDEWEB)

    Santoro, R.T. (Oak Ridge National Lab., TN (United States)); Whitaker, S.Y. (Clark Atlanta Univ., GA (United States))

    1993-03-01

    This report summarizes the Spring 1991 2-m Box experiments that were performed at the Army Pulse Radiation Facility (APRF) at Aberdeen Proving Ground. These studies were sponsored by the Defense Nuclear Agency (DNA) under the Radiation Environments Program to obtain measured data for benchmarking the Adjoint Monte Carlo Code System, MASH, Version 1.0. The MASH code system was developed for the Department of Defense and NATO for calculating neutron and gamma-ray radiation fields and shielding protection factors for armored vehicles and military structures against nuclear weapon radiation. In the 2-m Box experiments, neutron and gamma-ray dose rates and reduction factors were measured in the free-field and as a function of position on an anthropomorphic phantom that was placed outside and inside a borated polyethylene lined steel-walled 2-m box. The data were acquired at a distance of 400-m from the APRF reactor. The purpose of these experiments was to measure the neutron and gamma-ray dose rates as a function of detector location on the phantom for cases when the phantom was in the free-field and inside of the box. Neutron measurements were made using a BD-100R bubble detector and gamma-ray measurements were made using thermoluminescent detectors (TLD). Calculated and measured data were compared in terms of the C/M ratio. The calculated and measured neutron and gamma-ray dose rates and reduction factors agreed on the average within the [plus minus]20% limits mandated by DNA and demonstrate the capability of the MASH code system in reproducing measured data in nominally shielded assemblies.

  14. DNA Radiation Environments Program - Spring 1990 2-meter box experiments and analyses

    Energy Technology Data Exchange (ETDEWEB)

    Santoro, R.T [Oak Ridge National Lab., TN (United States); Whitaker, S.Y. [Clark Atlanta Univ., GA (United States)

    1992-09-01

    This report summarizes the Spring 1990 2-m Box Experiments performed at the Army Pulse Radiation Facility (APRF) at Aberdeen Proving Ground, Maryland. These studies were sponsored by the Defense Nuclear Agency (DNA) under the Radiation Environments Program to obtain measured data for benchmarking the Adjoint Monte Carlo Code System, MASH, Version 1.0. MASH was developed as the Department of Defense and NATO code system for calculating neutron and gamma-ray radiation fields and shielding protection factors for armored vehicles and military structures against nuclear weapon radiation. In the experiments, neutron and gamma-ray dose and reduction factors were measured in the free-field and as a function of position on an anthropomorphic phantom that was placed outside and inside the steel-walled 2-m box. The data were acquired at a distance of 400-m from the APRF reactor. The measurements were performed by APRF, Bubble Technology Industries, the Defence Research Establishment Ottawa, Establishment Technique Central de l`Armement, and Harry Diamond Laboratory. Calculations were carried out by the Oak Ridge National Laboratory and Science Applications International Corporation. The purpose of these experiments was to measure the neutron and gamma-ray dose as a function of detector location on the phantom for cases when the phantom was standing in the free-field and inside of the box. Neutron measurements were made using a BD-IOOR bubble detector and gamma-ray measurements were made using thermoluminescent detectors (TLD). Calculated and measured data were compared in terms of the C/M ratio. DNA mandated that C/M values of {plus_minus}20% define the acceptable limits for the comparison of the dose and reduction factor data and for qualifying the MASH code in replicating integral parameters.

  15. Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs.

    Science.gov (United States)

    Kellner, Ronny; Bhattacharyya, Amitava; Poppe, Stephan; Hsu, Tiffany Y; Brem, Rachel B; Stukenbrock, Eva H

    2014-05-14

    Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Mutational analyses of Epstein-Barr virus glycoprotein 42 reveal functional domains not involved in receptor binding but required for membrane fusion.

    Science.gov (United States)

    Silva, Amanda L; Omerovic, Jasmina; Jardetzky, Theodore S; Longnecker, Richard

    2004-06-01

    Epstein-Barr virus (EBV) is a human gammaherpesvirus associated with malignancies of both epithelial and lymphoid origin. Efficient infection of the latent host reservoir B lymphocytes involves the binding of glycoproteins gp350/220 for initial attachment, followed by the concerted action of gH, gL, gB, and gp42 for membrane fusion. The type II membrane protein gp42 is required for infection of B cells and assembles into a complex with gH and gL. The cellular host receptor for gp42, class II human leukocyte antigen (HLA), has been structurally verified by crystallization analyses of gp42 bound to HLA-DR1. Interestingly, the crystal structure revealed a hydrophobic pocket consisting of many aromatic and aliphatic residues from the predicted C-type lectin domain of gp42 that in other members of the C-type lectin family binds major histocompatibility complex class I or other diverse ligands. Although the hydrophobic pocket does not bind HLA class II, mutational analyses presented here indicate that this domain is essential for EBV-induced membrane fusion. In addition, mutational analysis of the region of gp42 contacting HLA class II in the gp42-HLA-DR1 cocrystal confirms that this region interacts with HLA class II and that this interaction is also important for EBV-induced membrane fusion.

  17. Genus-Wide Comparative Genome Analyses of Colletotrichum Species Reveal Specific Gene Family Losses and Gains during Adaptation to Specific Infection Lifestyles.

    Science.gov (United States)

    Gan, Pamela; Narusaka, Mari; Kumakura, Naoyoshi; Tsushima, Ayako; Takano, Yoshitaka; Narusaka, Yoshihiro; Shirasu, Ken

    2016-05-22

    Members from Colletotrichum genus adopt a diverse range of lifestyles during infection of plants and represent a group of agriculturally devastating pathogens. In this study, we present the draft genome of Colletotrichum incanum from the spaethianum clade of Colletotrichum and the comparative analyses with five other Colletotrichum species from distinct lineages. We show that the C. incanum strain, originally isolated from Japanese daikon radish, is able to infect both eudicot plants, such as certain ecotypes of the eudicot Arabidopsis, and monocot plants, such as lily. Being closely related to Colletotrichum species both in the graminicola clade, whose members are restricted strictly to monocot hosts, and to the destructivum clade, whose members are mostly associated with dicot infections, C. incanum provides an interesting model system for comparative genomics to study how fungal pathogens adapt to monocot and dicot hosts. Genus-wide comparative genome analyses reveal that Colletotrichum species have tailored profiles of their carbohydrate-degrading enzymes according to their infection lifestyles. In addition, we show evidence that positive selection acting on secreted and nuclear localized proteins that are highly conserved may be important in adaptation to specific hosts or ecological niches. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

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    Eunyoung Seo

    2016-08-01

    Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  19. The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    Directory of Open Access Journals (Sweden)

    Arzu Coleri Cihan

    2012-03-01

    Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

  20. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.

    Directory of Open Access Journals (Sweden)

    Philipp Wiemann

    Full Text Available The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs, but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19 and another that includes a non-ribosomal peptide synthetase gene (NRPS31 are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary

  1. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus.

    Science.gov (United States)

    Keller, J; Rousseau-Gueutin, M; Martin, G E; Morice, J; Boutte, J; Coissac, E; Ourari, M; Aïnouche, M; Salmon, A; Cabello-Hurtado, F; Aïnouche, A

    2017-08-01

    The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  2. Economic and policy instrument analyses in support of the scrap tire recycling program in Taiwan.

    Science.gov (United States)

    Chang, Ni-Bin

    2008-02-01

    Understanding the cost-effectiveness and the role of economic and policy instruments, such as the combined product tax-recycling subsidy scheme or a tradable permit, for scrap tire recycling has been of crucial importance in a market-oriented environmental management system. Promoting product (tire) stewardship on one hand and improving incentive-based recycling policy on the other hand requires a comprehensive analysis of the interfaces and interactions in the nexus of economic impacts, environmental management, environmental valuation, and cost-benefit analysis. This paper presents an assessment of the interfaces and interactions between the implementation of policy instruments and its associated economic evaluation for sustaining a scrap tire recycling program in Taiwan during the era of the strong economic growth of the late 1990s. It begins with an introduction of the management of the co-evolution between technology metrics of scrap tire recycling and organizational changes for meeting the managerial goals island-wide during the 1990s. The database collected and used for such analysis covers 17 major tire recycling firms and 10 major tire manufacturers at that time. With estimates of scrap tire generation and possible scale of subsidy with respect to differing tire recycling technologies applied, economic analysis eventually leads to identify the associated levels of product tax with respect to various sizes of new tires. It particularly demonstrates a broad perspective of how an integrated econometric and engineering economic analysis can be conducted to assist in implementing policy instruments for scrap tire management. Research findings indicate that different subsidy settings for collection, processing, and end use of scrap tires should be configured to ameliorate the overall managerial effectiveness. Removing the existing boundaries between designated service districts could strengthen the competitiveness of scrap tires recycling industry, helping to

  3. Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection.

    Science.gov (United States)

    Wang, Yong; Wu, Qiao-Feng; Chen, Chen; Wu, Ling-Yun; Yan, Xian-Zhong; Yu, Shu-Guang; Zhang, Xiang-Sun; Liang, Fan-Rong

    2012-01-01

    Acupuncture has been practiced in China for thousands of years as part of the Traditional Chinese Medicine (TCM) and has gradually accepted in western countries as an alternative or complementary treatment. However, the underlying mechanism of acupuncture, especially whether there exists any difference between varies acupoints, remains largely unknown, which hinders its widespread use. In this study, we develop a novel Linear Programming based Feature Selection method (LPFS) to understand the mechanism of acupuncture effect, at molecular level, by revealing the metabolite biomarkers for acupuncture treatment. Specifically, we generate and investigate the high-throughput metabolic profiles of acupuncture treatment at several acupoints in human. To select the subsets of metabolites that best characterize the acupuncture effect for each meridian point, an optimization model is proposed to identify biomarkers from high-dimensional metabolic data from case and control samples. Importantly, we use nearest centroid as the prototype to simultaneously minimize the number of selected features and the leave-one-out cross validation error of classifier. We compared the performance of LPFS to several state-of-the-art methods, such as SVM recursive feature elimination (SVM-RFE) and sparse multinomial logistic regression approach (SMLR). We find that our LPFS method tends to reveal a small set of metabolites with small standard deviation and large shifts, which exactly serves our requirement for good biomarker. Biologically, several metabolite biomarkers for acupuncture treatment are revealed and serve as the candidates for further mechanism investigation. Also biomakers derived from five meridian points, Zusanli (ST36), Liangmen (ST21), Juliao (ST3), Yanglingquan (GB34), and Weizhong (BL40), are compared for their similarity and difference, which provide evidence for the specificity of acupoints. Our result demonstrates that metabolic profiling might be a promising method to

  4. Epigenome-wide and transcriptome-wide analyses reveal gestational diabetes is associated with alterations in the human leukocyte antigen complex.

    Science.gov (United States)

    Binder, Alexandra M; LaRocca, Jessica; Lesseur, Corina; Marsit, Carmen J; Michels, Karin B

    2015-01-01

    Gestational diabetes mellitus (GDM) affects approximately 10 % of pregnancies in the United States and increases the risk of adverse health outcomes in the offspring. These adult disease propensities may be set by anatomical and molecular alterations in the placenta associated with GDM. To assess the mechanistic aspects of fetal programming, we measured genome-wide methylation (Infinium HumanMethylation450 BeadChips) and expression (Affymetrix transcriptome microarrays) in placental tissue of 41 GDM cases and 41 matched pregnancies without maternal complications from the Harvard Epigenetic Birth Cohort. Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study. Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region. This differential methylation and expression may be capturing shifts in cellular composition, reflecting physiological changes in the placenta associated with GDM. Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into how GDM shapes the intrauterine environment, which may have implications for fetal (re)programming.

  5. Response and Defense Mechanisms of Taxus chinensis Leaves Under UV-A Radiation are Revealed Using Comparative Proteomics and Metabolomics Analyses.

    Science.gov (United States)

    Zheng, Wen; Komatsu, Setsuko; Zhu, Wei; Zhang, Lin; Li, Ximin; Cui, Lei; Tian, Jingkui

    2016-09-01

    Taxus chinensis var. mairei is a species endemic to south-eastern China and one of the natural sources for the anticancer medicine paclitaxel. To investigate the molecular response and defense mechanisms of T. chinensis leaves to enhanced ultraviolet-A (UV-A) radiation, gel-free/label-free and gel-based proteomics and gas chromatography-mass spectrometry (GC-MS) analyses were performed. The transmission electron microscopy results indicated damage to the chloroplast under UV-A radiation. Proteomics analyses in leaves and chloroplasts showed that photosynthesis-, glycolysis-, secondary metabolism-, stress-, and protein synthesis-, degradation- and activation-related systems were mainly changed under UV-A radiation. Forty-seven PSII proteins and six PSI proteins were identified as being changed in leaves and chloroplasts under UV-A treatment. This indicated that PSII was more sensitive to UV-A than PSI as the target of UV-A light. Enhanced glycolysis, with four glycolysis-related key enzymes increased, provided precursors for secondary metabolism. The 1-deoxy-d-xylulose-5-phosphate reductoisomerase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase were identified as being significantly increased during UV-A radiation, which resulted in paclitaxel enhancement. Additionally, mRNA expression levels of genes involved in the paclitaxel biosynthetic pathway indicated a down-regulation under UV-A irradiation and up-regulation in dark incubation. These results reveal that a short-term high dose of UV-A radiation could stimulate the plant stress defense system and paclitaxel production. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

    Directory of Open Access Journals (Sweden)

    Alexander Lichius

    Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

  7. Mars Organic Matter Revealed by the Detection of Organo-chlorinated Molecules from Pyro-GCMS Analyses of Yellowknife Bay Mudstone

    Science.gov (United States)

    Szopa, C.; Freissinet, C.; Glavin, D. P.; Buch, A.; Coll, P. J.; Cabane, M.; Millan, M.; Belmahadi, I.; Navarro-Gonzalez, R.; Steele, A.; Summons, R. E.; Eigenbrode, J. L.; Mahaffy, P. R.

    2015-12-01

    Mudstones collected on the Yellowknife Bay site in Gale crater by the Curiosity rover, were analyzed with the Sample Analysis at Mars (SAM) chemical laboratory with the aim (among others) to detect and identify organic molecules in the Martian reglith [1]. The pyrolysis (to 900°C)-gas chromatography-mass spectrometry (Pyro-GCMS) analytical mode was systematically used to reach that goal. It revealed the existence of complex interactions between compounds present in the soil sample (e.g. oxychlorines [2]) and internal components of the SAM experiment (e.g. derivatization reactant) resulting in signals complex to interpret [3]. By comparing these results with those obtained for the other Mars samples analysed with SAM, and by carefully identifying, from laboratory work, the possible SAM internal contributions to the organic molecules detected [4], chlorobenzene has already been identified as mainly originating from organics present in the mudstone [5]. Since this discovery, we did additional studies of the chromatograms that reveal the presence of dichlorobenzene originating from an organic source endogenous to the sample. Even if the exact original source of these organic molecules cannot be strictly identified, the detection of several chlorinated aromatic molecules suggests the presence of a significant amount of aromatized materials which are in an oxidized state involving oxygen in the mudstone. We present here the corresponding results and the implication it can have on the origin of these organic materials References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Ming D. et al. (2013), Science 32, 64, [4] Miller K. et al. (In press), JGR, [5] Freissinet et al., (2015), JGR Pla. 120, 495.

  8. High-affinity nitrate/nitrite transporter genes (Nrt2) in Tisochrysis lutea: identification and expression analyses reveal some interesting specificities of Haptophyta microalgae.

    Science.gov (United States)

    Charrier, Aurélie; Bérard, Jean-Baptiste; Bougaran, Gaël; Carrier, Grégory; Lukomska, Ewa; Schreiber, Nathalie; Fournier, Flora; Charrier, Aurélie F; Rouxel, Catherine; Garnier, Matthieu; Cadoret, Jean-Paul; Saint-Jean, Bruno

    2015-08-01

    Microalgae have a diversity of industrial applications such as feed, food ingredients, depuration processes and energy. However, microalgal production costs could be substantially improved by controlling nutrient intake. Accordingly, a better understanding of microalgal nitrogen metabolism is essential. Using in silico analysis from transcriptomic data concerning the microalgae Tisochrysis lutea, four genes encoding putative high-affinity nitrate/nitrite transporters (TlNrt2) were identified. Unlike most of the land plants and microalgae, cloning of genomic sequences and their alignment with complementary DNA (cDNA) sequences did not reveal the presence of introns in all TlNrt2 genes. The deduced TlNRT2 protein sequences showed similarities to NRT2 proteins of other phyla such as land plants and green algae. However, some interesting specificities only known among Haptophyta were also revealed, especially an additional sequence of 100 amino acids forming an atypical extracellular loop located between transmembrane domains 9 and 10 and the function of which remains to be elucidated. Analyses of individual TlNrt2 gene expression with different nitrogen sources and concentrations were performed. TlNrt2.1 and TlNrt2.3 were strongly induced by low NO3 (-) concentration and repressed by NH4 (+) substrate and were classified as inducible genes. TlNrt2.2 was characterized by a constitutive pattern whatever the substrate. Finally, TlNrt2.4 displayed an atypical response that was not reported earlier in literature. Interestingly, expression of TlNrt2.4 was rather related to internal nitrogen quota level than external nitrogen concentration. This first study on nitrogen metabolism of T. lutea opens avenues for future investigations on the function of these genes and their implication for industrial applications. © 2015 Scandinavian Plant Physiology Society.

  9. Genetic structure of Mycobacterium avium subsp. paratuberculosis population in cattle herds in Quebec as revealed by using a combination of multilocus genomic analyses.

    Science.gov (United States)

    Sohal, Jagdip Singh; Arsenault, Julie; Labrecque, Olivia; Fairbrother, Julie-Hélène; Roy, Jean-Philippe; Fecteau, Gilles; L'Homme, Yvan

    2014-08-01

    Mycobacterium avium subsp. paratuberculosis is the etiological agent of paratuberculosis, a granulomatous enteritis affecting a wide range of domestic and wild ruminants worldwide. A variety of molecular typing tools are used to distinguish M. avium subsp. paratuberculosis strains, contributing to a better understanding of M. avium subsp. paratuberculosis epidemiology. In the present study, PCR-based typing methods, including mycobacterial interspersed repetitive units/variable-number tandem repeats (MIRU-VNTR) and small sequence repeats (SSR) in addition to IS1311 PCR-restriction enzyme analysis (PCR-REA), were used to investigate the genetic heterogeneity of 200 M. avium subsp. paratuberculosis strains from dairy herds located in the province of Quebec, Canada. The majority of strains were of the "cattle type," or type II, although 3 strains were of the "bison type." A total of 38 genotypes, including a novel one, were identified using a combination of 17 genetic markers, which generated a Simpson's index of genetic diversity of 0.876. Additional analyses revealed no differences in genetic diversity between environmental and individual strains. Of note, a spatial and spatiotemporal cluster was evidenced regarding the distribution of one of the most common genotypes. The population had an overall homogeneous genetic structure, although a few strains stemmed out of the consensus cluster, including the bison-type strains. The genetic structure of M. avium subsp. paratuberculosis populations within most herds suggested intraherd dissemination and microevolution, although evidence of interherd contamination was also revealed. The level of genetic diversity obtained by combining MIRU-VNTR and SSR markers shows a promising avenue for molecular epidemiology investigations of M. avium subsp. paratuberculosis transmission patterns. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  10. Impacts Analyses Supporting the National Environmental Policy Act Environmental Assessment for the Resumption of Transient Testing Program

    Energy Technology Data Exchange (ETDEWEB)

    Schafer, Annette L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Brown, LLoyd C. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Carathers, David C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Christensen, Boyd D. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Dahl, James J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Miller, Mark L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Farnum, Cathy Ottinger [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Peterson, Steven [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sondrup, A. Jeffrey [Idaho National Lab. (INL), Idaho Falls, ID (United States); Subaiya, Peter V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wachs, Daniel M. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Weiner, Ruth F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2014-02-01

    This document contains the analysis details and summary of analyses conducted to evaluate the environmental impacts for the Resumption of Transient Fuel and Materials Testing Program. It provides an assessment of the impacts for the two action alternatives being evaluated in the environmental assessment. These alternatives are (1) resumption of transient testing using the Transient Reactor Test Facility (TREAT) at Idaho National Laboratory (INL) and (2) conducting transient testing using the Annular Core Research Reactor (ACRR) at Sandia National Laboratory in New Mexico (SNL/NM). Analyses are provided for radiologic emissions, other air emissions, soil contamination, and groundwater contamination that could occur (1) during normal operations, (2) as a result of accidents in one of the facilities, and (3) during transport. It does not include an assessment of the biotic, cultural resources, waste generation, or other impacts that could result from the resumption of transient testing. Analyses were conducted by technical professionals at INL and SNL/NM as noted throughout this report. The analyses are based on bounding radionuclide inventories, with the same inventories used for test materials by both alternatives and different inventories for the TREAT Reactor and ACRR. An upper value on the number of tests was assumed, with a test frequency determined by the realistic turn-around times required between experiments. The estimates provided for impacts during normal operations are based on historical emission rates and projected usage rates; therefore, they are bounding. Estimated doses for members of the public, collocated workers, and facility workers that could be incurred as a result of an accident are very conservative. They do not credit safety systems or administrative procedures (such as evacuation plans or use of personal protective equipment) that could be used to limit worker doses. Doses estimated for transportation are conservative and are based on

  11. Comparative analyses of the proteomes of leaves and flowers at various stages of development reveal organ-specific functional differentiation of proteins in soybean.

    Science.gov (United States)

    Ahsan, Nagib; Komatsu, Setsuko

    2009-11-01

    The functional differentiation of protein networks in individual organs and tissues of soybean at various developmental stages was investigated by proteomic approach. Protein extraction by Mg/NP-40 buffer followed by alkaline phenol-based method was optimized for proteomic analysis. Proteome analyses of leaves at various developmental stages showed 26 differentially expressed proteins, wherein proteins in translocon at the outer/inner envelope membrane of chloroplast protein-transport machineries increased significantly at the first trifoliate. Immunoblot analysis showed chaperonin-60 expressed abundantly in young leaves, whereas HSP 70 and ATP-synthase beta were constitutively expressed in all tissues. The net photosynthesis rate and chlorophyll content showed an age-dependent correlation in leaves. These results suggest that proteins involved in carbon assimilation, folding and assembly, and energy may work synchronously and show a linear correlation to photosynthesis at developmental stages of leaves. Comparison of flower bud and flower proteome reveals 29 differentially expressed proteins, wherein proteins involved in mitochondrial protein transport and assembly, secondary metabolism, and pollen-tube growth were up-regulated during flower development. Together, these results suggest that during developmental stages, each type of tissue is associated with a specific group of proteins; wherein proteins involved in energy, sugar metabolism, and folding, assembly, and destination may play pivotal roles in the maturation process of each organ or tissue.

  12. Medulloblastoma in China: Clinicopathologic Analyses of SHH, WNT, and Non-SHH/WNT Molecular Subgroups Reveal Different Therapeutic Responses to Adjuvant Chemotherapy

    Science.gov (United States)

    Ren, Yong; Yao, Yu; Li, Kay Ka-Wai; Ng, Ho-Keung; Mao, Ying; Zhou, Liang-Fu; Zhong, Ping

    2014-01-01

    Medulloblastoma (MB) is one of the most common primary central nervous system tumors in children. Data is lacking of a large cohort of medulloblastoma patients in China. Also, our knowledge on the sensitivity of different molecular subgroups of MB to adjuvant radiation therapy (RT) or chemotherapy (CHT) is still limited. The authors performed a retrospective study of 173 medulloblastoma patients treated at two institutions from 2002 to 2011. Formalin-fixed paraffin embedded (FFPE) tissues were available in all the cases and sections were stained to classify histological and molecular subgroups. Univariate and multivariate analyses were used to investigate prognostic factors. Of 173 patients, there were 118 children and 55 adults, 112 males and 61 females. Estimated 5-year overall survival (OS) rates for all patients, children and adults were 52%, 48% and 63%, respectively. After multivariate analysis, postoperative primary radiation therapy (RT) and chemotherapy (CHT) were revealed as favorable prognostic factors influencing OS and EFS. Postoperative primary chemotherapy (CHT) was found significantly improving the survival of children (pmedulloblastoma (CMB) (OS pmedulloblastoma (DMB) (OS p = 0.361, EFS p = 0.834) and Non-SHH/WNT subgroup (OS p = 0.127, EFS p = 0.055). Our study showed postoperative primary CHT significantly influence the survival of CMB, SHH subgroup and WNT subgroup but not in DMB and Non-SHH/WNT subgroup of MB. PMID:24932704

  13. Possible Factors Promoting Car Evacuation in the 2011 Tohoku Tsunami Revealed by Analysing a Large-Scale Questionnaire Survey in Kesennuma City

    Directory of Open Access Journals (Sweden)

    Fumiyasu Makinoshima

    2017-11-01

    Full Text Available Excessive car evacuation can cause severe traffic jams that can lead to large numbers of casualties during tsunami disasters. Investigating the possible factors that lead to unnecessary car evacuation can ensure smoother tsunami evacuations and mitigate casualty damages in future tsunami events. In this study, we quantitatively investigated the possible factors that promote car evacuation, including both necessary and unnecessary usages, by statistically analysing a large amount of data on actual tsunami evacuation behaviours surveyed in Kesennuma, where devastating damage occurred during the 2011 Tohoku Tsunami. A straightforward statistical analysis revealed a high percentage of car evacuations (approx. 50%; however, this fraction includes a high number of unnecessary usage events that were distinguished based on mode choice reasons. In addition, a binary logistic regression was conducted to quantitatively evaluate the effects of several factors and to identify the dominant factor that affected evacuation mode choice. The regression results suggested that the evacuation distance was the dominant factor for choosing car evacuation relative to other factors, such as age and sex. The cross-validation test of the regression model demonstrated that the considered factors were useful for decision making and the prediction of evacuation mode choice in the target area.

  14. Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

    Science.gov (United States)

    James, Tamara; Hsieh, Meng-Lun; Knipling, Leslie; Hinton, Deborah

    2015-01-01

    Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex. We determined the position of the activator on the DNA from data generated using activator proteins that had been conjugated at specific residues with the chemical cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). These analyses were combined with 3-D models of the available structures of portions of the activator protein and B-form DNA to obtain a 3-D picture of the protein relative to the DNA. Finally, the Molsoft program was used to refine the position, revealing the architecture of the protein-DNA within the transcription complex.

  15. Consumer Loyalty and Loyalty Programs: a topographic examination of the scientific literature using bibliometrics, spatial statistics and network analyses

    Directory of Open Access Journals (Sweden)

    Viviane Moura Rocha

    2015-04-01

    Full Text Available This paper presents a topographic analysis of the fields of consumer loyalty and loyalty programs, vastly studied in the last decades and still relevant in the marketing literature. After the identification of 250 scientific papers that were published in the last ten years in indexed journals, a subset of 76 were chosen and their 3223 references were extracted. The journals in which these papers were published, their key words, abstracts, authors, institutions of origin and citation patterns were identified and analyzed using bibliometrics, spatial statistics techniques and network analyses. The results allow the identification of the central components of the field, as well as its main authors, journals, institutions and countries that intermediate the diffusion of knowledge, which contributes to the understanding of the constitution of the field by researchers and students.

  16. A FORTRAN 77 Program and User's Guide for the Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Helton, Jon C.; Shortencarier, Maichael J.

    1999-08-01

    A description and user's guide are given for a computer program, PATTRN, developed at Sandia National Laboratories for use in sensitivity analyses of complex models. This program is intended for use in the analysis of input-output relationships in Monte Carlo analyses when the input has been selected using random or Latin hypercube sampling. Procedures incorporated into the program are based upon attempts to detect increasingly complex patterns in scatterplots and involve the detection of linear relationships, monotonic relationships, trends in measures of central tendency, trends in measures of variability, and deviations from randomness. The program was designed to be easy to use and portable.

  17. Review of a licensed dengue vaccine: Inappropriate subgroup analyses and selective reporting may cause harm in mass vaccination programs.

    Science.gov (United States)

    Dans, Antonio L; Dans, Leonila F; Lansang, Mary Ann D; Silvestre, Maria Asuncion A; Guyatt, Gordon H

    2017-11-24

    Severe life-threatening dengue fever usually occurs when a child is infected by dengue virus a 2nd time. This is caused by a phenomenon called antibody dependent enhancement or ADE. Since dengue vaccines can mimic a first infection in seronegative children (those with no previous infection), a natural infection later in life could lead to severe disease. The possibility that dengue vaccines can cause severe dengue through ADE has led to serious concern regarding the safety of mass vaccination programs. A published meta-analysis addressed this safety issue for a new vaccine against dengue fever - Dengvaxia ™. The trials in this meta-analysis have been used to campaign for mass vaccination programs in developing countries. We discuss the results of this paper and point out problems in the analyses. Reporting the findings in an Asian trial (CYD14), the authors show a 7-fold rise in one outcome - hospitalization for dengue fever in children harm for another outcome - hospitalization for severe dengue fever (as confirmed by an independent data monitoring committee): 1. in children younger than 9 years, the relative risk was 8.5 [95% CI 0.5, 146.8], and 2. in the overall study group, the relative risk was 5.5 [95% CI: 0.9, 33] The authors conduct a subgroup analysis to support claims that the vaccine is probably safe among children aged 9 years or more. This subgroup analysis has limited credibility because: 1) it was a post-hoc analysis; 2) it was one of a large number of subgroup analyses; 3) the test of interaction was not reported; but was insignificant (p=0.14); and 4) there is no biological basis for a threshold age of 9 years. The more likely explanation for the higher risk in younger children is ADE, that is, more frequent seronegativity, rather than age itself. The selective reporting and inappropriate subgroup claims mask the potential harm of dengue mass vaccination programs. Countries planning public use of the vaccine must conduct diligent post

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

    Science.gov (United States)

    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.

  19. Physiological and proteomics analyses reveal the mechanism of Eichhornia crassipes tolerance to high-concentration cadmium stress compared with Pistia stratiotes.

    Science.gov (United States)

    Li, Xiong; Zhou, Yanli; Yang, Yunqiang; Yang, Shihai; Sun, Xudong; Yang, Yongping

    2015-01-01

    Cadmium (Cd) pollution is an environmental problem worldwide. Phytoremediation is a convenient method of removing Cd from both soil and water, but its efficiency is still low, especially in aquatic environments. Scientists have been trying to improve the ability of plants to absorb and accumulate Cd based on interactions between plants and Cd, especially the mechanism by which plants resist Cd. Eichhornia crassipes and Pistia stratiotes are aquatic plants commonly used in the phytoremediation of heavy metals. In the present study, we conducted physiological and biochemical analyses to compare the resistance of these two species to Cd stress at 100 mg/L. E. crassipes showed stronger resistance and was therefore used for subsequent comparative proteomics to explore the potential mechanism of E. crassipes tolerance to Cd stress at the protein level. The expression patterns of proteins in different functional categories revealed that the physiological activities and metabolic processes of E. crassipes were affected by exposure to Cd stress. However, when some proteins related to these processes were negatively inhibited, some analogous proteins were induced to compensate for the corresponding functions. As a result, E. crassipes could maintain more stable physiological parameters than P. stratiotes. Many stress-resistance substances and proteins, such as proline and heat shock proteins (HSPs) and post translational modifications, were found to be involved in the protection and repair of functional proteins. In addition, antioxidant enzymes played important roles in ROS detoxification. These findings will facilitate further understanding of the potential mechanism of plant response to Cd stress at the protein level.

  20. Physiological and proteomics analyses reveal the mechanism of Eichhornia crassipes tolerance to high-concentration cadmium stress compared with Pistia stratiotes.

    Directory of Open Access Journals (Sweden)

    Xiong Li

    Full Text Available Cadmium (Cd pollution is an environmental problem worldwide. Phytoremediation is a convenient method of removing Cd from both soil and water, but its efficiency is still low, especially in aquatic environments. Scientists have been trying to improve the ability of plants to absorb and accumulate Cd based on interactions between plants and Cd, especially the mechanism by which plants resist Cd. Eichhornia crassipes and Pistia stratiotes are aquatic plants commonly used in the phytoremediation of heavy metals. In the present study, we conducted physiological and biochemical analyses to compare the resistance of these two species to Cd stress at 100 mg/L. E. crassipes showed stronger resistance and was therefore used for subsequent comparative proteomics to explore the potential mechanism of E. crassipes tolerance to Cd stress at the protein level. The expression patterns of proteins in different functional categories revealed that the physiological activities and metabolic processes of E. crassipes were affected by exposure to Cd stress. However, when some proteins related to these processes were negatively inhibited, some analogous proteins were induced to compensate for the corresponding functions. As a result, E. crassipes could maintain more stable physiological parameters than P. stratiotes. Many stress-resistance substances and proteins, such as proline and heat shock proteins (HSPs and post translational modifications, were found to be involved in the protection and repair of functional proteins. In addition, antioxidant enzymes played important roles in ROS detoxification. These findings will facilitate further understanding of the potential mechanism of plant response to Cd stress at the protein level.

  1. Analyses of Sox-B and Sox-E Family Genes in the Cephalopod Sepia officinalis: Revealing the Conserved and the Unusual.

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    Laura Focareta

    Full Text Available Cephalopods provide an unprecedented opportunity for comparative studies of the developmental genetics of organ systems that are convergent with analogous vertebrate structures. The Sox-family of transcription factors is an important class of DNA-binding proteins that are known to be involved in many aspects of differentiation, but have been largely unstudied in lophotrochozoan systems. Using a degenerate primer strategy we have isolated coding sequence for three members of the Sox family of transcription factors from a cephalopod mollusk, the European cuttlefish Sepia officinalis: Sof-SoxE, Sof-SoxB1, and Sof-SoxB2. Analyses of their expression patterns during organogenesis reveals distinct spatial and temporal expression domains. Sof-SoxB1 shows early ectodermal expression throughout the developing epithelium, which is gradually restricted to presumptive sensory epithelia. Expression within the nervous system appears by mid-embryogenesis. Sof-SoxB2 expression is similar to Sof-SoxB1 within the developing epithelia in early embryogenesis, however appears in largely non-overlapping expression domains within the central nervous system and is not expressed in the maturing sensory epithelium. In contrast, Sof-SoxE is expressed throughout the presumptive mesodermal territories at the onset of organogenesis. As development proceeds, Sof-SoxE expression is elevated throughout the developing peripheral circulatory system. This expression disappears as the circulatory system matures, but expression is maintained within undifferentiated connective tissues throughout the animal, and appears within the nervous system near the end of embryogenesis. SoxB proteins are widely known for their role in neural specification in numerous phylogenetic lineages. Our data suggests that Sof-SoxB genes play similar roles in cephalopods. In contrast, Sof-SoxE appears to be involved in the early stages of vasculogenesis of the cephalopod closed circulatory system, a novel

  2. Analyses of Sox-B and Sox-E Family Genes in the Cephalopod Sepia officinalis: Revealing the Conserved and the Unusual.

    Science.gov (United States)

    Focareta, Laura; Cole, Alison G

    2016-01-01

    Cephalopods provide an unprecedented opportunity for comparative studies of the developmental genetics of organ systems that are convergent with analogous vertebrate structures. The Sox-family of transcription factors is an important class of DNA-binding proteins that are known to be involved in many aspects of differentiation, but have been largely unstudied in lophotrochozoan systems. Using a degenerate primer strategy we have isolated coding sequence for three members of the Sox family of transcription factors from a cephalopod mollusk, the European cuttlefish Sepia officinalis: Sof-SoxE, Sof-SoxB1, and Sof-SoxB2. Analyses of their expression patterns during organogenesis reveals distinct spatial and temporal expression domains. Sof-SoxB1 shows early ectodermal expression throughout the developing epithelium, which is gradually restricted to presumptive sensory epithelia. Expression within the nervous system appears by mid-embryogenesis. Sof-SoxB2 expression is similar to Sof-SoxB1 within the developing epithelia in early embryogenesis, however appears in largely non-overlapping expression domains within the central nervous system and is not expressed in the maturing sensory epithelium. In contrast, Sof-SoxE is expressed throughout the presumptive mesodermal territories at the onset of organogenesis. As development proceeds, Sof-SoxE expression is elevated throughout the developing peripheral circulatory system. This expression disappears as the circulatory system matures, but expression is maintained within undifferentiated connective tissues throughout the animal, and appears within the nervous system near the end of embryogenesis. SoxB proteins are widely known for their role in neural specification in numerous phylogenetic lineages. Our data suggests that Sof-SoxB genes play similar roles in cephalopods. In contrast, Sof-SoxE appears to be involved in the early stages of vasculogenesis of the cephalopod closed circulatory system, a novel role for a member of

  3. Stable isotope analyses on archived fish scales reveal the long-term effect of nitrogen loads on carbon cycling in rivers.

    Science.gov (United States)

    Roussel, Jean-Marc; Perrier, Charles; Erkinaro, Jaakko; Niemelä, Eero; Cunjak, Richard A; Huteau, Dominique; Riera, Pascal

    2014-02-01

    Stable isotope analysis of organic matter in sediment records has long been used to track historical changes in productivity and carbon cycling in marine and lacustrine ecosystems. While flow dynamics preclude stratigraphic measurements of riverine sediments, such retrospective analysis is important for understanding biogeochemical cycling in running waters. Unique collections of riverine fish scales were used to analyse δ(15) N and δ(13) C variations in the food web of two European rivers that experience different degrees of anthropogenic pressure. Over the past four decades, dissolved inorganic N loading remained low and constant in the Teno River (70°N, Finland); in contrast, N loading increased fourfold in the Scorff River (47°N, France) over the same period. Archived scales of Atlantic salmon parr, a riverine life-stage that feeds on aquatic invertebrates, revealed high δ(15) N values in the Scorff River reflecting anthropogenic N inputs to that riverine environment. A strong correlation between dissolved inorganic N loads and δ(13) C values in fish scales was observed in the Scorff River, whereas no trend was found in the Teno River. This result suggests that anthropogenic N-nutrients enhanced atmospheric C uptake by primary producers and its transfer to fish. Our results illustrate for the first time that, as for lakes and marine ecosystems, historical changes in anthropogenic N loading can affect C cycling in riverine food webs, and confirm the long-term interactions between N and C biogeochemical cycles in running waters. © 2013 John Wiley & Sons Ltd.

  4. Ancient DNA analyses of early archaeological sites in New Zealand reveal extreme exploitation of moa (Aves: Dinornithiformes) at all life stages

    Science.gov (United States)

    Oskam, Charlotte L.; Allentoft, Morten E.; Walter, Richard; Scofield, R. Paul; Haile, James; Holdaway, Richard N.; Bunce, Michael; Jacomb, Chris

    2012-10-01

    The human colonisation of New Zealand in the late thirteenth century AD led to catastrophic impacts on the local biota and is among the most compelling examples of human over-exploitation of native fauna, including megafauna. Nearly half of the species in New Zealand' s pre-human avifauna are now extinct, including all nine species of large, flightless moa (Aves: Dinornithiformes). The abundance of moa in early archaeological sites demonstrates the significance of these megaherbivores in the diet of the first New Zealanders. Combining moa assemblage data, based on DNA identification of eggshell and bone, with morphological identification of bone (literature and museum catalogued specimens), we present the most comprehensive audit of moa to date from several significant 13th-15th century AD archaeological deposits across the east coast of the South Island. Mitochondrial DNA (mtDNA) was amplified from 251 of 323 (78%) eggshell fragments and 22 of 27 (88%) bone samples, and the analyses revealed the presence of four moa species: Anomalopteryx didiformis; Dinornis robustus; Emeus crassus and Euryapteryx curtus. The mtDNA, along with polymorphic microsatellite markers, enabled an estimate of the minimum number of individual eggs consumed at each site. Remarkably, in one deposit over 50 individual eggs were identified - a number that likely represents a considerable proportion of the total reproductive output of moa in the area and emphasises that human predation of all life stages of moa was intense. Molecular sexing was conducted on bones (n = 11). Contrary to previous ancient DNA studies from natural sites that consistently report an excess of female moa, we observed an excess of males (2.7:1), suggestive that males were preferential targets. This could be related to different behaviour between the two highly size-dimorphic sexes in moa. Lastly, we investigated the moa species from recovered skeletal and eggshell remains from seven Wairau Bar burials, and identified

  5. An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies.

    Science.gov (United States)

    Broughton, Mary C; Davidson, Jane W

    2016-01-01

    observed, with judges revealing preferences for observing particular types of expressive bodily movements. The particular expressive bodily movements that are produced and perceived in marimba performance appear to be shaped by music-related and sound generating features, musical context, and observer music and motor expertise. With an understanding of bodily movements that are generated and perceived as expressive, embodied music performance training programs might be developed to enhance expressive performer-audience communication.

  6. An expressive bodily movement repertoire for marimba performance, revealed through observers’ Laban effort-shape analyses, and allied musical features: two case studies

    Directory of Open Access Journals (Sweden)

    Mary C Broughton

    2016-08-01

    types and locations of actions observed, with judges revealing preferences for observing particular types of expressive bodily movements. The particular expressive bodily movements that are produced and perceived in marimba performance appear to be shaped by music-related and sound generating features, musical context, and observer music and motor expertise. With an understanding of bodily movements that are generated and perceived as expressive, embodied music performance training programs might be developed to enhance expressive performer-audience communication.

  7. An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies

    Science.gov (United States)

    Broughton, Mary C.; Davidson, Jane W.

    2016-01-01

    observed, with judges revealing preferences for observing particular types of expressive bodily movements. The particular expressive bodily movements that are produced and perceived in marimba performance appear to be shaped by music-related and sound generating features, musical context, and observer music and motor expertise. With an understanding of bodily movements that are generated and perceived as expressive, embodied music performance training programs might be developed to enhance expressive performer-audience communication. PMID:27630585

  8. Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

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    Siddaramappa Shivakumara

    2012-08-01

    Full Text Available Abstract Background Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a distant relative of F. tularensis, is thought to constitute an environmental lineage along with Francisella novicida. Nevertheless, both F. philomiragia and F. novicida have been associated with human disease, primarily in immune-compromised individuals. To understand the genetic relationships and evolutionary contexts among different lineages within the genus Francisella, the genome of Francisella spp. strain TX07-7308 was sequenced and compared to the genomes of F. philomiragia strains ATCC 25017 and 25015, F. novicida strain U112, and F. tularensis strain Schu S4. Results The size of strain ATCC 25017 chromosome was 2,045,775 bp and contained 1,983 protein-coding genes. The size of strain TX07-7308 chromosome was 2,035,931 bp and contained 1,980 protein-coding genes. Pairwise BLAST comparisons indicated that strains TX07-7308 and ATCC 25017 contained 1,700 protein coding genes in common. NUCmer analyses revealed that the chromosomes of strains TX07-7308 and ATCC 25017 were mostly collinear except for a few gaps, translocations, and/or inversions. Using the genome sequence data and comparative analyses with other members of the genus Francisella (e.g., F. novicida strain U112 and F. tularensis strain Schu S4, several strain-specific genes were identified. Strains TX07-7308 and ATCC 25017 contained an operon with six open reading frames encoding proteins related to enzymes involved in thiamine biosynthesis that was absent in F. novicida strain U112 and F. tularensis strain Schu S4. Strain ATCC 25017 contained an operon putatively involved in lactose metabolism that was absent in strain TX07-7308, F. novicida strain U112, and F. tularensis strain Schu S4. In contrast, strain TX07-7308 contained an operon putatively

  9. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor.

    Directory of Open Access Journals (Sweden)

    Biaoyang Lin

    2009-08-01

    Full Text Available The androgen receptor (AR plays important roles in the development of male phenotype and in different human diseases including prostate cancers. The AR can act either as a promoter or a tumor suppressor depending on cell types. The AR proliferative response program has been well studied, but its prohibitive response program has not yet been thoroughly studied.Previous studies found that PC3 cells expressing the wild-type AR inhibit growth and suppress invasion. We applied expression profiling to identify the response program of PC3 cells expressing the AR (PC3-AR under different growth conditions (i.e. with or without androgens and at different concentration of androgens and then applied the newly developed ChIP-seq technology to identify the AR binding regions in the PC3 cancer genome. A surprising finding was that the comparison of MOCK-transfected PC3 cells with AR-transfected cells identified 3,452 differentially expressed genes (two fold cutoff even without the addition of androgens (i.e. in ethanol control, suggesting that a ligand independent activation or extremely low-level androgen activation of the AR. ChIP-Seq analysis revealed 6,629 AR binding regions in the cancer genome of PC3 cells with an FDR (false discovery rate cut off of 0.05. About 22.4% (638 of 2,849 can be mapped to within 2 kb of the transcription start site (TSS. Three novel AR binding motifs were identified in the AR binding regions of PC3-AR cells, and two of them share a core consensus sequence CGAGCTCTTC, which together mapped to 27.3% of AR binding regions (1,808/6,629. In contrast, only about 2.9% (190/6,629 of AR binding sites contains the canonical AR matrix M00481, M00447 and M00962 (from the Transfac database, which is derived mostly from AR proliferative responsive genes in androgen dependent cells. In addition, we identified four top ranking co-occupancy transcription factors in the AR binding regions, which include TEF1 (Transcriptional enhancer factor

  10. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Kwang-Soo, E-mail: shinks@dju.kr [Division of Life Science, Daejeon University, Daejeon, 300-716 (Korea, Republic of); Kim, Young Hwan [Biomedical Omics Team, Korea Basic Science Institute (KBSI), Ohcang, 368-883 (Korea, Republic of); Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 305-333 (Korea, Republic of); Yu, Jae-Hyuk, E-mail: jyu1@wisc.edu [Departments of Bacteriology and Genetics, The University of Wisconsin–Madison, Madison, WI, 53706 (United States)

    2015-07-31

    The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus.

  11. Medulloblastoma in China: clinicopathologic analyses of SHH, WNT, and non-SHH/WNT molecular subgroups reveal different therapeutic responses to adjuvant chemotherapy.

    Directory of Open Access Journals (Sweden)

    Zhen-Yu Zhang

    Full Text Available Medulloblastoma (MB is one of the most common primary central nervous system tumors in children. Data is lacking of a large cohort of medulloblastoma patients in China. Also, our knowledge on the sensitivity of different molecular subgroups of MB to adjuvant radiation therapy (RT or chemotherapy (CHT is still limited. The authors performed a retrospective study of 173 medulloblastoma patients treated at two institutions from 2002 to 2011. Formalin-fixed paraffin embedded (FFPE tissues were available in all the cases and sections were stained to classify histological and molecular subgroups. Univariate and multivariate analyses were used to investigate prognostic factors. Of 173 patients, there were 118 children and 55 adults, 112 males and 61 females. Estimated 5-year overall survival (OS rates for all patients, children and adults were 52%, 48% and 63%, respectively. After multivariate analysis, postoperative primary radiation therapy (RT and chemotherapy (CHT were revealed as favorable prognostic factors influencing OS and EFS. Postoperative primary chemotherapy (CHT was found significantly improving the survival of children (p<0.001 while it was not a significant prognostic factor for adult patients. Moreover, patients in WNT subtype had better OS (p = 0.028 than others (SHH and Non-SHH/WNT subtypes given postoperative adjuvant therapies. Postoperative primary RT was found to be a strong prognostic factor influencing the survival in all histological and molecular subgroups (p<0.001. Postoperative primary CHT was found significantly to influence the survival of classic medulloblastoma (CMB (OS p<0.001, EFS p<0.001, SHH subgroup (OS p = 0.020, EFS p = 0.049 and WNT subgroup (OS p = 0.003, EFS p = 0.016 but not in desmoplastic/nodular medulloblastoma (DMB (OS p = 0.361, EFS p = 0.834 and Non-SHH/WNT subgroup (OS p = 0.127, EFS p = 0.055. Our study showed postoperative primary CHT significantly influence the

  12. Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation.

    Science.gov (United States)

    Matthijnssens, Jelle; Miño, Samuel; Papp, Hajnalka; Potgieter, Christiaan; Novo, Luis; Heylen, Elisabeth; Zeller, Mark; Garaicoechea, Lorena; Badaracco, Alejandra; Lengyel, György; Kisfali, Péter; Cullinane, Ann; Collins, P J; Ciarlet, Max; O'Shea, Helen; Parreño, Viviana; Bányai, Krisztián; Barrandeguy, María; Van Ranst, Marc

    2012-04-01

    In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

  13. Impact of public programs on fertility and gender specific investment in human capital of children in rural India: cross sectional and time series analyses.

    Science.gov (United States)

    Duraisamy, P; Malathy, R

    1991-01-01

    Cross sectional and time series analyses are conducted with 1971 and 1981 rural district level data for India in order to estimate variations in program impacts on household decisionmaking concerning fertility, child mortality, and schooling; to analyze how the variation in public program subsidies and services influences sex specific investments in schooling; and to examine the bias in cross sectional estimates by employing fixed effects methodology. The theory of household production uses the framework development by Rosenzweig and Wolpin. The utility function is expressed as a function of families' desired number of children, sex specific investment in human capital of children measured by schooling of males and females, and a composite consumption good. Budget constraints are characterized in terms of the biological supply of births or natural fertility, the number of births averted by fertility control, exogenous money income, the prices of number of children, contraceptives, child schooling, and consumption of goods. Demand functions are constructed from maximizing the utility function subject to the budget constraint. Data constitute 40% of the total districts and 50% of the rural population. The empirical specification of the linear model and variable description are provided. Other explanatory variables included are adult educational attainment; % of scheduled castes and tribes and % Muslim; and % rural population. Estimation methods are described and justification is provided for the use of ordinary least squares and fixed effects methods. The results of the cross sectional analysis reveal that own-program effects of family planning and primary health centers reduced family size in 1971 and 81. The increase in secondary school enrollment is evidenced in only 1971. There is a significant effect of family planning (FP) clinics on the demand for surviving children only in 1971. The presence of a seconary school in a village reduces the demand for children in

  14. Giant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon

    Directory of Open Access Journals (Sweden)

    Caccone Adalgisa

    2007-02-01

    Full Text Available Abstract Background Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (Ne. Results We report here that an analysis of an additional 473 captive-bred tortoises released back to the island reveals an individual (E1465 that exhibits nuclear microsatellite alleles not found in any of the 15 breeders. Statistical analyses incorporating genotypes of 304 field-sampled individuals from all populations on the major islands indicate that E1465 is most probably a hybrid between an Española female tortoise and a male from the island of Pinzón, likely present on Española due to human transport. Conclusion Removal of E1465 as well as its father and possible (half-siblings is warranted to prevent further contamination within this taxon of particular conservation significance. Despite this detected single contamination, it is highly noteworthy to emphasize the success of this repatriation program conducted over nearly 40 years and involving release of over 2000 captive-bred tortoises that now reproduce in situ. The incorporation of molecular genetic analysis of the program is providing guidance that will aid in monitoring the genetic integrity of this ambitious effort to restore a unique linage of a spectacular animal.

  15. Integrated transcript and genome analyses reveal NKX2-1 and MEF2C as potential oncogenes in T cell acute lymphoblastic leukemia

    NARCIS (Netherlands)

    Homminga, I.; Pieters, R.; Langerak, A.W.; de Rooi, J.J.; Stubbs, A.; Verstegen, M.; Vuerhard, M.; Buijs-Gladdines, J.; Kooi, C.; Klous, P.; van Vlierberghe, P.; Ferrando, A.A.; Cayuela, J.M.; Verhaaf, B.; Beverloo, H.B.; Horstmann, M.; de Haas, V.; Wiekmeijer, A.S.; Pike-Overzet, K.; Staal, F.J.; de Laat, W.; Soulier, J.; Sigaux, F.; Meijerink, J.P.

    2011-01-01

    To identify oncogenic pathways in T cell acute lymphoblastic leukemia (T-ALL), we combined expression profiling of 117 pediatric patient samples and detailed molecular-cytogenetic analyses including the Chromosome Conformation Capture on Chip (4C) method. Two T-ALL subtypes were identified that

  16. ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs

    Directory of Open Access Journals (Sweden)

    Mark D. Borromeo

    2016-08-01

    Full Text Available Small cell lung carcinoma (SCLC is a high-grade pulmonary neuroendocrine tumor. The transcription factors ASCL1 and NEUROD1 play crucial roles in promoting malignant behavior and survival of human SCLC cell lines. Here, we find that ASCL1 and NEUROD1 identify heterogeneity in SCLC, bind distinct genomic loci, and regulate mostly distinct genes. ASCL1, but not NEUROD1, is present in mouse pulmonary neuroendocrine cells, and only ASCL1 is required in vivo for tumor formation in mouse models of SCLC. ASCL1 targets oncogenic genes including MYCL1, RET, SOX2, and NFIB while NEUROD1 targets MYC. ASCL1 and NEUROD1 regulate different genes that commonly contribute to neuronal function. ASCL1 also regulates multiple genes in the NOTCH pathway including DLL3. Together, ASCL1 and NEUROD1 distinguish heterogeneity in SCLC with distinct genomic landscapes and distinct gene expression programs.

  17. Rembrandt and/ or studio, Saul and David, c.1655: revealing the curtain using cross-section analyses and X-ray fluorescence imaging

    NARCIS (Netherlands)

    Noble, P.; van Loon, A.; Alfeld, M.; Janssens, K.; Dik, J.

    2012-01-01

    Recent technical investigation of a late Rembrandt painting - Saul and David, c.1655 - from the collection of the Mauritshuis in The Hague has revealed important new information regarding the picture’s condition and original appearance. As already known, at some point in the past, the two figures

  18. cDNA analyses of CAPN3 enhance mutation detection and reveal a low prevalence of LGMD2A patients in Denmark

    DEFF Research Database (Denmark)

    Duno, M.; Sveen, M.L.; Schwartz, M.

    2008-01-01

    suspected to have LGMD2A, based on western blot results. Four of these patients were shown to have LGMD2I upon molecular analysis, whereas 16 of the remaining 42 patients harbored mutations in CAPN3 by both direct genomic sequencing and cDNA analyses. In 10 patients, we identified both mutant alleles....... In three other, only one heterozygous mutation could be identified on the genomic level; however, CAPN3 cDNA analyses demonstrated homozygosity for the mutant allele, indicating the presence of an unidentified allele that somehow compromise correct CAPN3 RNA processing. In the three remaining patients......, only a single heterozygous mutation could be identified both at the genomic level and on full-length CAPN3 cDNA. All three patients exhibited a highly abnormal western blot for calpain-3 and clinical characteristics of LGMD2A. Only three of the genetically confirmed LGMD2A patients were of Danish...

  19. Parental Genome Separation and Elimination of Cells and Chromosomes Revealed by AFLP and GISH analyses in a Brassica carinata × Orychophragmus violaceus Cross

    OpenAIRE

    HUA, YU-WEI; LIU, MIN; LI, ZAI-YUN

    2006-01-01

    • Background and Aims The phenomenon of parental genome separation during the mitotic divisions of hybrid cells was proposed to occur under genetic control in intergeneric hybrids between cultivated Brassica species and Orychophragmus violaceus (2n = 24). To elucidate further the cytological and molecular mechanisms behind parental genome separation, Brassica carinata (2n = 34) × O. violaceus hybrids were resynthesized and their chromosome/genomic complements analysed.

  20. Global Analysis of Neutrophil Responses to Neisseria gonorrhoeae Reveals a Self-Propagating Inflammatory Program

    Science.gov (United States)

    Sintsova, Anna; Sarantis, Helen; Islam, Epshita A.; Sun, Chun Xiang; Amin, Mohsen; Chan, Carlos H. F.; Stanners, Clifford P.; Glogauer, Michael; Gray-Owen, Scott D.

    2014-01-01

    An overwhelming neutrophil-driven response causes both acute symptoms and the lasting sequelae that result from infection with Neisseria gonorrhoeae. Neutrophils undergo an aggressive opsonin-independent response to N. gonorrhoeae, driven by the innate decoy receptor CEACAM3. CEACAM3 is exclusively expressed by human neutrophils, and drives a potent binding, phagocytic engulfment and oxidative killing of Opa-expressing bacteria. In this study, we sought to explore the contribution of neutrophils to the pathogenic inflammatory process that typifies gonorrhea. Genome-wide microarray and biochemical profiling of gonococcal-infected neutrophils revealed that CEACAM3 engagement triggers a Syk-, PKCδ- and Tak1-dependent signaling cascade that results in the activation of an NF-κB-dependent transcriptional response, with consequent production of pro-inflammatory cytokines. Using an in vivo model of N. gonorrhoeae infection, we show that human CEACAM-expressing neutrophils have heightened migration toward the site of the infection where they may be further activated upon Opa-dependent binding. Together, this study establishes that the role of CEACAM3 is not restricted to the direct opsonin-independent killing by neutrophils, since it also drives the vigorous inflammatory response that typifies gonorrhea. By carrying the potential to mobilize increasing numbers of neutrophils, CEACAM3 thereby represents the tipping point between protective and pathogenic outcomes of N. gonorrhoeae infection. PMID:25188454

  1. Structural and Enzymatic Analyses Reveal the Binding Mode of a Novel Series of Francisella tularensis Enoyl Reductase (FabI) Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Mehboob, Shahila; Hevener, Kirk E.; Truong, Kent; Boci, Teuta; Santarsiero, Bernard D.; Johnson, Michael E. (UIC)

    2012-10-10

    Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.

  2. Reconstructed cell fate–regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis

    Science.gov (United States)

    Mendoza-Parra, Marco-Antonio; Malysheva, Valeriya; Mohamed Saleem, Mohamed Ashick; Lieb, Michele; Godel, Aurelie; Gronemeyer, Hinrich

    2016-01-01

    Cell lineages, which shape the body architecture and specify cell functions, derive from the integration of a plethora of cell intrinsic and extrinsic signals. These signals trigger a multiplicity of decisions at several levels to modulate the activity of dynamic gene regulatory networks (GRNs), which ensure both general and cell-specific functions within a given lineage, thereby establishing cell fates. Significant knowledge about these events and the involved key drivers comes from homogeneous cell differentiation models. Even a single chemical trigger, such as the morphogen all-trans retinoic acid (RA), can induce the complex network of gene-regulatory decisions that matures a stem/precursor cell to a particular step within a given lineage. Here we have dissected the GRNs involved in the RA-induced neuronal or endodermal cell fate specification by integrating dynamic RXRA binding, chromatin accessibility, epigenetic promoter epigenetic status, and the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. Our data reveal how RA induces a network of transcription factors (TFs), which direct the temporal organization of cognate GRNs, thereby driving neuronal/endodermal cell fate specification. Modeling signal transduction propagation using the reconstructed GRNs indicated critical TFs for neuronal cell fate specification, which were confirmed by CRISPR/Cas9-mediated genome editing. Overall, this study demonstrates that a systems view of cell fate specification combined with computational signal transduction models provides the necessary insight in cellular plasticity for cell fate engineering. The present integrated approach can be used to monitor the in vitro capacity of (engineered) cells/tissues to establish cell lineages for regenerative medicine. PMID:27650846

  3. Towards equitable access to medicines for the rural poor: analyses of insurance claims reveal rural pharmacy initiative triggers price competition in Kyrgyzstan.

    Science.gov (United States)

    Waning, Brenda; Maddix, Jason; Tripodis, Yorghos; Laing, Richard; Leufkens, Hubert Gm; Gokhale, Manjusha

    2009-12-14

    A rural pharmacy initiative (RPI) designed to increase access to medicines in rural Kyrgyzstan created a network of 12 pharmacies using a revolving drug fund mechanism in 12 villages where no pharmacies previously existed. The objective of this study was to determine if the establishment of the RPI resulted in the unforeseen benefit of triggering medicine price competition in pre-existing (non-RPI) private pharmacies located in the region. We conducted descriptive and multivariate analyses on medicine insurance claims data from Kyrgyzstan's Mandatory Health Insurance Fund for the Jumgal District of Naryn Province from October 2003 to December 2007. We compared average quarterly medicine prices in competitor pharmacies before and after the introduction of the rural pharmacy initiative in October 2004 to determine the RPI impact on price competition. Descriptive analyses suggest competitors reacted to RPI prices for 21 of 30 (70%) medicines. Competitor medicine prices from the quarter before RPI introduction to the end of the study period decreased for 17 of 30 (57%) medicines, increased for 4 of 30 (13%) medicines, and remained unchanged for 9 of 30 (30%) medicines. Among the 9 competitor medicines with unchanged prices, five initially decreased in price but later reverted back to baseline prices. Multivariate analyses on 19 medicines that met sample size criteria confirm these findings. Fourteen of these 19 (74%) competitor medicines changed significantly in price from the quarter before RPI introduction to the quarter after RPI introduction, with 9 of 19 (47%) decreasing in price and 5 of 19 (26%) increasing in price. The RPI served as a market driver, spurring competition in medicine prices in competitor pharmacies, even when they were located in different villages. Initiatives designed to increase equitable access to medicines in rural regions of developing and transitional countries should consider the potential to leverage medicine price competition as a means

  4. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L. Exposed to Water Deficit

    Directory of Open Access Journals (Sweden)

    Stefania Savoi

    2017-07-01

    Full Text Available Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  5. Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes.

    Science.gov (United States)

    Fracchia, Letizia; Dohrmann, Anja B; Martinotti, Maria Giovanna; Tebbe, Christoph C

    2006-08-01

    Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.

  6. Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster.

    Science.gov (United States)

    Lund, Steven T; Peng, Fred Y; Nayar, Tarun; Reid, Karen E; Schlosser, James

    2008-10-01

    Asynchronous ripening of individual grape berries within clusters can lead to inconsistent organoleptic characteristics for wine making. Ripening initiation in grape berries is non-climacteric and not well understood at the molecular level. Evidence is lacking for a single master switch controlling this process, such as the established role for ethylene in climacteric fruit ripening. We used Affymetrix microarray analyses of 32 individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at 50% ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that pigmentation is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. Abscisic acid has previously been demonstrated to be an important signaling component regulating ripening initiation in grapevine. We demonstrate via real-time RT-PCR analyses that up-regulation of a 9-cis-epoxycarotenoid gene family member, VvNCED2, in grape seed and pericarp and a putative ortholog to a reported abscisic acid receptor, VvGCR2, are correlated with ripening initiation. Our results suggest a role for these genes in abscisic acid signaling during ripening initiation.

  7. Genome-wide analyses of SWEET family proteins reveal involvement in fruit development and abiotic/biotic stress responses in banana.

    Science.gov (United States)

    Miao, Hongxia; Sun, Peiguang; Liu, Qing; Miao, Yulu; Liu, Juhua; Zhang, Kaixing; Hu, Wei; Zhang, Jianbin; Wang, Jingyi; Wang, Zhuo; Jia, Caihong; Xu, Biyu; Jin, Zhiqiang

    2017-06-14

    Sugars Will Eventually be Exported Transporters (SWEET) are a novel type of sugar transporter that plays crucial roles in multiple biological processes. From banana, for the first time, 25 SWEET genes which could be classified into four subfamilies were identified. Majority of MaSWEETs in each subfamily shared similar gene structures and conserved motifs. Comprehensive transcriptomic analysis of two banana genotypes revealed differential expression patterns of MaSWEETs in different tissues, at various stages of fruit development and ripening, and in response to abiotic and biotic stresses. More than 80% MaSWEETs were highly expressed in BaXi Jiao (BX, Musa acuminata AAA group, cv. Cavendish), in sharp contrast to Fen Jiao (FJ, M. acuminata AAB group) when pseudostem was first emerged. However, MaSWEETs in FJ showed elevated expression under cold, drought, salt, and fungal disease stresses, but not in BX. Interaction networks and co-expression assays further revealed that MaSWEET-mediated networks participate in fruit development signaling and abiotic/biotic stresses, which was strongly activated during early stage of fruit development in BX. This study provides new insights into the complex transcriptional regulation of SWEETs, as well as numerous candidate genes that promote early sugar transport to improve fruit quality and enhance stress resistance in banana.

  8. Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata.

    Directory of Open Access Journals (Sweden)

    Ting Guo

    Full Text Available Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata ("Tianma", are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca ("Brown Tianma" and G. elata f. elata ("Red Tianma", two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China.

  9. 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.

    Directory of Open Access Journals (Sweden)

    Simone Marcelletti

    Full Text Available 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.

  10. Towards equitable access to medicines for the rural poor: analyses of insurance claims reveal rural pharmacy initiative triggers price competition in Kyrgyzstan

    Directory of Open Access Journals (Sweden)

    Leufkens Hubert GM

    2009-12-01

    Full Text Available Abstract Background A rural pharmacy initiative (RPI designed to increase access to medicines in rural Kyrgyzstan created a network of 12 pharmacies using a revolving drug fund mechanism in 12 villages where no pharmacies previously existed. The objective of this study was to determine if the establishment of the RPI resulted in the unforeseen benefit of triggering medicine price competition in pre-existing (non-RPI private pharmacies located in the region. Methods We conducted descriptive and multivariate analyses on medicine insurance claims data from Kyrgyzstan's Mandatory Health Insurance Fund for the Jumgal District of Naryn Province from October 2003 to December 2007. We compared average quarterly medicine prices in competitor pharmacies before and after the introduction of the rural pharmacy initiative in October 2004 to determine the RPI impact on price competition. Results Descriptive analyses suggest competitors reacted to RPI prices for 21 of 30 (70% medicines. Competitor medicine prices from the quarter before RPI introduction to the end of the study period decreased for 17 of 30 (57% medicines, increased for 4 of 30 (13% medicines, and remained unchanged for 9 of 30 (30% medicines. Among the 9 competitor medicines with unchanged prices, five initially decreased in price but later reverted back to baseline prices. Multivariate analyses on 19 medicines that met sample size criteria confirm these findings. Fourteen of these 19 (74% competitor medicines changed significantly in price from the quarter before RPI introduction to the quarter after RPI introduction, with 9 of 19 (47% decreasing in price and 5 of 19 (26% increasing in price. Conclusions The RPI served as a market driver, spurring competition in medicine prices in competitor pharmacies, even when they were located in different villages. Initiatives designed to increase equitable access to medicines in rural regions of developing and transitional countries should consider the

  11. Phylogeographic Analyses Reveal a Crucial Role of Xinjiang in HIV-1 CRF07_BC and HCV 3a Transmissions in Asia

    Science.gov (United States)

    Liu, Jun; Zhang, Chiyu

    2011-01-01

    Background China faces an increasing prevalence of two HIV-1 circulating recombinant forms (CRFs) 07_BC and 08_BC. Both CRFs_BC were previously demonstrated to originate in Yunnan and spread to Liaoning from Yunnan via injection drug use (IDU) in China. Supposing it is true, we are unable to answer why only CRF07_BC, rather than both CRFs_BC together, was transmitted to Xinjiang. Methodology/Principal Findings We investigated the phylogeography of CRF07_BC and CRF08_BC using multiple HIV-1 genomic regions with Bayesian phylogeography method. Phylogenetic reconstructions showed that all CRF07_BC sequences were divided into two clades, Yunnan and Xinjiang, and all strains from other regions of mainland China clustered within the Xinjiang clade. Significant geographic diffusion links of Xinjiang with other regions (including Liaoning, Beijing, Jiangsu and Guangdong) were supported by Bayes factor tests. The temporal dynamics analyses showed that CRF07_BC spread from Xinjiang to Liaoning in 1996.10, and to Jiangsu in 2000.9. The analyses of CRF08_BC not only confirmed the previous conclusion on temporal and spatial dynamics of CRF08_BC, but also indicated that the CRF08_BC strains from Guangdong and Shanghai originated from Yunnan. The analyses of HCV 3a showed that it was introduced into Xinjiang in the early 1980s, and spread from Xinjiang to Yunnan in 1990.10 and to Jiangsu in 1999.2, and further from Yunnan to Guangxi in 1995.3. The temporal and spatial dynamics of HCV 3a were similar to some extent to that of HIV-1 CRF07_BC and/or CRF08_BC, suggesting a possible association in migration patterns between HCV and HIV-1 through IDU. In addition, HCV 3a spread from Xinjiang to Pakistan, implying a drug trafficking route linking them. Conclusions/Significance Xinjiang, as the most important transfer station for drug trafficking from Golden Crescent to other regions of China, plays a very crucial role in the transmission of viruses (e.g., HIV-1 and HCV) through IDU in

  12. RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

    DEFF Research Database (Denmark)

    Salleh, M. S.; Mazzoni, G.; Höglund, J. K.

    2017-01-01

    The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high......-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate...... genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency...

  13. RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle.

    Science.gov (United States)

    Salleh, M S; Mazzoni, G; Höglund, J K; Olijhoek, D W; Lund, P; Løvendahl, P; Kadarmideen, H N

    2017-03-24

    The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP's and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins.

  14. The Acinetobacter Outer Membrane Contains Multiple Specific Channels for Carbapenem β-Lactams as Revealed by Kinetic Characterization Analyses of Imipenem Permeation into Acinetobacter baylyi Cells.

    Science.gov (United States)

    Morán-Barrio, Jorgelina; Cameranesi, María M; Relling, Verónica; Limansky, Adriana S; Brambilla, Luciano; Viale, Alejandro M

    2017-03-01

    The number and type of outer membrane (OM) channels responsible for carbapenem uptake in Acinetobacter are still not well defined. Here, we addressed these questions by using Acinetobacter baylyi as a model species and a combination of methodologies aimed to characterize OM channels in their original membrane environment. Kinetic and competition analyses of imipenem (IPM) uptake by A. baylyi whole cells allowed us to identify different carbapenem-specific OM uptake sites. Comparative analyses of IPM uptake by A. baylyi wild-type (WT) cells and ΔcarO mutants lacking CarO indicated that this OM protein provided a carbapenem uptake site displaying saturable kinetics and common binding sites for basic amino acids compatible with a specific channel. The kinetic analysis uncovered another carbapenem-specific channel displaying a somewhat lower affinity for IPM than that of CarO and, in addition, common binding sites for basic amino acids as determined by competition studies. The use of A. baylyi gene deletion mutants lacking OM proteins proposed to function in carbapenem uptake in Acinetobacter baumannii indicated that CarO and OprD/OccAB1 mutants displayed low but consistent reductions in susceptibility to different carbapenems, including IPM, meropenem, and ertapenem. These two mutants also showed impaired growth on l-Arg but not on other carbon sources, further supporting a role of CarO and OprD/OccAB1 in basic amino acid and carbapenem uptake. A multiple-carbapenem-channel scenario may provide clues to our understanding of the contribution of OM channel loss or mutation to the carbapenem-resistant phenotype evolved by pathogenic members of the Acinetobacter genus. Copyright © 2017 American Society for Microbiology.

  15. Host-dependent differences in resource use associated with Anilocra spp. parasitism in two coral reef fishes, as revealed by stable carbon and nitrogen isotope analyses

    Science.gov (United States)

    Welicky, Rachel; Demopoulos, Amanda W. J.; Sikkel, Paul C.

    2017-01-01

    The role of parasites in trophic ecology is poorly understood in marine ecosystems. Stable isotope analyses (SIA) have been widely used in studies of trophic ecology, but have rarely been applied to study the role of parasites. Considering that some parasites are associated with altered host foraging patterns, SIA can help elucidate whether parasitism influences host trophic interactions. French grunt (Haemulon flavolineatum), an abundant Caribbean coral reef fish, contributes greatly to trophic connectivity. They typically depart the reef at dusk, feed overnight in seagrass beds, and return to the reef at dawn. The large parasitic isopod Anilocra haemuli commonly infects French grunt, and infected fish are less likely to complete their diel migration, and are in poorer condition than uninfected conspecifics. Brown chromis (Chromis multilineata) are diurnally feeding planktivores and infection by Anilocra chromis does not influence host condition. To determine if Anilocra infection influences host diet and foraging locality, we conducted stable carbon and nitrogen isotope analyses on scale, muscle, heart and gill tissues of infected and uninfected French grunt and brown chromis. We determined that all French grunt had δ13C values representative of seagrass habitats, but infected French grunt were significantly enriched in 13C and 15N compared to uninfected conspecifics. This suggests that compared to uninfected conspecifics, infected French grunt forage in seagrass, but on isotopically enriched prey, and/or are in poorer condition, which can elevate δ13C and δ15N values. For brown chromis, infection did not significantly influence any δ13C and δ15N values; hence they all foraged in the same environment and on similar prey. This is the first study to use SIA to examine differences in resource use by Caribbean coral reef fishes associated with parasitism and to evaluate how closely related parasites might have host-dependent effects on host trophic ecology.

  16. Transcriptome-Wide Mega-Analyses Reveal Joint Dysregulation of Immunologic Genes and Transcription Regulators in Brain and Blood in Schizophrenia

    Science.gov (United States)

    Hess, Jonathan L.; Tylee, Daniel S.; Barve, Rahul; de Jong, Simone; Ophoff, Roel A.; Kumarasinghe, Nishantha; Tooney, Paul; Schall, Ulrich; Gardiner, Erin; Beveridge, Natalie Jane; Scott, Rodney J.; Yasawardene, Surangi; Perera, Antionette; Mendis, Jayan; Carr, Vaughan; Kelly, Brian; Cairns, Murray; Tsuang, Ming T.; Glatt, Stephen J.

    2016-01-01

    The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n = 315) and from ex-vivo blood tissues (n = 578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia. PMID:27450777

  17. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    Directory of Open Access Journals (Sweden)

    David Kamanda Ngugi

    Full Text Available Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C and salinity (~41 psu from the mixed layer (~200 m to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS region of SAR11 in different depths of the Red Sea's water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen on the population dynamics of this ubiquitous marine bacterium.

  18. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  19. Mycorrhiza analyses in New Zealand truffières reveal frequent but variable persistence of Tuber melanosporum in co-existence with other truffle species.

    Science.gov (United States)

    Guerin-Laguette, Alexis; Cummings, Nicholas; Hesom-Williams, Nina; Butler, Ruth; Wang, Yun

    2013-02-01

    This study compiles the results from an examination of mycorrhizae on root samples from Tuber melanosporum truffières in New Zealand. Samples were taken over 5 years from 328 trees in 43 truffières established with nursery-inoculated trees. Mycorrhizae were analysed using a combination of morphological and molecular techniques, focusing on the identification of Tuber species. Results show that 49% of the trees, and nearly 90% of the truffières, retained T. melanosporum mycorrhizae up to 21 years after planting. Tuber mycorrhizae with spiky cystidia were found on 26.9% of the tested trees: Tuber brumale (5.5%), Tuber maculatum (10.7%), and unidentified Tuber species (10.7%), and were detected in 67% of the truffières tested. T. brumale was found in 28% and T. maculatum in 35% of the truffières. In 56% of the truffières, T. melanosporum was found to occur with spiky Tuber species. The existence of T. brumale and T. maculatum in the same truffière was recorded only once. Forty-four percent of trees examined had Scleroderma-like (SCL) mycorrhizae and 50% of trees hosted other ectomycorrhizal species (OE). For all categories of mycorrhizal species examined, the variation between truffières was greater than variation within each truffière. Overall results indicate that Corylus avellana tends to be more receptive to mycorrhizae of Tuber species than Quercus robur but is not necessarily more productive. In productive truffières, Q. robur appears to host SCL mycorrhizae more often than C. avellana. This is the first study of its scale to analyse the mycorrhizal species associated with T. melanosporum truffières in the Southern Hemisphere.

  20. Transcriptional Profiling Reveals a Common Metabolic Program in High-Risk Human Neuroblastoma and Mouse Neuroblastoma Sphere-Forming Cells

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    Mengling Liu

    2016-10-01

    Full Text Available High-risk neuroblastoma remains one of the deadliest childhood cancers. Identification of metabolic pathways that drive or maintain high-risk neuroblastoma may open new avenues of therapeutic interventions. Here, we report the isolation and propagation of neuroblastoma sphere-forming cells with self-renewal and differentiation potential from tumors of the TH-MYCN mouse, an animal model of high-risk neuroblastoma with MYCN amplification. Transcriptional profiling reveals that mouse neuroblastoma sphere-forming cells acquire a metabolic program characterized by transcriptional activation of the cholesterol and serine-glycine synthesis pathways, primarily as a result of increased expression of sterol regulatory element binding factors and Atf4, respectively. This metabolic reprogramming is recapitulated in high-risk human neuroblastomas and is prognostic for poor clinical outcome. Genetic and pharmacological inhibition of the metabolic program markedly decreases the growth and tumorigenicity of both mouse neuroblastoma sphere-forming cells and human neuroblastoma cell lines. These findings suggest a therapeutic strategy for targeting the metabolic program of high-risk neuroblastoma.

  1. Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus and other eukaryote species revealed by nucleotide and amino acid sequence analyses

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    Andréia B. Poletto

    2008-01-01

    Full Text Available Actin-encoding cDNAs of Nile tilapia (Oreochromis niloticus were isolated by RT-PCR using total RNA samples of different tissues and further characterized by nucleotide sequencing and in silico amino acid (aa sequence analysis. Comparisons among the actin gene sequences of O. niloticus and those of other species evidenced that the isolated genes present a high similarity to other fish and other vertebrate actin genes. The highest nucleotide resemblance was observed between O. niloticus and O. mossambicus a-actin and b-actin genes. Analysis of the predicted aa sequences revealed two distinct types of cytoplasmic actins, one cardiac muscle actin type and one skeletal muscle actin type that were expressed in different tissues of Nile tilapia. The evolutionary relationships between the Nile tilapia actin genes and diverse other organisms is discussed.

  2. Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).

    Science.gov (United States)

    Zhu, Haifeng; Wang, Hua; Zhu, Yifang; Zou, Jianwen; Zhao, Fang-Jie; Huang, Chao-Feng

    2015-01-21

    Similar to common buckwheat (Fagopyrum esculentum), tartary buckwheat (Fagopyrum tataricum) shows a high level of aluminum (Al) tolerance and accumulation. However, the molecular mechanisms for Al detoxification and accumulation are still poorly understood. To begin to elucidate the molecular basis of Al tolerance and accumulation, we used the Illumina high-throughput mRNA sequencing (RNA-seq) technology to conduct a genome-wide transcriptome analysis on both tip and basal segments of the roots exposed to Al. By using the Trinity method for the de novo assembly and cap3 software to reduce the redundancy and chimeras of the transcripts, we constructed 39,815 transcripts with an average length of 1184 bp, among which 20,605 transcripts were annotated by BLAST searches in the NCBI non-redundant protein database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that expression of genes involved in the defense of cell wall toxicity and oxidative stress was preferentially induced by Al stress. Our RNA-seq data also revealed that organic acid metabolism was unlikely to be a rate-limiting step for the Al-induced secretion of organic acids in buckwheat. We identified two citrate transporter genes that were highly induced by Al and potentially involved in the release of citrate into the xylem. In addition, three of four conserved Al-tolerance genes were found to be duplicated in tartary buckwheat and display diverse expression patterns. Nearly 40,000 high quality transcript contigs were de novo assembled for tartary buckwheat, providing a reference platform for future research work in this plant species. Our differential expression and phylogenetic analysis revealed novel aspects of Al-tolerant mechanisms in buckwheat.

  3. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence.

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    Dawoon Chung

    2014-11-01

    Full Text Available The Aspergillus fumigatus sterol regulatory element binding protein (SREBP SrbA belongs to the basic Helix-Loop-Helix (bHLH family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA. How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4-sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveal new insights into SREBPs' complex role in infection site adaptation and fungal virulence.

  4. Combining surface weathering analyses and cosmogenic 36Cl dating on the Pisia fault plane (Eastern Gulf of Corinth) to reveal the Holocene earthquake history

    Science.gov (United States)

    Mechernich, Silke; Schneiderwind, Sascha; Mason, Jack; Papanikolaou, Ioannis; Binnie, Steven A.; Dunai, Tibor J.; Reicherter, Klaus

    2017-04-01

    The deformation of the Corinth rift (Greece) is distributed along several E-W trending active normal faults like the 25-km-long Pisia fault, which experienced up to 110 cm of coseismic displacement during the 1981 Alkyonides earthquake sequence (Mw 6.7). Ages of paleoearthquakes and slip rate estimates of the Pisia fault are not known so far, despite the faults recent strong shaking and its significant destruction that reached until Athens. We mapped the continuous bedrock fault scarp of the central Pisia fault and revealed at least six different weathering stripes, which are interpreted as coseismic slip that stepwise exhumed the Pisia fault plane. The stripes were detected by color changes, lichen colonization, karst features (pitting and solution flute termination), and by the laser backscatter intensity. Their width and thus the amount of coseismic displacement ranges from 50-110 cm suggesting that six to seven paleoearthquakes of Mw 6.5-6.7 have exhumed the lower 5.15 m of the free-face. Forward modeling of 32 36Cl concentrations indicates that the Pisia fault moved at an average slip rate of 0.7 mm/yr during the Holocene. Modeled ages of individual earthquake events reveal recurrence intervals ranging between 0.2 and 3.1 kyr and a declined tectonic activity from this fault during the past 4.5 kyr. The exposure time in between most events was too narrow to be able to differentiate consecutive events based on cusps in the cosmogenic 36Cl concentrations as there is a rather low local 36Cl production rate (38°N, 625 m a.s.l.). Since such recurrence intervals and earthquake clustering phenomena appear to be quite common on active faults, mapping of independent offset features are often necessary to accurately restore the earthquake history on similarly located bedrock fault planes.

  5. Chromosome analyses in dogs.

    Science.gov (United States)

    Reimann-Berg, N; Bullerdiek, J; Murua Escobar, H; Nolte, I

    2012-01-01

    Cytogenetics is the study of normal and abnormal chromosomes. Every species is characterized by a given number of chromosomes that can be recognized by their specific shape. The chromosomes are arranged according to standard classification schemes for the respective species. While pre- and postnatal chromosome analyses investigate the constitutional karyotype, tumor cytogenetics is focused on the detection of clonal acquired, tumor-associated chromosome aberrations. Cytogenetic investigations in dogs are of great value especially for breeders dealing with fertility problems within their pedigrees, for veterinarians and last but not least for the dog owners. Dogs and humans share a variety of genetic diseases, including cancer. Thus, the dog has become an increasingly important model for genetic diseases. However, cytogenetic analyses of canine cells are complicated by the complex karyotype of the dog. Only just 15 years ago, a standard classification scheme for the complete canine karyotype was established. For chromosome analyses of canine cells the same steps of chromosome preparation are used as in human cytogenetics. There are few reports about cytogenetic changes in non-neoplastic cells, involving predominantly the sex chromosomes. Cytogenetic analyses of different entities of canine tumors revealed that, comparable to human tumors, tumors of the dog are often characterized by clonal chromosome aberrations, which might be used as diagnostic and prognostic markers. The integration of modern techniques (molecular genetic approaches, adaptive computer programs) will facilitate and complete conventional cytogenetic studies. However, conventional cytogenetics is still non-replaceable.

  6. Controls on the long term earthquake behavior of an intraplate fault revealed by U-Th and stable isotope analyses of syntectonic calcite veins

    Science.gov (United States)

    Williams, Randolph; Goodwin, Laurel; Sharp, Warren; Mozley, Peter

    2017-04-01

    U-Th dates on calcite precipitated in coseismic extension fractures in the Loma Blanca normal fault zone, Rio Grande rift, NM, USA, constrain earthquake recurrence intervals from 150-565 ka. This is the longest direct record of seismicity documented for a fault in any tectonic environment. Combined U-Th and stable isotope analyses of these calcite veins define 13 distinct earthquake events. These data show that for more than 400 ka the Loma Blanca fault produced earthquakes with a mean recurrence interval of 40 ± 7 ka. The coefficient of variation for these events is 0.40, indicating strongly periodic seismicity consistent with a time-dependent model of earthquake recurrence. Stochastic statistical analyses further validate the inference that earthquake behavior on the Loma Blanca was time-dependent. The time-dependent nature of these earthquakes suggests that the seismic cycle was fundamentally controlled by a stress renewal process. However, this periodic cycle was punctuated by an episode of clustered seismicity at 430 ka. Recurrence intervals within the earthquake cluster were as low as 5-11 ka. Breccia veins formed during this episode exhibit carbon isotope signatures consistent with having formed through pronounced degassing of a CO2 charged brine during post-failure, fault-localized fluid migration. The 40 ka periodicity of the long-term earthquake record of the Loma Blanca fault is similar in magnitude to recurrence intervals documented through paleoseismic studies of other normal faults in the Rio Grande rift and Basin and Range Province. We propose that it represents a background rate of failure in intraplate extension. The short-term, clustered seismicity that occurred on the fault records an interruption of the stress renewal process, likely by elevated fluid pressure in deeper structural levels of the fault, consistent with fault-valve behavior. The relationship between recurrence interval and inferred fluid degassing suggests that pore fluid pressure

  7. Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora.

    Science.gov (United States)

    Heizer, Esley; Zarlenga, Dante S; Rosa, Bruce; Gao, Xin; Gasser, Robin B; De Graef, Jessie; Geldhof, Peter; Mitreva, Makedonka

    2013-02-22

    Cooperia oncophora and Ostertagia ostertagi are among the most important gastrointestinal nematodes of cattle worldwide. The economic losses caused by these parasites are on the order of hundreds of millions of dollars per year. Conventional treatment of these parasites is through anthelmintic drugs; however, as resistance to anthelmintics increases, overall effectiveness has begun decreasing. New methods of control and alternative drug targets are necessary. In-depth analysis of transcriptomic data can help provide these targets. The assembly of 8.7 million and 11 million sequences from C. oncophora and O. ostertagi, respectively, resulted in 29,900 and 34,792 transcripts. Among these, 69% and 73% of the predicted peptides encoded by C. oncophora and O. ostertagi had homologues in other nematodes. Approximately 21% and 24% were constitutively expressed in both species, respectively; however, the numbers of transcripts that were stage specific were much smaller (~1% of the transcripts expressed in a stage). Approximately 21% of the transcripts in C. oncophora and 22% in O. ostertagi were up-regulated in a particular stage. Functional molecular signatures were detected for 46% and 35% of the transcripts in C. oncophora and O. ostertagi, respectively. More in-depth examinations of the most prevalent domains led to knowledge of gene expression changes between the free-living (egg, L1, L2 and L3 sheathed) and parasitic (L3 exsheathed, L4, and adult) stages. Domains previously implicated in growth and development such as chromo domains and the MADF domain tended to dominate in the free-living stages. In contrast, domains potentially involved in feeding such as the zinc finger and CAP domains dominated in the parasitic stages. Pathway analyses showed significant associations between life-cycle stages and peptides involved in energy metabolism in O. ostertagi whereas metabolism of cofactors and vitamins were specifically up-regulated in the parasitic stages of C

  8. Comparative proteomic and metabolomic analyses reveal mechanisms of improved cold stress tolerance in bermudagrass (Cynodon dactylon (L.) Pers.) by exogenous calcium.

    Science.gov (United States)

    Shi, Haitao; Ye, Tiantian; Zhong, Bao; Liu, Xun; Chan, Zhulong

    2014-11-01

    As an important second messenger, calcium is involved in plant cold stress response, including chilling (stress tolerances, while ethylene glycol-bis-(β-aminoethyl) ether-N,N,N,N-tetraacetic acid (EGTA) reversed CaCl2 effects in bermudagrass (Cynodon dactylon (L.) Pers.). Physiological analyses showed that CaCl2 treatment alleviated the reactive oxygen species (ROS) burst and cell damage triggered by chilling stress, via activating antioxidant enzymes, non-enzymatic glutathione antioxidant pool, while EGTA treatment had the opposite effects. Additionally, comparative proteomic analysis identified 51 differentially expressed proteins that were enriched in redox, tricarboxylicacid cycle, glycolysis, photosynthesis, oxidative pentose phosphate pathway, and amino acid metabolisms. Consistently, 42 metabolites including amino acids, organic acids, sugars, and sugar alcohols were regulated by CaCl2 treatment under control and cold stress conditions, further confirming the common modulation of CaCl2 treatment in carbon metabolites and amino acid metabolism. Taken together, this study reported first evidence of the essential and protective roles of endogenous and exogenous calcium in bermudagrass response to cold stress, partially via activation of the antioxidants and modulation of several differentially expressed proteins and metabolic homeostasis in the process of cold acclimation. © 2014 Institute of Botany, Chinese Academy of Sciences.

  9. Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    Science.gov (United States)

    Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

    2011-01-01

    Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. PMID:21980283

  10. Comparative genomic and transcriptional analyses of the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant roles during infection and development.

    Science.gov (United States)

    Lyu, Xueliang; Shen, Cuicui; Fu, Yanping; Xie, Jiatao; Jiang, Daohong; Li, Guoqing; Cheng, Jiasen

    2015-11-04

    Our comparative genomic analysis showed that the numbers of plant cell wall (PCW)- and fungal cell wall (FCW)-degradation-associated carbohydrate-active enzymes (CAZymes) in necrotrophic and hemibiotrophic fungi are significantly larger than that in most biotrophic fungi. However, our transcriptional analyses of CAZyme-encoding genes in Melampsora larici-populina, Puccinia graminis and Sclerotinia sclerotiorum showed that many genes encoding PCW- and FCW-degradation-associated CAZymes were significantly up-regulated during the infection of both necrotrophic fungi and biotrophic fungi, indicating an existence of a universal mechanism underlying PCW degradation and FCW reorganization or modification, which are both intimately involved in necrotrophic and biotrophic fungal infection. Furthermore, our results showed that the FCW reorganization or modification was also related to the fungal development. Additionally, our transcriptional analysis of the secretome of S. sclerotiorum showed that many secreted protein-encoding genes were dramatically induced during infection. Among them, a small, cysteine-rich protein SsCVNH was experimentally confirmed to be essential for the virulence and sclerotial development, indicating that the small secreted proteins might also play crucial roles as potential effectors in host-non-specific necrotrophic fungi.

  11. Likelihood and Bayesian analyses reveal major genes affecting body composition, carcass, meat quality and the number of false teats in a Chinese European pig line

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    Le Roy Pascale

    2003-07-01

    Full Text Available Abstract Segregation analyses were performed using both maximum likelihood – via a Quasi Newton algorithm – (ML-QN and Bayesian – via Gibbs sampling – (Bayesian-GS approaches in the Chinese European Tiameslan pig line. Major genes were searched for average ultrasonic backfat thickness (ABT, carcass fat (X2 and X4 and lean (X5 depths, days from 20 to 100 kg (D20100, Napole technological yield (NTY, number of false (FTN and good (GTN teats, as well as total teat number (TTN. The discrete nature of FTN was additionally considered using a threshold model under ML methodology. The results obtained with both methods consistently suggested the presence of major genes affecting ABT, X2, NTY, GTN and FTN. Major genes were also suggested for X4 and X5 using ML-QN, but not the Bayesian-GS, approach. The major gene affecting FTN was confirmed using the threshold model. Genetic correlations as well as gene effect and genotype frequency estimates suggested the presence of four different major genes. The first gene would affect fatness traits (ABT, X2 and X4, the second one a leanness trait (X5, the third one NTY and the last one GTN and FTN. Genotype frequencies of breeding animals and their evolution over time were consistent with the selection performed in the Tiameslan line.

  12. Rasch analysis reveals comparative analyses of activities of daily living/instrumental activities of daily living summary scores from different residential settings is inappropriate.

    Science.gov (United States)

    Lutomski, Jennifer E; Krabbe, Paul F M; den Elzen, Wendy P J; Olde-Rikkert, Marcel G M; Steyerberg, Ewout W; Muntinga, Maaike E; Bleijenberg, Nienke; Kempen, Gertrudis I J M; Melis, René J F

    2016-06-01

    To internally validate a 15-item dichotomous activities of daily living (ADL) and instrumental activities of daily living (IADL) index. Data were extracted from The Older Persons and Informal Caregivers Survey Minimum DataSet (TOPICS-MDS). Using Rasch modeling, six aspects of the ADL/IADL scale were assessed: (1) overall fit, (2) internal consistency, (3) individual item and person fit, (4) local dependency, (5) targeting, and (6) differential item functioning (DIF) (RUMM 2030). All analyses were stratified by living situation [community-dwelling (n = 21,926) or residential care facility (n = 2,458)]. In both settings, "eating" was the easiest activity on the scale and "performing household tasks" was the most difficult activity. However, based on the location on the logit scale, the level of difficulty for certain items varied between residential settings, suggesting summary scores are not equivalent between these settings. DIF by gender and age group was observed for several items, indicating potential measurement bias in the scale. Unless adjustments are undertaken, ADL/IADL summary scores retrieved from older persons residing in the community or residential care facilities should not be directly compared. This 15-item scale is poorly targeted for a community-dwelling older population, underscoring the need for items with improved discriminative ability. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Transcriptional and physiological analyses of Fe deficiency response in maize reveal the presence of Strategy I components and Fe/P interactions.

    Science.gov (United States)

    Zanin, Laura; Venuti, Silvia; Zamboni, Anita; Varanini, Zeno; Tomasi, Nicola; Pinton, Roberto

    2017-02-13

    Under limited iron (Fe) availability maize, a Strategy II plant, improves Fe acquisition through the release of phytosiderophores (PS) into the rhizosphere and the subsequent uptake of Fe-PS complexes into root cells. Occurrence of Strategy-I-like components and interactions with phosphorous (P) nutrition has been hypothesized based on molecular and physiological studies in grasses. In this report transcriptomic analysis (NimbleGen microarray) of Fe deficiency response revealed that maize roots modulated the expression levels of 724 genes (508 up- and 216 down-regulated, respectively). As expected, roots of Fe-deficient maize plants overexpressed genes involved in the synthesis and release of 2'-deoxymugineic acid (the main PS released by maize roots). A strong modulation of genes involved in regulatory aspects, Fe translocation, root morphological modification, primary metabolic pathways and hormonal metabolism was induced by the nutritional stress. Genes encoding transporters for Fe(2+) (ZmNRAMP1) and P (ZmPHT1;7 and ZmPHO1) were also up-regulated under Fe deficiency. Fe-deficient maize plants accumulated higher amounts of P than the Fe-sufficient ones, both in roots and shoots. The supply of 1 μM (59)Fe, as soluble (Fe-Citrate and Fe-PS) or sparingly soluble (Ferrihydrite) sources to deficient plants, caused a rapid down-regulation of genes coding for PS and Fe(III)-PS transport, as well as of ZmNRAMP1 and ZmPHT1;7. Levels of (32)P absorption essentially followed the rates of (59)Fe uptake in Fe-deficient plants during Fe resupply, suggesting that P accumulation might be regulated by Fe uptake in maize plants. The transcriptional response to Fe-deficiency in maize roots confirmed the modulation of known genes involved in the Strategy II and revealed the presence of Strategy I components usually described in dicots. Moreover, data here presented provide evidence of a close relationship between two essential nutrients for plants, Fe and P, and highlight a key

  14. Genome-wide identification, phylogeny, and expression analyses of the 14-3-3 family reveal their involvement in the development, ripening and abiotic stress response in banana

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    meiying li

    2016-09-01

    Full Text Available Plant 14-3-3 proteins act as critical components of various cellular signaling processes and play an important role in regulating multiple physiological processes. However, less information is known about the 14-3-3 gene family in banana. In this study, 25 14-3-3 genes were identified from the banana genome. Based on the evolutionary analysis, banana 14-3-3 proteins were clustered into ε and non-ε groups. Conserved motif analysis showed that all identified banana 14-3-3 genes had the typical 14-3-3 motif. The gene structure of banana 14-3-3 genes showed distinct class-specific divergence between the ε group and the non-ε group. Most banana 14-3-3 genes showed strong transcript accumulation changes during fruit development and postharvest ripening in two banana varieties, indicating that they might be involved in regulating fruit development and ripening. Moreover, some 14-3-3 genes also showed great changes after osmotic, cold, and salt treatments in two banana varieties, suggested their potential role in regulating banana response to abiotic stress. Taken together, this systemic analysis reveals the involvement of banana 14-3-3 genes in fruit development, postharvest ripening, and response to abiotic stress and provides useful information for understanding the functions of 14-3-3 genes in banana.

  15. Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range.

    Science.gov (United States)

    Wei, Shu-Jun; Cao, Li-Jun; Gong, Ya-Jun; Shi, Bao-Cai; Wang, Su; Zhang, Fan; Guo, Xiao-Jun; Wang, Yuan-Min; Chen, Xue-Xin

    2015-08-01

    The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  16. Crystal structure and biochemical analyses reveal that the Arabidopsis triphosphate tunnel metalloenzyme AtTTM3 is a tripolyphosphatase involved in root development.

    Science.gov (United States)

    Moeder, Wolfgang; Garcia-Petit, Christel; Ung, Huoi; Fucile, Geoffrey; Samuel, Marcus A; Christendat, Dinesh; Yoshioka, Keiko

    2013-11-01

    The Arabidopsis protein AtTTM3 belongs to the CYTH superfamily named after its two founding members, the CyaB adenylate cyclase from Aeromonas hydrophila and the mammalian thiamine triphosphatase. In this study we report the three-dimensional structure of a plant CYTH domain protein, AtTTM3, determined at 1.9 Å resolution. The crystal structure revealed the characteristic tunnel architecture of CYTH proteins, which specialize in the binding of nucleotides and other organic phosphates and in phosphoryl transfer reactions. The β barrel is composed of eight antiparallel β strands with a cluster of conserved inwardly facing acidic and basic amino acid residues. Mutagenesis of these residues in the catalytic core led to an almost complete loss of enzymatic activity. We established that AtTTM3 is not an adenylate cyclase. Instead, the enzyme displayed weak NTP phosphatase as well as strong tripolyphosphatase activities similar to the triphosphate tunnel metalloenzyme proteins from Clostridium thermocellum (CthTTM) and Nitrosomonas europaea (NeuTTM). AtTTM3 is most highly expressed in the proximal meristematic zone of the plant root. Furthermore, an AtTTM3 T-DNA insertion knockout line displayed a delay in root growth as well as reduced length and number of lateral roots, suggesting a role for AtTTM3 in root development. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  17. 13C-Tracer and Gas Chromatography-Mass Spectrometry Analyses Reveal Metabolic Flux Distribution in the Oleaginous Microalga Chlorella protothecoides1[C][W][OA

    Science.gov (United States)

    Xiong, Wei; Liu, Lixia; Wu, Chao; Yang, Chen; Wu, Qingyu

    2010-01-01

    The green alga Chlorella protothecoides has received considerable attention because it accumulates neutral triacylglycerols, commonly regarded as an ideal feedstock for biodiesel production. In order to gain a better understanding of its metabolism, tracer experiments with [U-13C]/[1-13C]glucose were performed with heterotrophic growth of C. protothecoides for identifying the metabolic network topology and estimating intracellular fluxes. Gas chromatography-mass spectrometry analysis tracked the labeling patterns of protein-bound amino acids, revealing a metabolic network consisting of the glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle with inactive glyoxylate shunt. Evidence of phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme activity was also obtained. It was demonstrated that the relative activity of the pentose phosphate pathway to glycolysis under nitrogen-limited environment increased, reflecting excess NADPH requirements for lipid biosynthesis. Although the growth rate and cellular oil content were significantly altered in response to nitrogen limitation, global flux distribution of C. protothecoides remained stable, exhibiting the rigidity of central carbon metabolism. In conclusion, quantitative knowledge on the metabolic flux distribution of oleaginous alga obtained in this study may be of value in designing strategies for metabolic engineering of desirable bioproducts. PMID:20720172

  18. Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain.

    Directory of Open Access Journals (Sweden)

    Ruben Pérez

    Full Text Available Canine parvovirus (CPV, a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population and a major recombinant strain (86.7%. The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity.

  19. Phylogenetic and Genome-Wide Deep-Sequencing Analyses of Canine Parvovirus Reveal Co-Infection with Field Variants and Emergence of a Recent Recombinant Strain

    Science.gov (United States)

    Pérez, Ruben; Calleros, Lucía; Marandino, Ana; Sarute, Nicolás; Iraola, Gregorio; Grecco, Sofia; Blanc, Hervé; Vignuzzi, Marco; Isakov, Ofer; Shomron, Noam; Carrau, Lucía; Hernández, Martín; Francia, Lourdes; Sosa, Katia; Tomás, Gonzalo; Panzera, Yanina

    2014-01-01

    Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity. PMID:25365348

  20. Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Science.gov (United States)

    Seo, Eunyoung; Kim, Seungill; Yeom, Seon-In; Choi, Doil

    2016-01-01

    Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analysis of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding. PMID:27559340

  1. SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus

    Science.gov (United States)

    Li, Bing; Tian, Xiaofang; Wang, Chunlan; Zeng, Xu; Xing, Yongmei; Ling, Hong; Yin, Wanqiang; Tian, Lixia; Meng, Zhixia; Zhang, Jihui; Guo, Shunxing

    2017-01-01

    Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.

  2. Food web of a confined and anthropogenically affected coastal basin (the Mar Piccolo of Taranto) revealed by carbon and nitrogen stable isotopes analyses.

    Science.gov (United States)

    Bongiorni, Lucia; Fiorentino, Federica; Auriemma, Rocco; Aubry, Fabrizio Bernardi; Camatti, Elisa; Camin, Federica; Nasi, Federica; Pansera, Marco; Ziller, Luca; Grall, Jacques

    2016-07-01

    Carbon and nitrogen stable isotope analysis was used to examine the food web of the Mar Piccolo of Taranto, a coastal basin experiencing several anthropogenic impacts. Main food sources (algal detritus, seaweeds, particulate organic matter (POM) and sediment organic matter (SOM)) and benthic and pelagic consumers were collected during two contrasting seasons (June and April), at four sites distributed over two inlets, and characterized by different level of confinements, anthropogenic inputs and the presence of mussels farming. δ(13)C values of organic sources revealed an important contribution of POM to both planktonic and benthic pathways, as well as the influence of terrigenous inputs within both inlets, probably due to high seasonal land runoff. Although δ(13)C of both sources and consumers varied little between sampling sites and dates, δ(15)N spatial variability was higher and clearly reflected the organic enrichment in the second inlet as well as the uptake of anthropogenically derived material by benthic consumers. On the other hand, within the first inlet, the isotopic composition of consumers did not change in response to chemical contamination. However, the impact of polluted sediments near the Navy Arsenal in the first inlet was detectable at the level of the macrobenthic trophic structure, showing high dominance of motile, upper level consumers capable to face transient conditions and the reduction of the more resident deposit feeders. We therefore underline the great potential of matching stable isotope analysis with quantitative studies of community structure to assess the effects of multiple anthropogenic stressors.

  3. Morphological and Proteomic Analyses Reveal that Unsaturated Guluronate Oligosaccharide Modulates Multiple Functional Pathways in Murine Macrophage RAW264.7 Cells

    Directory of Open Access Journals (Sweden)

    Xu Xu

    2015-03-01

    Full Text Available Alginate is a natural polysaccharide extracted from various species of marine brown algae. Alginate-derived guluronate oligosaccharide (GOS obtained by enzymatic depolymerization has various pharmacological functions. Previous studies have demonstrated that GOS can trigger the production of inducible nitric oxide synthase (iNOS/nitric oxide (NO, reactive oxygen species (ROS and tumor necrosis factor (TNF-α by macrophages and that it is involved in the nuclear factor (NF-κB and mitogen-activated protein (MAP kinase signaling pathways. To expand upon the current knowledge regarding the molecular mechanisms associated with the GOS-induced immune response in macrophages, comparative proteomic analysis was employed together with two-dimensional electrophoresis (2-DE, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS and Western blot verification. Proteins showing significant differences in expression in GOS-treated cells were categorized into multiple functional pathways, including the NF-κB signaling pathway and pathways involved in inflammation, antioxidant activity, glycolysis, cytoskeletal processes and translational elongation. Moreover, GOS-stimulated changes in the morphologies and actin cytoskeleton organization of RAW264.7 cells were also investigated as possible adaptations to GOS. This study is the first to reveal GOS as a promising agent that can modulate the proper balance between the pro- and anti-inflammatory immune responses, and it provides new insights into pharmaceutical applications of polysaccharides.

  4. The regulatory mechanism of fruit ripening revealed by analyses of direct targets of the tomato MADS-box transcription factor RIPENING INHIBITOR.

    Science.gov (United States)

    Fujisawa, Masaki; Ito, Yasuhiro

    2013-06-01

    The developmental process of ripening is unique to fleshy fruits and a key factor in fruit quality. The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN), one of the earliest-acting ripening regulators, is required for broad aspects of ripening, including ethylene-dependent and -independent pathways. However, our knowledge of direct RIN target genes has been limited, considering the broad effects of RIN on ripening. In a recent work published in The Plant Cell, we identified 241 direct RIN target genes by chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip) and transcriptome analysis. Functional classification of the targets revealed that RIN participates in the regulation of many biological processes including well-known ripening processes such as climacteric ethylene production and lycopene accumulation. In addition, we found that ethylene is required for the full expression of RIN and several RIN-targeting transcription factor genes at the ripening stage. Here, based on our recently published findings and additional data, we discuss the ripening processes regulated by RIN and the interplay between RIN and ethylene.

  5. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios.

    Science.gov (United States)

    Kao, Damian; Felix, Daniel; Aboobaker, Aziz

    2013-11-16

    Planarians can regenerate entire animals from a small fragment of the body. The regenerating fragment is able to create new tissues and remodel existing tissues to form a complete animal. Thus different fragments with very different starting components eventually converge on the same solution. In this study, we performed an extensive RNA-seq time-course on regenerating head and tail fragments to observe the differences and similarities of the transcriptional landscape between head and tail fragments during regeneration. We have consolidated existing transcriptomic data for S. mediterranea to generate a high confidence set of transcripts for use in genome wide expression studies. We performed a RNA-seq time-course on regenerating head and tail fragments from 0 hours to 3 days. We found that the transcriptome profiles of head and tail regeneration were very different at the start of regeneration; however, an unexpected convergence of transcriptional profiles occurred at 48 hours when head and tail fragments are still morphologically distinct. By comparing differentially expressed transcripts at various time-points, we revealed that this divergence/convergence pattern is caused by a shared regulatory program that runs early in heads and later in tails.Additionally, we also performed RNA-seq on smed-prep(RNAi) tail fragments which ultimately fail to regenerate anterior structures. We find the gene regulation program in response to smed-prep(RNAi) to display the opposite regulatory trend compared to the previously mentioned share regulatory program during regeneration. Using annotation data and comparative approaches, we also identified a set of approximately 4,800 triclad specific transcripts that were enriched amongst the genes displaying differential expression during the regeneration time-course. The regeneration transcriptome of head and tail regeneration provides us with a rich resource for investigating the global expression changes that occurs during

  6. Mutational analyses on X-linked adrenoleukodystrophy reveal a novel cryptic splicing and three missense mutations in the ABCD1 gene.

    Science.gov (United States)

    Hung, Kun-Long; Wang, Jinn-Shyan; Keng, Wee Teik; Chen, Hui-Ju; Liang, Jao-Shwann; Ngu, Lock Hock; Lu, Jyh-Feng

    2013-09-01

    X-linked adrenoleukodystrophy is caused by a defective peroxisomal membrane transporter, ABCD1, responsible for transporting very-long-chain fatty acid substrate into peroxisomes for degradation. The main biochemical defect, which is also one of the major diagnostic hallmarks, of X-linked adrenoleukodystrophy is the accumulation of saturated very-long-chain fatty acids in all tissues and body fluids. Direct and reverse-transcribed polymerase chain reactions followed by DNA sequencing-based mutational analyses were performed on one Taiwanese and three Malaysian X-linked adrenoleukodystrophy families. A novel splicing donor site mutation (c.1272+1g>a) was identified in a Taiwanese X-linked adrenoleukodystrophy patient, resulting in a deletion of 121 bp and a premature stop codon (p.Val425fs*92) in messenger-RNA transcript. This deletion is caused by the activation of a cryptic splicing donor site in exon 4 of the ABCD1 gene, which is consistent with the prediction by several online algorithms. In addition, three previously described missense mutations (c.965T>C, c.1978C>T, and c.2006A>G), leading to aberrant ABCD1 of p.Leu322Pro, p.Arg660Trp, and p.His669Arg, were also identified in Malaysian probands. This is the first report to unveil unequivocally that cryptic splicing-induced aberrant messenger-RNA carrying an internal frameshift deletion results from an intronic mutation in the ABCD1 gene. Furthermore, a polymorphism in intron 9 (c.1992-32c/t; refSNP: rs4898368) of the ABCD1 gene was commonly observed in both Taiwanese and Malaysian populations. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Parental Genome Separation and Elimination of Cells and Chromosomes Revealed by AFLP and GISH analyses in a Brassica carinata × Orychophragmus violaceus Cross

    Science.gov (United States)

    HUA, YU-WEI; LIU, MIN; LI, ZAI-YUN

    2006-01-01

    • Background and Aims The phenomenon of parental genome separation during the mitotic divisions of hybrid cells was proposed to occur under genetic control in intergeneric hybrids between cultivated Brassica species and Orychophragmus violaceus (2n = 24). To elucidate further the cytological and molecular mechanisms behind parental genome separation, Brassica carinata (2n = 34) × O. violaceus hybrids were resynthesized and their chromosome/genomic complements analysed. • Methods F1 hybrids of the cross were obtained following embryo rescue, and were investigated for their cytological behaviour and subjected to genomic in situ hybridization (GISH) and amplified fragment length polymorphism (AFLP) to determine the contribution of parental genomes. • Key Results All the F1 plants with high fertility closely resembled B. carinata in morphological attributes. These were mixoploids with 2n chromosome numbers ranging from 17 to 35; however, 34, the same number as in B. carinata, was the most frequent number of chromosomes in ovary and pollen mother cells (PMCs). GISH clearly identified 16 chromosomes of B. nigra in ovary cells and PMCs with 2n = 34 and 35. However, no O. violaceus chromosome was detected, indicating the presence of the intact B. carinata genome and elimination of the entire O. violaceus genome. However, some AFLP bands specific for O. violaceus and novel for the two parents were detected in the leaves. Cells with fewer than 34 chromosomes had lost some B. oleracea chromosomes. F2 plants were predominantly like B. carinata, but some contained O. violaceus characters. • Conclusions The cytological mechanism for the results involves complete and partial genome separation at mitosis in embryos of F1 plants followed by chromosome doubling, elimination of cells with O. violaceus chromosomes and some introgression of O. violaceus genetic information. PMID:16624845

  8. Parental genome separation and elimination of cells and chromosomes revealed by AFLP and GISH analyses in a Brassica carinata x Orychophragmus violaceus cross.

    Science.gov (United States)

    Hua, Yu-Wei; Liu, Min; Li, Zai-Yun

    2006-06-01

    The phenomenon of parental genome separation during the mitotic divisions of hybrid cells was proposed to occur under genetic control in intergeneric hybrids between cultivated Brassica species and Orychophragmus violaceus (2n = 24). To elucidate further the cytological and molecular mechanisms behind parental genome separation, Brassica carinata (2n = 34) x O. violaceus hybrids were resynthesized and their chromosome/genomic complements analysed. F(1) hybrids of the cross were obtained following embryo rescue, and were investigated for their cytological behaviour and subjected to genomic in situ hybridization (GISH) and amplified fragment length polymorphism (AFLP) to determine the contribution of parental genomes. All the F(1) plants with high fertility closely resembled B. carinata in morphological attributes. These were mixoploids with 2n chromosome numbers ranging from 17 to 35; however, 34, the same number as in B. carinata, was the most frequent number of chromosomes in ovary and pollen mother cells (PMCs). GISH clearly identified 16 chromosomes of B. nigra in ovary cells and PMCs with 2n = 34 and 35. However, no O. violaceus chromosome was detected, indicating the presence of the intact B. carinata genome and elimination of the entire O. violaceus genome. However, some AFLP bands specific for O. violaceus and novel for the two parents were detected in the leaves. Cells with fewer than 34 chromosomes had lost some B. oleracea chromosomes. F(2) plants were predominantly like B. carinata, but some contained O. violaceus characters. The cytological mechanism for the results involves complete and partial genome separation at mitosis in embryos of F(1) plants followed by chromosome doubling, elimination of cells with O. violaceus chromosomes and some introgression of O. violaceus genetic information.

  9. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Guanhui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); University of Chinese Academy of Sciences, Beijing (China); Dong, Hongjun; Zhu, Yan; Mao, Shaoming [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Zhang, Tianrui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin (China); Zhang, Yanping [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Chen, Zugen [Department of Human Genetics, School of Medicine, University of California, Los Angeles, CA 90095 (United States); Li, Yin, E-mail: yli@im.ac.cn [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China)

    2014-08-08

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance.

  10. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  11. Genetic Analyses Reveal Differences in the VP7 and VP4 Antigenic Epitopes between Human Rotaviruses Circulating in Belgium and Rotaviruses in Rotarix and RotaTeq

    Science.gov (United States)

    Zeller, Mark; Patton, John T.; Heylen, Elisabeth; De Coster, Sarah; Ciarlet, Max; Van Ranst, Marc

    2012-01-01

    Two live-attenuated rotavirus group A (RVA) vaccines, Rotarix (G1P[8]) and RotaTeq (G1-G4, P[8]), have been successfully introduced in many countries worldwide, including Belgium. The parental RVA strains used to generate the vaccines were isolated more than 20 years ago in France (G4 parental strain in RotaTeq) and the United States (all other parental strains). At present, little is known about the relationship between currently circulating human RVAs and the vaccine strains. In this study, we determined sequences for the VP7 and VP4 outer capsid proteins of representative G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G12P[8] RVAs circulating in Belgium during 2007 to 2009. The analyses showed that multiple amino acid differences existed between the VP7 and VP4 antigenic epitopes of the vaccine viruses and the Belgian isolates, regardless of their G and P genotypes. However, the highest variability was observed among the circulating G1P[8] RVA strains and the G1 and P[8] components of both RVA vaccines. In particular, RVA strains of the P[8] lineage 4 (OP354-like) showed a significant number of amino acid differences with the P[8] VP4 of both vaccines. In addition, the circulating Belgian G3 RVA strains were found to possibly possess an extra N-linked glycosylation site compared to the G3 RVA vaccine strain of RotaTeq. These results indicate that the antigenic epitopes of RVA strains contained in the vaccines differ substantially from those of the currently circulating RVA strains in Belgium. Over time, these differences might result in selection for strains that escape the RVA neutralizing-antibody pressure induced by vaccines. PMID:22189107

  12. Koala retrovirus genotyping analyses reveal a low prevalence of KoRV-A in Victorian koalas and an association with clinical disease.

    Science.gov (United States)

    Legione, Alistair R; Patterson, Jade L S; Whiteley, Pam; Firestone, Simon M; Curnick, Megan; Bodley, Kate; Lynch, Michael; Gilkerson, James R; Sansom, Fiona M; Devlin, Joanne M

    2017-02-01

    Koala retrovirus (KoRV) is undergoing endogenization into the genome of koalas in Australia, providing an opportunity to assess the effect of retrovirus infection on the health of a population. The prevalence of KoRV in north-eastern Australia (Queensland and New South Wales) is 100 %, whereas previous preliminary investigations in south-eastern Australia (Victoria) suggested KoRV is present at a lower prevalence, although the values have varied widely. Here, we describe a large study of free-ranging koalas in Victoria to estimate the prevalence of KoRV and assess the clinical significance of KoRV infection in wild koalas. Blood or spleen samples from 648 koalas where tested for KoRV provirus, and subsequently genotyped, using PCRs to detect the pol and env genes respectively. Clinical data was also recorded where possible and analysed in comparison to infection status. The prevalence of KoRV was 24.7 % (160/648). KoRV-A was detected in 141/160 cases, but KoRV-B, a genotype associated with neoplasia in captive koalas, was not detected. The genotype in 19 cases could not be determined. Genomic differences between KoRV in Victoria and type strains may have impacted genotyping. Factors associated with KoRV infection, based on multivariable analysis, were low body condition score, region sampled, and 'wet bottom' (a staining of the fur around the rump associated with chronic urinary incontinence). Koalas with wet bottom were nearly twice as likely to have KoRV provirus detected than those without wet bottom (odds ratio=1.90, 95 % confidence interval 1.21, 2.98). Our findings have important implications for the conservation of this iconic species, particularly regarding translocation potential of Victorian koalas.

  13. Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations

    Directory of Open Access Journals (Sweden)

    Accili Eric A

    2008-06-01

    Full Text Available Abstract Background Mutations in HERG and KCNQ1 potassium channels have been associated with Long QT syndrome and atrial fibrillation, and more recently with sudden infant death syndrome and sudden unexplained death. In other proteins, disease-associated amino acid mutations have been analyzed according to the chemical severity of the changes and the locations of the altered amino acids according to their conservation over metazoan evolution. Here, we present the first such analysis of arrhythmia-associated mutations (AAMs in the HERG and KCNQ1 potassium channels. Results Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains. Non-synonymous single nucleotide polymorphisms (nsSNPs are under-represented at evolutionarily conserved sites in HERG, but distribute randomly in KCNQ1. AAMs are chemically more severe, according to Grantham's Scale, than changes observed in evolution and their severity correlates with the expected chemical severity of the involved codon. Expected chemical severity of a given amino acid also correlates with its relative contribution to arrhythmias. At evolutionarily variable sites, the chemical severity of the changes is also correlated with the expected chemical severity of the involved codon. Conclusion Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution. Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

  14. Magma mixing and crystal exchange at Yellowstone caldera revealed though sub-crystal-scale age, trace-element, and Hf-isotopic analyses of zircons

    Science.gov (United States)

    Stelten, M. E.; Cooper, K. M.; Vazquez, J. A.; Wimpenny, J.; Yin, Q.

    2011-12-01

    We examine magma mixing and crystal exchange in a young magma reservoir by correlating sub-crystal-scale SIMS age, SIMS trace element, and LA-MC-ICPMS Hf-isotopic data from zircons in the coeval ca. 100ka, yet compositionally distinct rhyolites of the Solfatara Plateau flow (SPF) and Hayden Valley flow (HVF) at Yellowstone Caldera. The SPF and HVF lavas are part of the Central Plateau Member (CPM) of the Plateau Rhyolite that is composed of the youngest intracaldera rhyolite flows at Yellowstone, erupted between ca. 170-70ka. We compare these data to age and trace element data from zircons in 1) the Pitchstone Plateau Flow, West Yellowstone Flow, and Dry Creek Flow of the CPM as representative of main reservoir zircons, 2) the ca. 118ka extracaldera Gibbon River Flow rhyolite (GRF), and 3) the ca. 260ka Scaup Lake Flow of the Upper Basin Member rhyolites. Additionally, we compare the zircon data to new MC-ICPMS Hf-isotopic data from CPM glasses. Correlating age, trace element, and Hf-isotopic data from zircons in the HVF and SPF reveals the presence of four zircon populations. Main reservoir-like (MR-like) zircons have trace element compositions similar to main CPM reservoir zircons, young ages (Lastly, a population of zircons (which we interpret to be inherited) have cores with older ages (>350ka), a range in trace element compositions, and high ɛHf (-5.8 to -3.6) whereas the rims have restricted MR-like trace element compositions and ɛHf within error of CPM glasses. The sense of core to rim zoning specific to each population suggests that each population has its own unique history. The core to rim zoning in MR-like and inherited zircons, from cores with a range of Hf-isotopic compositions to rims similar to CPM glasses, suggests that MR-like and inherited zircons in the SPF and HVF came from distinct high ɛHf magmas and were incorporated into the CPM reservoir. For mixed zircons, the zoning from MR-like or EC-like cores to intermediate rim compositions

  15. Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced and splicing changes that classify brain region transcriptomes

    Directory of Open Access Journals (Sweden)

    Lilach eSoreq

    2013-05-01

    Full Text Available MicroRNAs (miRNAs are key post transcriptional regulators of their multiple target genes. However, the detailed profile of miRNA expression in Parkinson's disease, the second most common neurodegenerative disease worldwide and the first motor disorder has not been charted yet. Here, we report comprehensive miRNA profiling by next-generation small-RNA sequencing, combined with targets inspection by splice-junction and exon arrays interrogating leukocyte RNA in Parkinson’s disease patients before and after deep brain stimulation (DBS treatment and of matched healthy control volunteers (HC. RNA-Seq analysis identified 254 miRNAs and 79 passenger strand forms as expressed in blood leukocytes, 16 of which were modified in patients pre treatment as compared to HC. 11 miRNAs were modified following brain stimulation, 5 of which were changed inversely to the disease induced changes. Stimulation cessation further induced changes in 11 miRNAs. Transcript isoform abundance analysis yielded 332 changed isoforms in patients compared to HC, which classified brain transcriptomes of 47 PD and control independent microarrays. Functional enrichment analysis highlighted mitochondrion organization. DBS induced 155 splice changes, enriched in ubiquitin homeostasis. Cellular composition analysis revealed immune cell activity pre and post treatment. Overall, 217 disease and 74 treatment alternative isoforms were predictably targeted by modified miRNAs within both 3’ and 5’ untranslated ends and coding sequence sites. The stimulation-induced network sustained 4 miRNAs and 7 transcripts of the disease network. We believe that the presented dynamic networks provide a novel avenue for identifying disease and treatment-related therapeutic targets. Furthermore, the identification of these networks is a major step forward in the road for understanding the molecular basis for neurological and neurodegenerative diseases and assessment of the impact of brain stimulation

  16. Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family.

    Science.gov (United States)

    Hrle, Ajla; Maier, Lisa-Katharina; Sharma, Kundan; Ebert, Judith; Basquin, Claire; Urlaub, Henning; Marchfelder, Anita; Conti, Elena

    2014-01-01

    Upon pathogen invasion, bacteria and archaea activate an RNA-interference-like mechanism termed CRISPR (clustered regularly interspaced short palindromic repeats). A large family of Cas (CRISPR-associated) proteins mediates the different stages of this sophisticated immune response. Bioinformatic studies have classified the Cas proteins into families, according to their sequences and respective functions. These range from the insertion of the foreign genetic elements into the host genome to the activation of the interference machinery as well as target degradation upon attack. Cas7 family proteins are central to the type I and type III interference machineries as they constitute the backbone of the large interference complexes. Here we report the crystal structure of Thermofilum pendens Csc2, a Cas7 family protein of type I-D. We found that Csc2 forms a core RRM-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. Comparison with other Cas7 family proteins reveals a set of similar structural features both in the core and in the peripheral domains, despite the absence of significant sequence similarity. T. pendens Csc2 binds single-stranded RNA in vitro in a sequence-independent manner. Using a crosslinking - mass-spectrometry approach, we mapped the RNA-binding surface to a positively charged surface patch on T. pendens Csc2. Thus our analysis of the key structural and functional features of T. pendens Csc2 highlights recurring themes and evolutionary relationships in type I and type III Cas proteins.

  17. Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes

    Science.gov (United States)

    Soreq, Lilach; Salomonis, Nathan; Bronstein, Michal; Greenberg, David S.; Israel, Zvi; Bergman, Hagai; Soreq, Hermona

    2013-01-01

    MicroRNAs (miRNAs) are key post transcriptional regulators of their multiple target genes. However, the detailed profile of miRNA expression in Parkinson's disease, the second most common neurodegenerative disease worldwide and the first motor disorder has not been charted yet. Here, we report comprehensive miRNA profiling by next-generation small-RNA sequencing, combined with targets inspection by splice-junction and exon arrays interrogating leukocyte RNA in Parkinson's disease patients before and after deep brain stimulation (DBS) treatment and of matched healthy control volunteers (HC). RNA-Seq analysis identified 254 miRNAs and 79 passenger strand forms as expressed in blood leukocytes, 16 of which were modified in patients pre-treatment as compared to HC. 11 miRNAs were modified following brain stimulation 5 of which were changed inversely to the disease induced changes. Stimulation cessation further induced changes in 11 miRNAs. Transcript isoform abundance analysis yielded 332 changed isoforms in patients compared to HC, which classified brain transcriptomes of 47 PD and control independent microarrays. Functional enrichment analysis highlighted mitochondrion organization. DBS induced 155 splice changes, enriched in ubiquitin homeostasis. Cellular composition analysis revealed immune cell activity pre and post treatment. Overall, 217 disease and 74 treatment alternative isoforms were predictably targeted by modified miRNAs within both 3′ and 5′ untranslated ends and coding sequence sites. The stimulation-induced network sustained 4 miRNAs and 7 transcripts of the disease network. We believe that the presented dynamic networks provide a novel avenue for identifying disease and treatment-related therapeutic targets. Furthermore, the identification of these networks is a major step forward in the road for understanding the molecular basis for neurological and neurodegenerative diseases and assessment of the impact of brain stimulation on human diseases

  18. Time-course global proteome analyses reveal an inverse correlation between Aβ burden and immunoglobulin M levels in the APPNL-F mouse model of Alzheimer disease.

    Science.gov (United States)

    Wang, Hansen; Williams, Declan; Griffin, Jennifer; Saito, Takashi; Saido, Takaomi C; Fraser, Paul E; Rogaeva, Ekaterina; Schmitt-Ulms, Gerold

    2017-01-01

    Alzheimer disease (AD) stands out amongst highly prevalent diseases because there is no effective treatment nor can the disease be reliably diagnosed at an early stage. A hallmark of AD is the accumulation of aggregation-prone amyloid β peptides (Aβ), the main constituent of amyloid plaques. To identify Aβ-dependent changes to the global proteome we used the recently introduced APPNL-F mouse model of AD, which faithfully recapitulates the Aβ pathology of the disease, and a workflow that interrogated the brain proteome of these mice by quantitative mass spectrometry at three different ages. The elevated Aβ burden in these mice was observed to cause almost no changes to steady-state protein levels of the most abundant >2,500 brain proteins, including 12 proteins encoded by well-confirmed AD risk loci. The notable exception was a striking reduction in immunoglobulin heavy mu chain (IGHM) protein levels in homozygote APPNL-F/NL-F mice, relative to APPNL-F/wt littermates. Follow-up experiments revealed that IGHM levels generally increase with age in this model. Although discovered with brain samples, the relative IGHM depletion in APPNL-F/NL-F mice was validated to manifest systemically in the blood, and did not extend to other blood proteins, including immunoglobulin G. Results presented are consistent with a cause-effect relationship between the excessive accumulation of Aβ and the selective depletion of IGHM levels, which may be of relevance for understanding the etiology of the disease and ongoing efforts to devise blood-based AD diagnostics.

  19. DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and gamma-rays.

    Science.gov (United States)

    Kimura, Shinzo; Ishidou, Emi; Kurita, Sakiko; Suzuki, Yoshiteru; Shibato, Junko; Rakwal, Randeep; Iwahashi, Hitoshi

    2006-07-21

    Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma (gamma)-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and gamma-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and gamma-rays). Similarly, for X- and gamma-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and gamma-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-à-vis their energy levels.

  20. Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits

    Directory of Open Access Journals (Sweden)

    Thangasamy Saminathan

    2018-01-01

    concept to incorporate associated microbiomes in breeding programs.

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

    Directory of Open Access Journals (Sweden)

    Karmali Mohamed A

    2009-06-01

    methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

  2. Molecular analyses reveal an abundant diversity of ticks and rickettsial agents associated with wild birds in two regions of primary Brazilian Atlantic Rainforest.

    Science.gov (United States)

    Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; McIntosh, Douglas

    2017-06-01

    Brazilian wild birds are recognized as frequent and important hosts for immature stages of more than half of the 32 recognized species of Amblyomma ticks recorded in that country. Several species of Amblyomma harbor rickettsial agents, including members of the spotted fever group (SFG). Most studies on this topic relied primarily on morphological characterization and reported large portions of the collected ticks at the genus rather than species level. Clearly, this factor may have contributed to an underestimation of tick diversity and distribution and makes comparisons between studies difficult. The current investigation combined morphological and molecular analyses to assess the diversity of ticks and rickettsial agents associated with wild birds, captured in two regions of native Atlantic rainforest, in the state of Rio de Janeiro, Brazil. A total of 910 birds were captured, representing two orders, 34 families and 106 species, among which 93 specimens (10.2%), were parasitized by 138 immature ticks (60 larvae and 78 nymphs), representing 10 recognized species of the genus Amblyomma; together with two reasonably well classified haplotypes (Amblyomma sp. haplotype Nazaré and Amblyomma sp. strain USNTC 6792). Amplification by PCR and sequencing of rickettsial genes (htrA, gltA, ompA and ompB), demonstrated the presence of Rickettsia DNA in 48 (34%) of the ticks. Specifically, Rickettsia bellii was detected in a single larva and a single nymph of A. aureolatum; R. amblyomatis was found in 16 of 37 A. longirostre and was recorded for the first time in three nymphs of A. calcaratum; R. rhipicephali was detected in 9 (47%) of 19 Amblyomma sp. haplotype Nazaré ticks. The remaining ticks were infected with genetic variants of R. parkeri, namely strain ApPR in 12 A. parkeri and seven Amblyomma sp. haplotype Nazaré ticks, with the strain NOD found in two specimens of A. nodosum. Interestingly, a single larvae of A. ovale was shown to be infected with the emerging

  3. A 2000-yr record of the extent of decomposition and vegetation change in peats from the Western Siberian Lowland as revealed from carbohydrate, lignin and amino acid analyses

    Science.gov (United States)

    Benner, R. H.; Kaiser, K.; Philben, M. J.; Beilman, D.; MacDonald, G. M.

    2011-12-01

    The Western Siberian Lowland is among the largest wetlands in the world, and it is estimated to store ~70 Pg C as peat. Based on radiocarbon dating, peat accumulation rates at sites south of 60°N are higher than those at more northerly sites during the past 2000 yr. The biochemical composition of peat from high-resolution sampling in four cores was analyzed to investigate the influence of current and past climatic events on the decomposition and diagenetic alteration of the accumulated peat. The analyzed cores were collected from 56.8°N (SIB04), 58.4°N (SIB06), 63.8°N (G137) and 66.5°N (E113). Molecular analyses of hydrolysable neutral sugars, amino acids and lignin phenols accounted for about 36% of the C and 50% of the N in the peat samples, indicating the observed compositional trends are generally representative of bulk C and N dynamics. Prominent compositional anomalies were observed in the upper 6-43 cm of SIB04, the most southern core. An 8-fold decline in Sphagnum-derived p-hydroxy phenols was accompanied by a 5-fold increase in gymnosperm-derived vanillyl phenols in the upper SIB04 core, indicating a shift in vegetation that was also observed at 5 other depths in the core. The yield of neutral sugars decreased from 27% to 10% of total C in peat deposited over a span of about 230 yr. The C/N ratio declined from 68 to 45, and the yield of amino acids increased two-fold. These changes indicate extensive decomposition of the surface (6-9 cm) peat occurred during the last few decades, a period of significant warming in the region. We estimate a 50-65% mass loss in surface peat at the SIB04 site. No apparent indication of extensive decomposition was observed in surface peat at the SIB06 site located 2° further north. About 33% of total C was accounted for in neutral sugars, the C/N ratio was above 100 and amino acid yields were relatively low. A 2-fold increase in vanillyl and syringyl phenols indicates the input of angiosperm vegetation in the upper SIB06

  4. Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Men, Yujie; Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa; Liu, Shuang-Jiang

    2017-02-10

    ABSTRACT

    The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

    IMPORTANCEThe key

  5. A study of common Mendelian disease carriers across ageing British cohorts: meta-analyses reveal heterozygosity for alpha 1-antitrypsin deficiency increases respiratory capacity and height.

    Science.gov (United States)

    North, Teri-Louise; Ben-Shlomo, Yoav; Cooper, Cyrus; Deary, Ian J; Gallacher, John; Kivimaki, Mika; Kumari, Meena; Martin, Richard M; Pattie, Alison; Sayer, Avan Aihie; Starr, John M; Wong, Andrew; Kuh, Diana; Rodriguez, Santiago; Day, Ian N M

    2016-04-01

    Several recessive Mendelian disorders are common in Europeans, including cystic fibrosis (CFTR), medium-chain-acyl-Co-A-dehydrogenase deficiency (ACADM), phenylketonuria (PAH) and alpha 1-antitrypsin deficiency (SERPINA1). In a multicohort study of >19,000 older individuals, we investigated the relevant phenotypes in heterozygotes for these genes: lung function (forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC)) for CFTR and SERPINA1; cognitive measures for ACADM and PAH; and physical capability for ACADM, PAH and SERPINA1. Findings were mostly negative but lung function in SERPINA1 (protease inhibitor (PI) Z allele, rs28929474) showed enhanced FEV1 and FVC (0.13 z-score increase in FEV1 (p=1.7 × 10(-5)) and 0.16 z-score increase in FVC (p=5.2 × 10(-8))) in PI-MZ individuals. Height adjustment (a known, strong correlate of FEV1 and FVC) revealed strong positive height associations of the Z allele (1.50 cm increase in height (p=3.6 × 10(-10))). The PI-MZ rare (2%) SNP effect is nearly four times greater than the 'top' common height SNP in HMGA2. However, height only partially attenuates the SERPINA1-FEV1 or FVC association (around 50%) and vice versa. Height SNP variants have recently been shown to be positively selected collectively in North versus South Europeans, while the Z allele high frequency is localised to North Europe. Although PI-ZZ is clinically disadvantageous to lung function, PI-MZ increases both height and respiratory function; potentially a balanced polymorphism. Partial blockade of PI could conceivably form part of a future poly-therapeutic approach in very short children. The notion that elastase inhibition should benefit patients with chronic obstructive pulmonary disease may also merit re-evaluation. PI is already a therapeutic target: our findings invite a reconsideration of the optimum level in respiratory care and novel pathway potential for development of agents for the management of growth disorders. Published by

  6. The global pediatric antiretroviral market: analyses of product availability and utilization reveal challenges for development of pediatric formulations and HIV/AIDS treatment in children

    Directory of Open Access Journals (Sweden)

    Jambert Elodie

    2010-10-01

    Full Text Available Abstract Background Important advances in the development and production of quality-certified pediatric antiretroviral (ARV formulations have recently been made despite significant market disincentives for manufacturers. This progress resulted from lobbying and innovative interventions from HIV/AIDS activists, civil society organizations, and international organizations. Research on uptake and dispersion of these improved products across countries and international organizations has not been conducted but is needed to inform next steps towards improving child health. Methods We used information from the World Health Organization Prequalification Programme and the United States Food and Drug Administration to describe trends in quality-certification of pediatric formulations and used 7,989 donor-funded, pediatric ARV purchase transactions from 2002-2009 to measure uptake and dispersion of new pediatric ARV formulations across countries and programs. Prices for new pediatric ARV formulations were compared to alternative dosage forms. Results Fewer ARV options exist for HIV/AIDS treatment in children than adults. Before 2005, most pediatric ARVs were produced by innovator companies in single-component solid and liquid forms. Five 2-in1 and four 3-in-1 generic pediatric fixed-dose combinations (FDCs in solid and dispersible forms have been quality-certified since 2005. Most (67% of these were produced by one quality-certified manufacturer. Uptake of new pediatric FDCs outside of UNITAID is low. UNITAID accounted for 97-100% of 2008-2009 market volume. In total, 33 and 34 countries reported solid or dispersible FDC purchases in 2008 and 2009, respectively, but most purchases were made through UNITAID. Only three Global Fund country recipients reported purchase of these FDCs in 2008. Prices for pediatric FDCs were considerably lower than liquids but typically higher than half of an adult FDC. Conclusion Pediatric ARV markets are more fragile than

  7. The global pediatric antiretroviral market: analyses of product availability and utilization reveal challenges for development of pediatric formulations and HIV/AIDS treatment in children.

    Science.gov (United States)

    Waning, Brenda; Diedrichsen, Ellen; Jambert, Elodie; Bärnighausen, Till; Li, Yun; Pouw, Mieke; Moon, Suerie

    2010-10-17

    Important advances in the development and production of quality-certified pediatric antiretroviral (ARV) formulations have recently been made despite significant market disincentives for manufacturers. This progress resulted from lobbying and innovative interventions from HIV/AIDS activists, civil society organizations, and international organizations. Research on uptake and dispersion of these improved products across countries and international organizations has not been conducted but is needed to inform next steps towards improving child health. We used information from the World Health Organization Prequalification Programme and the United States Food and Drug Administration to describe trends in quality-certification of pediatric formulations and used 7,989 donor-funded, pediatric ARV purchase transactions from 2002-2009 to measure uptake and dispersion of new pediatric ARV formulations across countries and programs. Prices for new pediatric ARV formulations were compared to alternative dosage forms. Fewer ARV options exist for HIV/AIDS treatment in children than adults. Before 2005, most pediatric ARVs were produced by innovator companies in single-component solid and liquid forms. Five 2-in1 and four 3-in-1 generic pediatric fixed-dose combinations (FDCs) in solid and dispersible forms have been quality-certified since 2005. Most (67%) of these were produced by one quality-certified manufacturer. Uptake of new pediatric FDCs outside of UNITAID is low. UNITAID accounted for 97-100% of 2008-2009 market volume. In total, 33 and 34 countries reported solid or dispersible FDC purchases in 2008 and 2009, respectively, but most purchases were made through UNITAID. Only three Global Fund country recipients reported purchase of these FDCs in 2008. Prices for pediatric FDCs were considerably lower than liquids but typically higher than half of an adult FDC. Pediatric ARV markets are more fragile than adult markets. Ensuring a long-term supply of quality, well

  8. Metabolomics Reveals Relationship between Plasma Inositols and Birth Weight: Possible Markers for Fetal Programming of Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Pia Marlene Nissen

    2011-01-01

    Full Text Available Epidemiological studies in man and with experimental animal models have shown that intrauterine growth restriction (IUGR resulting in low birth weight is associated with higher risk of programming welfare diseases in later life. In the pig, severe IUGR occurs naturally and contribute substantially to a large intralitter variation in birth weight and may therefore be a good model for man. In the present paper the natural form of IUGR in pigs was studied close to term by nuclear magnetic resonance (NMR-based metabolomics. The NMR-based investigations revealed different metabolic profiles of plasma samples from low-birth weight (LW and high-birth weight (HW piglets, respectively, and differences were assigned to levels of glucose and myo-inositol. Further studies by GC-MS revealed that LW piglets had a significant higher concentration of myoinositol and D-chiro-inositol in plasma compared to larger littermates. Myo-inositol and D-chiro-inositol have been coupled with glucose intolerance and insulin resistance in adults, and the present paper therefore suggests that IUGR is related to impaired glucose metabolism during fetal development, which may cause type 2 diabetes in adulthood.

  9. Metabolomics reveals relationship between plasma inositols and birth weight: possible markers for fetal programming of type 2 diabetes.

    Science.gov (United States)

    Nissen, Pia Marlene; Nebel, Caroline; Oksbjerg, Niels; Bertram, Hanne Christine

    2011-01-01

    Epidemiological studies in man and with experimental animal models have shown that intrauterine growth restriction (IUGR) resulting in low birth weight is associated with higher risk of programming welfare diseases in later life. In the pig, severe IUGR occurs naturally and contribute substantially to a large intralitter variation in birth weight and may therefore be a good model for man. In the present paper the natural form of IUGR in pigs was studied close to term by nuclear magnetic resonance (NMR-)based metabolomics. The NMR-based investigations revealed different metabolic profiles of plasma samples from low-birth weight (LW) and high-birth weight (HW) piglets, respectively, and differences were assigned to levels of glucose and myo-inositol. Further studies by GC-MS revealed that LW piglets had a significant higher concentration of myoinositol and D-chiro-inositol in plasma compared to larger littermates. Myo-inositol and D-chiro-inositol have been coupled with glucose intolerance and insulin resistance in adults, and the present paper therefore suggests that IUGR is related to impaired glucose metabolism during fetal development, which may cause type 2 diabetes in adulthood.

  10. Analyses of computer programs for the probabilistic estimation of design earthquake and seismological characteristics of the Korean Peninsula

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Gi Hwa [Seoul National Univ., Seoul (Korea, Republic of)

    1997-11-15

    The purpose of the present study is to develop predictive equations from simulated motions which are adequate for the Korean Peninsula and analyze and utilize the computer programs for the probabilistic estimation of design earthquakes. In part I of the report, computer programs for the probabilistic estimation of design earthquake are analyzed and applied to the seismic hazard characterizations in the Korean Peninsula. In part II of the report, available instrumental earthquake records are analyzed to estimate earthquake source characteristics and medium properties, which are incorporated into simulation process. And earthquake records are simulated by using the estimated parameters. Finally, predictive equations constructed from the simulation are given in terms of magnitude and hypocentral distances.

  11. Adult-onset obesity reveals prenatal programming of glucose-insulin sensitivity in male sheep nutrient restricted during late gestation.

    Directory of Open Access Journals (Sweden)

    Philip Rhodes

    Full Text Available BACKGROUND: Obesity invokes a range of metabolic disturbances, but the transition from a poor to excessive nutritional environment may exacerbate adult metabolic dysfunction. The current study investigated global maternal nutrient restriction during early or late gestation on glucose tolerance and insulin sensitivity in the adult offspring when lean and obese. METHODS/PRINCIPAL FINDINGS: Pregnant sheep received adequate (1.0M; CE, n = 6 or energy restricted (0.7M diet during early (1-65 days; LEE, n = 6 or late (65-128 days; LEL, n = 7 gestation (term approximately 147 days. Subsequent offspring remained on pasture until 1.5 years when all received glucose and insulin tolerance tests (GTT & ITT and body composition determination by dual energy x-ray absorptiometry (DXA. All animals were then exposed to an obesogenic environment for 6-7 months and all protocols repeated. Prenatal dietary treatment had no effect on birth weight or on metabolic endpoints when animals were 'lean' (1.5 years. Obesity revealed generalised metabolic 'inflexibility' and insulin resistance; characterised by blunted excursions of plasma NEFA and increased insulin(AUC (from 133 to 341 [s.e.d. 26] ng.ml(-1.120 mins during a GTT, respectively. For LEL vs. CE, the peak in plasma insulin when obese was greater (7.8 vs. 4.7 [s.e.d. 1.1] ng.ml(-1 and was exacerbated by offspring sex (i.e. 9.8 vs. 4.4 [s.e.d. 1.16] ng.ml(-1; LEL male vs. CE male, respectively. Acquisition of obesity also significantly influenced the plasma lipid and protein profile to suggest, overall, greater net lipogenesis and reduced protein metabolism. CONCLUSIONS: This study indicates generalised metabolic dysfunction with adult-onset obesity which also exacerbates and 'reveals' programming of glucose-insulin sensitivity in male offspring prenatally exposed to maternal undernutrition during late gestation. Taken together, the data suggest that metabolic function appears little compromised in young

  12. Analyse the risks of ad hoc programming in web development and develop a metrics of appropriate tools

    OpenAIRE

    Gubhaju, Manish; Al-Sherbaz, Ali

    2013-01-01

    Today the World Wide Web has become one of the most powerful tools for business promotion and social networking. As the use of websites and web applications to promote the businesses has increased drastically over the past few years, the complexity of managing them and protecting them from security threats has become a complicated task for the organizations. On the other hand, most of the web projects are at risk and less secure due to lack of quality programming. Although there are plenty of...

  13. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.

    Science.gov (United States)

    Excoffier, Laurent; Lischer, Heidi E L

    2010-05-01

    We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework. © 2010 Blackwell Publishing Ltd.

  14. COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians.

    Directory of Open Access Journals (Sweden)

    Martis W Cowles

    2014-10-01

    Full Text Available Members of the COE family of transcription factors are required for central nervous system (CNS development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals.

  15. COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians.

    Science.gov (United States)

    Cowles, Martis W; Omuro, Kerilyn C; Stanley, Brianna N; Quintanilla, Carlo G; Zayas, Ricardo M

    2014-10-01

    Members of the COE family of transcription factors are required for central nervous system (CNS) development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured) planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals.

  16. Heart of endosymbioses: transcriptomics reveals a conserved genetic program among arbuscular mycorrhizal, actinorhizal and legume-rhizobial symbioses.

    Directory of Open Access Journals (Sweden)

    Alexandre Tromas

    Full Text Available To improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. A few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. Fossil and molecular data suggest that the molecular mechanisms involved in these root nodule symbioses (RNS have been partially recycled from more ancient and widespread arbuscular mycorrhizal (AM symbiosis. We used a comparative transcriptomics approach to identify genes involved in establishing these 3 endosymbioses and their functioning. We analysed global changes in gene expression in AM in the actinorhizal tree C. glauca. A comparison with genes induced in AM in Medicago truncatula and Oryza sativa revealed a common set of genes induced in AM. A comparison with genes induced in nitrogen-fixing nodules of C. glauca and M. truncatula also made it possible to define a common set of genes induced in these three endosymbioses. The existence of this core set of genes is in accordance with the proposed recycling of ancient AM genes for new functions related to nodulation in legumes and actinorhizal plants.

  17. Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses

    Science.gov (United States)

    Tromas, Alexandre; Parizot, Boris; Diagne, Nathalie; Champion, Antony; Hocher, Valérie; Cissoko, Maïmouna; Crabos, Amandine; Prodjinoto, Hermann; Lahouze, Benoit; Bogusz, Didier; Laplaze, Laurent; Svistoonoff, Sergio

    2012-01-01

    To improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. A few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. Fossil and molecular data suggest that the molecular mechanisms involved in these root nodule symbioses (RNS) have been partially recycled from more ancient and widespread arbuscular mycorrhizal (AM) symbiosis. We used a comparative transcriptomics approach to identify genes involved in establishing these 3 endosymbioses and their functioning. We analysed global changes in gene expression in AM in the actinorhizal tree C. glauca. A comparison with genes induced in AM in Medicago truncatula and Oryza sativa revealed a common set of genes induced in AM. A comparison with genes induced in nitrogen-fixing nodules of C. glauca and M. truncatula also made it possible to define a common set of genes induced in these three endosymbioses. The existence of this core set of genes is in accordance with the proposed recycling of ancient AM genes for new functions related to nodulation in legumes and actinorhizal plants. PMID:22970303

  18. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri.

    Science.gov (United States)

    Su, Andreas A H; Tripp, Vanessa; Randau, Lennart

    2013-07-01

    The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.

  19. Systematic review of model-based analyses reporting the cost-effectiveness and cost-utility of cardiovascular disease management programs.

    Science.gov (United States)

    Maru, Shoko; Byrnes, Joshua; Whitty, Jennifer A; Carrington, Melinda J; Stewart, Simon; Scuffham, Paul A

    2015-02-01

    The reported cost effectiveness of cardiovascular disease management programs (CVD-MPs) is highly variable, potentially leading to different funding decisions. This systematic review evaluates published modeled analyses to compare study methods and quality. Articles were included if an incremental cost-effectiveness ratio (ICER) or cost-utility ratio (ICUR) was reported, it is a multi-component intervention designed to manage or prevent a cardiovascular disease condition, and it addressed all domains specified in the American Heart Association Taxonomy for Disease Management. Nine articles (reporting 10 clinical outcomes) were included. Eight cost-utility and two cost-effectiveness analyses targeted hypertension (n=4), coronary heart disease (n=2), coronary heart disease plus stoke (n=1), heart failure (n=2) and hyperlipidemia (n=1). Study perspectives included the healthcare system (n=5), societal and fund holders (n=1), a third party payer (n=3), or was not explicitly stated (n=1). All analyses were modeled based on interventions of one to two years' duration. Time horizon ranged from two years (n=1), 10 years (n=1) and lifetime (n=8). Model structures included Markov model (n=8), 'decision analytic models' (n=1), or was not explicitly stated (n=1). Considerable variation was observed in clinical and economic assumptions and reporting practices. Of all ICERs/ICURs reported, including those of subgroups (n=16), four were above a US$50,000 acceptability threshold, six were below and six were dominant. The majority of CVD-MPs was reported to have favorable economic outcomes, but 25% were at unacceptably high cost for the outcomes. Use of standardized reporting tools should increase transparency and inform what drives the cost-effectiveness of CVD-MPs. © The European Society of Cardiology 2014.

  20. Programs in Fortran language for reporting the results of the analyses by ICP emission spectroscopy; Programas en lenguaje Fortran para la informacion de los resultados de los analisis efectuados mediante Espectroscopia Optica de emision con fuente de plasma

    Energy Technology Data Exchange (ETDEWEB)

    Roca, M.

    1985-07-01

    Three programs, written in FORTRAN IV language, for reporting the results of the analyses by ICP emission spectroscopy from data stored in files on floppy disks have been developed. They are intended, respectively, for the analyses of: 1) waters, 2) granites and slates, and 3) different kinds of geological materials. (Author) 8 refs.

  1. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    2016-11-01

    Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

  2. Temporal lineage tracing of Aire-expressing cells reveals a requirement for Aire in their maturation program.

    Science.gov (United States)

    Nishikawa, Yumiko; Nishijima, Hitoshi; Matsumoto, Minoru; Morimoto, Junko; Hirota, Fumiko; Takahashi, Satoru; Luche, Hervé; Fehling, Hans Joerg; Mouri, Yasuhiro; Matsumoto, Mitsuru

    2014-03-15

    Understanding the cellular dynamics of Aire-expressing lineage(s) among medullary thymic epithelial cells (AEL-mTECs) is essential for gaining insight into the roles of Aire in establishment of self-tolerance. In this study, we monitored the maturation program of AEL-mTECs by temporal lineage tracing, in which bacterial artificial chromosome transgenic mice expressing tamoxifen-inducible Cre recombinase under control of the Aire regulatory element were crossed with reporter strains. We estimated that the half-life of AEL-mTECs subsequent to Aire expression was ∼7-8 d, which was much longer than that reported previously, owing to the existence of a post-Aire stage. We found that loss of Aire did not alter the overall lifespan of AEL-mTECs, inconsistent with the previous notion that Aire expression in medullary thymic epithelial cells (mTECs) might result in their apoptosis for efficient cross-presentation of self-antigens expressed by AEL-mTECs. In contrast, Aire was required for the full maturation program of AEL-mTECs, as exemplified by the lack of physiological downregulation of CD80 during the post-Aire stage in Aire-deficient mice, thus accounting for the abnormally increased CD80(high) mTECs seen in such mice. Of interest, increased CD80(high) mTECs in Aire-deficient mice were not mTEC autonomous and were dependent on cross-talk with thymocytes. These results further support the roles of Aire in the differentiation program of AEL-mTECs.

  3. Integrative Analyses of Uterine Transcriptome and MicroRNAome Reveal Compromised LIF-STAT3 Signaling and Progesterone Response in the Endometrium of Patients with Recurrent/Repeated Implantation Failure (RIF.

    Directory of Open Access Journals (Sweden)

    Youngsok Choi

    Full Text Available Intimate two-way interactions between the implantation-competent blastocyst and receptive uterus are prerequisite for successful embryo implantation. In humans, recurrent/repeated implantation failure (RIF may occur due to altered uterine receptivity with aberrant gene expression in the endometrium as well as genetic defects in embryos. Several studies have been performed to understand dynamic changes of uterine transcriptome during menstrual cycles in humans. However, uterine transcriptome of the patients with RIF has not been clearly investigated yet. Here we show that several signaling pathways as well as many genes and microRNAs are dysregulated in the endometrium of patients with RIF (RIFE. Whereas unsupervised hierarchical clustering showed that overall mRNA and microRNA profiles of RIFE were similar to those of endometria of healthy women, many genes were significantly dysregulated in RIFE (cut off at 1.5 fold change. The majority (~75% of differentially expressed genes in RIFE including S100 calcium binding protein P (S100P, Chemokine (C-X-C motif ligand 13 (CXCL13 and SIX homeobox 1 (SIX1 were down-regulated, suggesting that reduced uterine expression of these genes is associated with RIF. Gene Set Enrichment analyses (GSEA for mRNA microarrays revealed that various signaling pathways including Leukemia inhibitory factor (LIF signaling and a P4 response were dysregulated in RIFE although expression levels of Estrogen receptor α (ERα and Progesterone receptor (PR were not significantly altered in RIFE. Furthermore, expression and phosphorylation of Signal transducer and activator of transcription 3 (STAT3 are reduced and a gene set associated with Janus kinase (JAK-STAT signaling pathway is systemically down-regulated in these patients. Pairwise analyses of microRNA arrays with prediction of dysregulated microRNAs based on mRNA expression datasets demonstrated that 6 microRNAs are aberrantly regulated in RIFE. Collectively, we here

  4. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis

    Science.gov (United States)

    Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Mittal, Inna; Mobeen, Ahmed; Ramachandran, Srinivasan

    2016-01-01

    Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness. PMID:27000948

  5. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis.

    Science.gov (United States)

    Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Mittal, Inna; Mobeen, Ahmed; Ramachandran, Srinivasan

    2016-03-22

    Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness.

  6. VH Replacement Footprint Analyser-I (VHRFA-I, a Java based Computer Program for Analyses of Immunoglobulin Heavy Chain Genes and Potential VH Replacement Products in Human and Mouse

    Directory of Open Access Journals (Sweden)

    Lin eHuang

    2014-02-01

    Full Text Available VH replacement occurs through RAG-mediated secondary recombination between a rearranged VH gene and an upstream unrearranged VH gene. Due to the location of the cryptic Recombination Signal Sequence (cRSS, TACTGTG at the 3’ end of VH gene coding region, a short stretch of nucleotides from the previous rearranged VH gene can be retained in the newly formed VH-DH junction as a footprint of VH replacement. Such footprints can be used as markers to identify IgH genes potentially generated through VH replacement. To explore the contribution of VH replacement products to the antibody repertoire, we developed a Java based computer program, VH replacement footprint analyzer-I (VHRFA-I, to analyze published or newly obtained IgH genes from human or mouse. The VHRFA-1 program has multiple functional modules: it first uses service provided by the IMGT/V-QUEST program to assign potential VH, DH, and JH germline genes; then, it searches for VH replacement footprint motifs within the VH-DH junction (N1 regions of IgH gene sequences to identify potential VH replacement products; it can also analyze the frequencies of VH replacement products in correlation with publications, keywords, or VH, DH, and JH gene usages, and mutation status; it can further analyze the amino acid usages encoded by the identified VH replacement footprints. In summary, this program provides a useful computation tool for exploring the biological significance of VH replacement products in human and mouse.

  7. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    . Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  8. Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation.

    Science.gov (United States)

    Strelkov, Sergei V; Burkhard, Peter

    2002-01-01

    Alpha-helical coiled coils represent a widespread protein structure motif distinguished by a seven-residue periodicity of apolar residues in the primary sequence. A characteristic "knobs-into-holes" packing of these residues into a hydrophobic core results in a superhelical, usually left-handed, rope of two or more alpha-helices. Such a geometry can be parameterized. For this purpose, a new computer program, TWISTER, was developed. With the three-dimensional coordinates as input, TWISTER uses an original algorithm to determine the local coiled-coil parameters as a function of residue number. In addition, heptad positions are assigned based on structural criteria. It is known that frequently encountered discontinuities in the heptad repeat, such as stutters and skips, can be tolerated within a continuous coiled coil but result in a local distortion of its geometry. This was explored in detail with the help of TWISTER for several two- and three-stranded coiled coils. Depending on the particular protein, stutters were found to be compensated locally by an unwinding of the superhelix, alpha-helical unwinding, or both. In the first case, there is often a local switch from a left-handed to a right-handed superhelix. In general, the geometrical distortion is confined to about two alpha-helical turns at either side of the stutter. Furthermore, stutters result in a local increase of the coiled-coil radius. (c) 2002 Elsevier Science (USA).

  9. Effects of reduced natural background radiation on Drosophila melanogaster growth and development as revealed by the FLYINGLOW program.

    Science.gov (United States)

    Morciano, Patrizia; Iorio, Roberto; Iovino, Daniela; Cipressa, Francesca; Esposito, Giuseppe; Porrazzo, Antonella; Satta, Luigi; Alesse, Edoardo; Tabocchini, Maria Antonella; Cenci, Giovanni

    2018-01-01

    Natural background radiation of Earth and cosmic rays played a relevant role during the evolution of living organisms. However, how chronic low doses of radiation can affect biological processes is still unclear. Previous data have indicated that cells grown at the Gran Sasso Underground Laboratory (LNGS, L'Aquila) of National Institute of Nuclear Physics (INFN) of Italy, where the dose rate of cosmic rays and neutrons is significantly reduced with respect to the external environment, elicited an impaired response against endogenous damage as compared to cells grown outside LNGS. This suggests that environmental radiation contributes to the development of defense mechanisms at cellular level. To further understand how environmental radiation affects metabolism of living organisms, we have recently launched the FLYINGLOW program that aims at exploiting Drosophila melanogaster as a model for evaluating the effects of low doses/dose rates of radiation at the organismal level. Here, we will present a comparative data set on lifespan, motility and fertility from different Drosophila strains grown in parallel at LNGS and in a reference laboratory at the University of L'Aquila. Our data suggest the reduced radiation environment can influence Drosophila development and, depending on the genetic background, may affect viability for several generations even when flies are moved back to normal background radiation. As flies are considered a valuable model for human biology, our results might shed some light on understanding the effect of low dose radiation also in humans. © 2017 Wiley Periodicals, Inc.

  10. Requirements for implementation of Kuessner and Wagner indicial lift growth functions into the FLEXSTAB computer program system for use in dynamic loads analyses

    Science.gov (United States)

    Miller, R. D.; Rogers, J. T.

    1975-01-01

    General requirements for dynamic loads analyses are described. The indicial lift growth function unsteady subsonic aerodynamic representation is reviewed, and the FLEXSTAB CPS is evaluated with respect to these general requirements. The effects of residual flexibility techniques on dynamic loads analyses are also evaluated using a simple dynamic model.

  11. Root Cause Analyses of Nunn-McCurdy Breaches. Volume 2: Excalibur Artillery Projectile and the Navy Enterprise Resource Planning Program, with an Approach to Analyzing Program Complexity and Risk

    Science.gov (United States)

    2012-01-01

    extraordinarily helpful discussions about the program. We thank John McNair and Dennis Taitano for their insights regarding the creation and expectations of...Program Deviation Report PEO-AMMO Program Executive Officer for Ammunition PMP parts management program POM Program Objectives Memorandum RCA root cause

  12. Variations of GHGs from the lower-troposphere to the UT/LS revealed by two Japanese regular aircraft observation programs

    Science.gov (United States)

    Niwa, Yosuke; Machida, Toshinobu; Sawa, Yousuke; Tsuboi, Kazuhiro; Matsueda, Hidekazu; Imasu, Ryoichi

    2014-05-01

    A Japan-centered observation network consisting of two regular aircraft programs have revealed the greenhouse gases variations from the lower-troposphere to the upper-troposphere/lower-stratosphere (UT/LS) regions. In the Comprehensive Observation Network for Trace gases by Airliner (CONTRAIL) project, in-situ continuous measurement equipment (CME) onboard commercial passenger aircraft world-widely observes CO2 profiles in vertical over tens of airports and in horizontal in the UT/LS regions. The CONTRAIL-CME has revealed three-dimensional structure of the global CO2 distribution and has exposed significant inter-hemispheric transport of CO2 through the upper-troposphere. In inverse modeling, the CME data have provided strong constraints on CO2 flux estimation especially for the Asian tropics. Automatic flask air sampling equipment (ASE) is also onboard the CONTRAIL aircraft and has been observing CO2 mixing ratios as well as those of methane, carbon monoxide, nitrous oxide and other trace species in the upper-troposphere between Japan and Australia. The observation period of the ASE has reached 20 years. In recent years, the ASE program has extended to the northern subarctic UT/LS region and has given an insight of transport mechanisms in the UT/LS by observing seasonal GHGs variations. In the other aircraft observation program by Japan Meteorological Agency, variations of GHGs have been observed by flask-sampling onboard a C-130H aircraft horizontally in the mid-troposphere over the western North Pacific as well as vertically over Minamitorishima-Island. The C-130H aircraft has persistently observed high mixing ratios of CH4 in the mid-troposphere, which seems to be originated from fossil fuel combustion throughout the year as well as from biogenic sources during summer in the Asian regions. Those above aircraft observation programs have a significant role for constraining GHGs flux estimates by filling the data gap of the existing surface measurement network

  13. Calibration exercise for the Community Aquatic Monitoring Program (CAMP) nutrient analyses: establishing variability between filtered and unfiltered water samples and two analytical laboratories

    National Research Council Canada - National Science Library

    Thériault, M.-H; Courtenay, S.C

    2012-01-01

    As part of the Community Aquatic Monitoring Program (CAMP) unfiltered water samples were collected between 2006 and 2008 and analyzed for dissolved inorganic nutrients (i.e., nitrate + nitrite (NO3 + NO2...

  14. RNA-Seq-based transcriptomic and metabolomic analysis reveal stress responses and programmed cell death induced by acetic acid in Saccharomyces cerevisiae

    Science.gov (United States)

    Dong, Yachen; Hu, Jingjin; Fan, Linlin; Chen, Qihe

    2017-01-01

    As a typical harmful inhibitor in cellulosic hydrolyzates, acetic acid not only hinders bioethanol production, but also induces cell death in Saccharomyces cerevisiae. Herein, we conducted both transcriptomic and metabolomic analyses to investigate the global responses under acetic acid stress at different stages. There were 295 up-regulated and 427 down-regulated genes identified at more than two time points during acetic acid treatment (150 mM, pH 3.0). These differentially expressed genes (DEGs) were mainly involved in intracellular homeostasis, central metabolic pathway, transcription regulation, protein folding and stabilization, ubiquitin-dependent protein catabolic process, vesicle-mediated transport, protein synthesis, MAPK signaling pathways, cell cycle, programmed cell death, etc. The interaction network of all identified DEGs was constructed to speculate the potential regulatory genes and dominant pathways in response to acetic acid. The transcriptional changes were confirmed by metabolic profiles and phenotypic analysis. Acetic acid resulted in severe acidification in both cytosol and mitochondria, which was different from the effect of extracellular pH. Additionally, the imbalance of intracellular acetylation was shown to aggravate cell death under this stress. Overall, this work provides a novel and comprehensive understanding of stress responses and programmed cell death induced by acetic acid in yeast. PMID:28209995

  15. VH Replacement Footprint Analyzer-I, a Java-Based Computer Program for Analyses of Immunoglobulin Heavy Chain Genes and Potential VH Replacement Products in Human and Mouse.

    Science.gov (United States)

    Huang, Lin; Lange, Miles D; Zhang, Zhixin

    2014-01-01

    VH replacement occurs through RAG-mediated secondary recombination between a rearranged VH gene and an upstream unrearranged VH gene. Due to the location of the cryptic recombination signal sequence (cRSS, TACTGTG) at the 3' end of VH gene coding region, a short stretch of nucleotides from the previous rearranged VH gene can be retained in the newly formed VH-DH junction as a "footprint" of VH replacement. Such footprints can be used as markers to identify Ig heavy chain (IgH) genes potentially generated through VH replacement. To explore the contribution of VH replacement products to the antibody repertoire, we developed a Java-based computer program, VH replacement footprint analyzer-I (VHRFA-I), to analyze published or newly obtained IgH genes from human or mouse. The VHRFA-1 program has multiple functional modules: it first uses service provided by the IMGT/V-QUEST program to assign potential VH, DH, and JH germline genes; then, it searches for VH replacement footprint motifs within the VH-DH junction (N1) regions of IgH gene sequences to identify potential VH replacement products; it can also analyze the frequencies of VH replacement products in correlation with publications, keywords, or VH, DH, and JH gene usages, and mutation status; it can further analyze the amino acid usages encoded by the identified VH replacement footprints. In summary, this program provides a useful computation tool for exploring the biological significance of VH replacement products in human and mouse.

  16. Optimizing the analysis strategy for the CANVAS Program : A prespecified plan for the integrated analyses of the CANVAS and CANVAS-R trials

    NARCIS (Netherlands)

    Neal, Bruce; Perkovic, Vlado; Mahaffey, Kenneth W.; Fulcher, Greg; Erondu, Ngozi; Desai, Mehul; Shaw, Wayne; Law, Gordon; Walton, Marc K.; Rosenthal, Norm; de Zeeuw, Dick; Matthews, David R.

    Two large cardiovascular outcome trials of canagliflozin, comprising the CANVAS Program, will complete in early 2017: the CANagliflozin cardioVascular Assessment Study (CANVAS) and the CANagliflozin cardioVascular Assessment Study-Renal (CANVAS-R). Accruing data for the sodium glucose co-transporter

  17. An analysis of the costs of Uganda's Child Days Plus: do low costs reveal an efficient program or an underfinanced one?

    Science.gov (United States)

    Fiedler, John L; Semakula, Richard

    2014-03-01

    Twice annually, Uganda implements Child Days Plus (CDP), a month-long outreach activity that distributes vitamin A capsules to preschool children and deworms children 6 months to 14 years old. Introduced initially as a temporary, interim strategy, CDP is now a decade old. To assess how well CDP is implemented using an activity-based cost analysis. In the absence of a cost-accounting system for CDP, we defined the six major CDP activities as cost centers and identified five important subactivities required to implement a round of CDP. Based on a purposive sample, we conducted a structured interview survey of 59 Ministry of Health facilities, 9 district offices, and national-level CDP staff. Only one-third of the facilities implemented all 11 CDP core activities. The survey revealed that Ministry of Health staff and volunteers are frequently paid substantially less in allowances than they are entitled to for their CDP outreach activities. Viewing these two practices--nonimplementation and less-than-full-reimbursement--as indicators of CDP's underfinancing, we estimate the program is underfinanced by the equivalent of 37% of its 'full implementation" costs. Two-thirds of underfinancing is manifested in nonimplementation and one-third as less-than full-reimbursement. CDP exploits economies of scale and scope and has an average cost per child served of US$0.22. We estimate that it annually saves 367,000 disability-adjusted life-years (DALYs) at an average cost of US$12.5, making it--despite its underfinancing--highly cost-effective. Increased CDP funding would enable its vitamin A coverage rate of 58% and its deworming coverage rate of 62% to be increased, thereby increasing its effectiveness and efficiency. CDP should be "relaunched," as part of an effort to improve the structure of the program, set expectations about it, and earmark a minimum of resources for CDP. The Ministry of Health should demonstrate its new, greater commitment to CDP by introducing a program

  18. (In)security factor atomic bomb. An analysis of the crisis with the Iranian nuclear program; (Un-)Sicherheitsfaktor Atombombe. Eine Analyse der Krise um das iranische Nuklearprogramm

    Energy Technology Data Exchange (ETDEWEB)

    Bock, Andreas [Augsburg Univ. (Germany). Lehrstuhl fuer Friedens- und Konfliktforschung

    2012-04-15

    Iran is a rational actor in the international politics that decides on the basis of the perception of threat. Iran's security situation is comparable with that of Israel with the rational consequence to rely on the atomic program with respect to deterrence and self-defense. The solution of the Iran crisis is basically dependent on a change of the perception of threat. A military act against the Iranian nuclear facilities would be counterproductive, would only slowing down the program but not prevent further activities. In fact a military act would enhance the perception of threat. For the analysis of the Iran crises the author used the Cuba crisis as blueprint, were mislead perceptions were responsible for the escalation.

  19. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

    Directory of Open Access Journals (Sweden)

    Diogo M O Ogawa

    Full Text Available We propose the technique of biogeochemical typing (BGC typing as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES; and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR spectroscopy and proton nuclear magnetic resonance (1H-NMR all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that

  20. Analyse d'une formation plurilingue à distance : actions et interactions Analysis of a plurilingual e-learning program: action and interaction

    Directory of Open Access Journals (Sweden)

    Monica Masperi

    2006-04-01

    Full Text Available Cette contribution s'attache à analyser trois sessions de formation à l'intercompréhension en langues romanes qui se sont déroulées selon un scénario semblable depuis une plateforme Internet spécifiquement développée pour cet usage : la plateforme Galanet. Les formations Galanet réunissent un nombre important d'étudiants (entre cent et deux cents en général, répartis au sein de plusieurs établissements universitaires et investis dans un projet à réaliser en commun, soit un "dossier de presse" quadrilingue publié sur la Toile. Nous mènerons notre étude selon deux axes complémentaires : une analyse quantitative des messages déposés, pour chacune des sessions, dans l'espace forum de la plateforme et une analyse qualitative d'un échantillon d'interventions générées dans une de ces sessions. La première approche, quantitative et comparative, devrait nous permettre de tirer un certain nombre d'enseignements sur le déroulement de la formation dans ses grandes lignes, ainsi que sur l'action de ses participants (étudiants et tuteurs. La seconde nous permettra en revanche de mieux cerner les pratiques discursives suscitées par le scénario pédagogique et la dimension plurilingue des échanges.This paper focuses on analysing three sessions of cross-comprehension training in romance languages which took place using similar scenarii on the e-learning platform "Galanet". "Galanet" learning schemes assemble large groups of students (from one to two hundred in general who are geographically located in different universities and committed to completing common tasks the final objective of which is to create a quadrilingual press file publication online. The present study will be developed along two complementary axes: 1. a quantitative analysis of the messages posted on the forum page of the platform for each session. 2. a qualitative analysis of sample interventions generated in one of these sessions. On the one hand, the

  1. Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development.

    Science.gov (United States)

    Agarwal, Aakrati; Mudgil, Yashwanti; Pandey, Saurabh; Fartyal, Dhirendra; Reddy, Malireddy K

    2016-01-01

    Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants.

  2. Introduction of Transplant Registry Unified Management Program 2 (TRUMP2): scripts for TRUMP data analyses, part I (variables other than HLA-related data).

    Science.gov (United States)

    Atsuta, Yoshiko

    2016-01-01

    Collection and analysis of information on diseases and post-transplant courses of allogeneic hematopoietic stem cell transplant recipients have played important roles in improving therapeutic outcomes in hematopoietic stem cell transplantation. Efficient, high-quality data collection systems are essential. The introduction of the Second-Generation Transplant Registry Unified Management Program (TRUMP2) is intended to improve data quality and more efficient data management. The TRUMP2 system will also expand possible uses of data, as it is capable of building a more complex relational database. The construction of an accessible data utilization system for adequate data utilization by researchers would promote greater research activity. Study approval and management processes and authorship guidelines also need to be organized within this context. Quality control of processes for data manipulation and analysis will also affect study outcomes. Shared scripts have been introduced to define variables according to standard definitions for quality control and improving efficiency of registry studies using TRUMP data.

  3. Image-Guided Analyses Reveal that Non-CD4 Splenocytes Contribute to CD4+ T Cell–Mediated Inflammation Leading to Islet Destruction by Altering Their Local Function and Not Systemic Trafficking Patterns

    Directory of Open Access Journals (Sweden)

    Mi-Heon Lee

    2007-11-01

    Full Text Available Recruitment of CD4+ T cells into islets is a critical component of islet inflammation (insulitis leading to type 1 diabetes; therefore, determining if conditions used to treat diabetes change their trafficking patterns is relevant to the outcome. Cotransfer of CD4+BDC2.5 (BDC cells with non-CD4 splenocytes obtained from newly diabetic NOD mice, but not when they are transferred alone, induces accelerated diabetes. It is unclear whether these splenocytes affect diabetes development by altering the systemic and/or local trafficking and proliferation patterns of BDC cells in target and nontarget tissues. To address these questions, we developed an animal model to visualize BDC cell trafficking and proliferation using whole-body in vivo bioluminescence imaging and used the images to direct tissue sampling for further analyses of the cell distribution within tissues. The whole-body, or macroscopic, trafficking patterns were not dramatically altered in both groups of recipient mice. However, the local patterns of cell distribution were distinct, which led to invasive insulitis only in cotransferred mice with an increased number of islet-infiltrating CD11b+ and CD11c+ cells. Taken together, the non-CD4 splenocytes act locally by promoting invasive insulitis without altering the systemic trafficking patterns or proliferation of BDC cells and thus contributing to diabetes by altering the localization within the tissue.

  4. Analysing small insect glands with UV-LDI MS: high-resolution spatial analysis reveals the chemical composition and use of the osmeterium secretion in Themira superba (Sepsidae: Diptera).

    Science.gov (United States)

    Araujo, D P; Tuan, M J M; Yew, J Y; Meier, R

    2014-08-01

    For many insect species, pheromones are important communication tools, but chemical analysis and experimental study can be technically challenging because they require the detection and handling of complex chemicals in small quantities. One drawback of traditional mass spectrometry methods such as gas chromatography mass spectrometry is that whole-body extractions from one to several hundred individuals are required, with the consequence that intra- and interindividual differences cannot be detected. Here, we used the recently introduced UV-LDI MS (ultraviolet laser desorption/ionization mass spectrometry) to profile the 'osmeterium' of the sepsid fly Themira superba that is located on the edge of the hind tibia of males. Based on analyses of individual legs, we established that the gland produced a secretion that consisted of oxygenated hydrocarbons and putative isoprenoids. The secretion was first detected 24 h after eclosion, and its transfer to the wings of females during mating was demonstrated using UV-LDI MS. We then tested whether the secretion had an anti-aphrodisiac function, but experimental transfer of the secretion to virgin females did not affect mating success or copulation duration. Throughout the study, UV-LDI MS proved invaluable, because it allowed tracking the natural and experimental transfer of small quantities of pheromones to specific body parts of small flies. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  5. Sequence analyses reveal that a TPR–DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR–DP domains and prokaryotic GerD proteins

    Science.gov (United States)

    Papandreou, Nikolaos; Chomilier, Jacques

    2008-01-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR–DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR–DP domains. Electronic supplementary material The online version of this article (doi:10.1007/s12192-008-0083-8) contains supplementary material, which is available to authorized users. PMID:18987995

  6. Sequence analyses reveal that a TPR-DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR-DP domains and prokaryotic GerD proteins.

    Science.gov (United States)

    Hernández Torres, Jorge; Papandreou, Nikolaos; Chomilier, Jacques

    2009-05-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR-DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR-DP domains.

  7. Consistent C3 plant habitat of hominins during 400-300 ka at the Longyadong Cave site (Luonan Basin, central China) revealed by stable carbon isotope analyses of loess deposits

    Science.gov (United States)

    Zhang, Hongyan; Lu, Huayu; Wang, Shejiang

    2017-04-01

    The proportions of woody and grassland taxa in terrestrial ecosystems played an important role in the origin and evolution of early Palaeolithic hominins. However the influence of ecosystem changes on hominin behavior and adaptations in Asia has not been studied in detail. Hominins have exploited the Luonan Basin in the Eastern Qinling Mountains, central China, since the early Paleolithic. Dated sites, consisting of alternating loess and soil deposits with in situ artefacts, are common in the region, and provide a detailed record of Early to Middle Pleistocene hominin environments. Here, we present the results of measurements of the stable carbon isotopic composition of soil organic matter (δ13C) in the loess-paleosol sequences from the Longyadong Cave site. Our analyses of δ13C show that for at least 400 ka the Longyadong Cave site and its surroundings were dominated by C3 woody plants, whereas the nearby Liuwan site was dominated by C4 and C3 mixed grassland or woody grassland vegetation. These findings demonstrate that between 400 and 300 ka in the Luonan Basin, hominins occupied a habitat consisting of a mosaic of grassland and woodland/forest. Although the vegetation of the region changed in response to the glacial-interglacial climatic cycles, patches of woody vegetation in landscapes such as at Longyadong Cave site persisted continuously. Such environments seem to be have been favored by hominins living in the Luonan Basin, possibly because they provided a diverse range of food resources during both glacial and interglacial intervals of the Middle Pleistocene, when most of northern China was experiencing an increasing trend of drying and cooling and steppe environments were expanding. Thus, the Luonan Basin would have served as a refugium for hominin occupation in China during the Middle Pleistocene.

  8. Seasonal dynamics of particulate organic matter and its response to flooding in the Pearl River Estuary, China, revealed by stable isotope (δ13C and δ15N) analyses

    Science.gov (United States)

    Ye, Feng; Guo, Wei; Shi, Zhen; Jia, Guodong; Wei, Gangjian

    2017-08-01

    Nine cruises were conducted on a seasonal basis from 2013 to 2015 to investigate the spatial distribution and seasonal variability of δ13C and δ15N in particulate organic matter (POM), and its response to flooding in the Pearl River Estuary (PRE), south China. Our study reveals highly variable isotope ratios between seasons in this subtropical estuary, following seasonal climatic and hydrological cycles. Wet seasons had more isotopically depleted δ13C values, indicating the dominance of terrestrial and freshwater algae POM, whereas the contribution from marine phytoplankton (16%-59%) was higher during the dry seasons. In contrast, δ15N exhibited a sharp increase (up to 17.6‰) at low salinities (0-5) during high flow seasons. This was consistent with high NO3- concentrations, reflecting phytoplankton and bacteria assimilation of δ15N enriched-NO3- as well as notable isotope fractionation during microbial mineralization. There was little annual variability in δ13C over the 2 year period; however, particulate nitrogen (PN) exhibited lower concentrations but more enriched isotope values in 2015 than in 2014. This can be best explained by temperature-modulated biological processing of particulate organic nitrogen, partially due to different biogeochemical responses during normal (2014) and strong El Niño (2015) years. After flooding in June 2015, terrestrial organic matter and freshwater phytoplankton were the major components of POM within the estuary and shelf areas, whereas marine phytoplankton was the dominant component in the adjacent coastal waters with mid-salinities (10 10 μg L-1) and δ13C-enriched but δ15N-depleted POM.

  9. A persistent Holocene wetting trend in arid central Asia, with wettest conditions in the late Holocene, revealed by multi-proxy analyses of loess-paleosol sequences in Xinjiang, China

    Science.gov (United States)

    Chen, Fahu; Jia, Jia; Chen, Jianhui; Li, Guoqiang; Zhang, Xiaojian; Xie, Haichao; Xia, Dunsheng; Huang, Wei; An, Chengbang

    2016-08-01

    There are significant differences in the interpretation of the moisture (precipitation) history of arid central Asia (ACA) during the Holocene, as inferred on one hand from speleothem oxygen isotope records, and on the other from lake sediments. Here we present the results of measurements of climatically-sensitive magnetic properties and soil color from four well-dated loess-paleosol sequences from the northern slopes of the Tienshan Mountains and the Yili River valley, Xinjiang, China, in the core area of ACA. Our results demonstrate that the characteristic Holocene paleosol, indicating relatively moist conditions, generally formed after ∼6 ka (1 ka = 1000 cal yr BP) in the study region, and that the accumulation of unweathered loess prevailed during the early Holocene, indicating a dry climate at that time. The magnetic proxies further reveal a trend of generally increasing moisture since the Last Glacial Maximum, with the wettest climate occurring during the late Holocene. This trend of increasing moisture during the Holocene is representative of the Xinjiang region and possibly of the whole of the core area of ACA, and is in marked contrast both to the mid-Holocene moisture maximum observed in the East Asian summer monsoon region and to the general decrease in the strength of the Indian summer monsoon since the early Holocene. Our findings are supported by the results of a climate simulation which indicate a trend of increasing summer and winter precipitation during the Holocene in the core area of ACA, caused mainly by an increase in the strength of the westerlies effected by an increasing latitudinal insolation gradient and by a negative trend of the Arctic Oscillation (AO) or North Atlantic Oscillation (NAO).

  10. Virus-induced Gene Silencing-based Functional Analyses Revealed the Involvement of Several Putative Trehalose-6-Phosphate Synthase/Phosphatase Genes in Disease Resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato

    Directory of Open Access Journals (Sweden)

    Huijuan Zhang

    2016-08-01

    Full Text Available Trehalose and its metabolism have been demonstrated to play important roles in control of plant growth, development and stress responses. However, direct genetic evidence supporting the functions of trehalose and its metabolism in defense response against pathogens is lacking. In the present study, genome-wide characterization of putative trehalose-related genes identified 11 SlTPSs for trehalose-6-phosphate synthase, 8 SlTPPs for trehalose-6-phosphate phosphatase and one SlTRE1 for trehalase in tomato genome. Nine SlTPSs, 4 SlTPPs and SlTRE1 were selected for functional analyses to explore their involvement in tomato disease resistance. Some selected SlTPSs, SlTPPs and SlTRE1 responded with distinct expression induction patterns to Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst DC3000 as well as to defense signaling hormones (e.g. salicylic acid, jasmonic acid and a precursor of ethylene. Virus-induced gene silencing-mediated silencing of SlTPS3, SlTPS4 or SlTPS7 led to deregulation of ROS accumulation and attenuated the expression of defense-related genes upon pathogen infection and thus deteriorated the resistance against B. cinerea or Pst DC3000. By contrast, silencing of SlTPS5 or SlTPP2 led to an increased expression of the defense-related genes upon pathogen infection and conferred an increased resistance against Pst DC3000. Silencing of SlTPS3, SlTPS4, SlTPS5, SlTPS7 or SlTPP2 affected trehalose level in tomato plants with or without infection of B. cinerea or Pst DC3000. These results demonstrate that SlTPS3, SlTPS4, SlTPS5, SlTPS7 and SlTPP2 play roles in resistance against B. cinerea and Pst DC3000, implying the importance of trehalose and tis metabolism in regulation of defense response against pathogens in tomato.

  11. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.

    Science.gov (United States)

    Linguiti, Giovanna; Antonacci, Rachele; Tasco, Gianluca; Grande, Francesco; Casadio, Rita; Massari, Serafina; Castelli, Vito; Consiglio, Arianna; Lefranc, Marie-Paule; Ciccarese, Salvatrice

    2016-08-15

    those of the so far examined artiodactyls, genomic results highlight in dolphin an unusually simple TRG locus. The cDNA analysis reveal productive TRA/TRD transcripts and unusual ratios of productive/unproductive TRG transcripts. Comparing multiple different individuals, evidence is found for a "public" gamma delta TCR repertoire thus suggesting that in dolphins as in human the gamma delta TCR repertoire is accompanied by selection for public gamma chain.

  12. Genome-wide mRNA expression analysis of hepatic adaptation to high-fat diets reveals switch from an inflammatory to steatotic transcriptional program.

    Directory of Open Access Journals (Sweden)

    Marijana Radonjic

    Full Text Available BACKGROUND: Excessive exposure to dietary fats is an important factor in the initiation of obesity and metabolic syndrome associated pathologies. The cellular processes associated with the onset and progression of diet-induced metabolic syndrome are insufficiently understood. PRINCIPAL FINDINGS: To identify the mechanisms underlying the pathological changes associated with short and long-term exposure to excess dietary fat, hepatic gene expression of ApoE3Leiden mice fed chow and two types of high-fat (HF diets was monitored using microarrays during a 16-week period. A functional characterization of 1663 HF-responsive genes reveals perturbations in lipid, cholesterol and oxidative metabolism, immune and inflammatory responses and stress-related pathways. The major changes in gene expression take place during the early (day 3 and late (week 12 phases of HF feeding. This is also associated with characteristic opposite regulation of many HF-affected pathways between these two phases. The most prominent switch occurs in the expression of inflammatory/immune pathways (early activation, late repression and lipogenic/adipogenic pathways (early repression, late activation. Transcriptional network analysis identifies NF-kappaB, NEMO, Akt, PPARgamma and SREBP1 as the key controllers of these processes and suggests that direct regulatory interactions between these factors may govern the transition from early (stressed, inflammatory to late (pathological, steatotic hepatic adaptation to HF feeding. This transition observed by hepatic gene expression analysis is confirmed by expression of inflammatory proteins in plasma and the late increase in hepatic triglyceride content. In addition, the genes most predictive of fat accumulation in liver during 16-week high-fat feeding period are uncovered by regression analysis of hepatic gene expression and triglyceride levels. CONCLUSIONS: The transition from an inflammatory to a steatotic transcriptional program

  13. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    2015-03-12

    Mar 12, 2015 ... ethnic, linguistic and geographic diversity of India. In the present study we aimed to find out whether the. Indian populations differ in risk allele frequencies (RAFs) at. NAFLD-associated candidate SNPs, and also to predict the genetic risk score of NAFLD in different Indian populations, as well as to compare ...

  14. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    Author Affiliations. Ankita Chatterjee1 Analabha Basu1 Abhijit Chowdhury2 3 Kausik Das2 Neeta Sarkar-Roy1 Partha P. Majumder1 Priyadarshi Basu1 3. National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. Hospital), Kalyani 741 251, India; Institute of Post Graduate Medical Education and Research, ...

  15. Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles

    CERN Document Server

    Breuer, David; Sampathkumar, Arun; Hollandt, Florian; Persson, Staffan; Nikoloski, Zoran

    2015-01-01

    The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microtubule dynamics have been intensively studied, principles that govern the cytoskeleton organization remain largely unexplored. Here, we captured biologically relevant characteristics of the plant cytoskeleton through a network-driven imaging-based approach allowing to quantitatively assess dynamic features of the cytoskeleton. By introducing suitable null models, we demonstrate that the plant cytoskeletal networks exhibit properties required for efficient transport, namely, short average path lengths and high robustness. We further show that these advantageous features are maintained during temporal cytoskeletal re-arrangements. Interestingly, man-made transportation networks exhibit similar properties, suggesting general laws of network organization supporting diverse transport processes. The proposed network-driven analysis can be ...

  16. Autism cornered: network analyses reveal mechanisms of autism spectrum disorders

    OpenAIRE

    Auffray, Charles

    2014-01-01

    Despite a wealth of behavioral, cognitive, biological, and genetic studies, the causes of autism have remained largely unknown. In their recent work, Snyder and colleagues (Li et?al, 2014) use a systems biology approach and shed light on the molecular and cellular mechanisms underlying autism, thus opening novel avenues for understanding the disease and developing potential treatments.

  17. Análise comparativa da aplicação do programa Seis Sigma em processos de manufatura e serviços Comparative analyses of Six-Sigma program application in manufacturing and services process

    Directory of Open Access Journals (Sweden)

    Luis Ricardo Galvani

    2013-01-01

    Full Text Available O programa Seis Sigma nasceu e evoluiu em ambiente de manufatura, mas também pode ser utilizado em processos de serviços. Porém sua utilização nesse ambiente tem sido feita de forma mais modesta, com menor participação de empresas e, consequentemente, menor número de casos e relatos divulgados. Este trabalho buscou comparar e analisar a aplicação do programa Seis Sigma em manufatura e serviços, por meio de revisão da literatura, análise de projetos vivenciados pelo autor e pesquisa de campo em empresas praticantes do programa. Apesar da limitação da amostra, os resultados mostram fortes indícios de diferenças significativas cuja melhor compreensão pode ajudar a obter melhores resultados em aplicações em serviços.The Six-sigma program has its roots in the manufacturing field, but it can be applied to a service process. However, this application has been done in a modest manner, with the participation of few companies and, as a consequence, few cases, projects, and papers have been exposed. This paper presents a comparative analysis of Six-sigma program application in manufacturing and services process by literature review, comparative analyses of Six-sigma projects experienced by the author, and case studies with companies that apply the program in the manufacturing and services field. Even with sample restriction, the results show key differences that can lead to benefits to services application.

  18. Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

    OpenAIRE

    Karunakaran, Devi Krishna Priya; Al Seesi, Sahar; Banday, Abdul Rouf; Baumgartner, Marybeth; Olthof, Anouk; Lemoine, Christopher; M?ndoiu, Ion I.; Kanadia, Rahul N

    2016-01-01

    Background The retina as a model system with extensive information on genes involved in development/maintenance is of great value for investigations employing deep sequencing to capture transcriptome change over time. This in turn could enable us to find patterns in gene expression across time to reveal transition in biological processes. Methods We developed a bioinformatics pipeline to categorize genes based on their differential expression and their alternative splicing status across time ...

  19. Task 1 Report - Assessment of Data Availability to Inform Energy Planning Analyses: Energy Alternatives Study for the Lao People's Democratic Republic: Smart Infrastructure for the Mekong Program

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Nathan [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Lopez, Anthony J. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Katz, Jessica R. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Cardoso de Oliveira, Ricardo P. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hayter, Sheila J. [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-01-24

    In an effort to address concerns such as energy security, reliability, affordability, and other objectives, the Government of the Lao People's Democratic Republic (Lao PDR) is seeking to advance its expertise and experience in energy system analysis and planning to explore energy alternatives. Assessing the potential and alternatives for deploying energy technology options is often an early step - and, in most cases, an ongoing process - in planning for the development of the energy sector as a whole. Reliable and robust data are crucial to conducting these types of planning-related analyses in a transparent manner that builds confidence among power sector stakeholders and encourages investment in future energy project development and infrastructure opportunities. This report represents the first output of the Energy Alternatives Study for the Lao PDR (Energy Alternatives Study), a collaboration between Ministry of Energy and Mines and the United States Agency for International Development (USAID) under the auspices of the Smart Infrastructure for the Mekong (SIM) program. The Energy Alternatives Study includes five tasks that build upon each other to meet the goal of the project. The report summarizes the availability, quality, and accessibility of data that serve as key inputs to energy planning activities for the power sector. The purpose of this data assessment is two-fold: 1. To facilitate the informed use of existing data by highlighting applications for these data as they relate to priority energy planning analyses; and 2. To inform future investments in energy data collection and management by identifying significant data gaps and providing guidance on how to fill these gaps.

  20. A Novel Function for Arabidopsis CYCLASE1 in Programmed Cell Death Revealed by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Analysis of Extracellular Matrix Proteins.

    Science.gov (United States)

    Smith, Sarah J; Kroon, Johan T M; Simon, William J; Slabas, Antoni R; Chivasa, Stephen

    2015-06-01

    Programmed cell death is essential for plant development and stress adaptation. A detailed understanding of the signal transduction pathways that regulate plant programmed cell death requires identification of the underpinning protein networks. Here, we have used a protagonist and antagonist of programmed cell death triggered by fumonisin B1 as probes to identify key cell death regulatory proteins in Arabidopsis. Our hypothesis was that changes in the abundance of cell death-regulatory proteins induced by the protagonist should be blocked or attenuated by concurrent treatment with the antagonist. We focused on proteins present in the mobile phase of the extracellular matrix on the basis that they are important for cell-cell communications during growth and stress-adaptive responses. Salicylic acid, a plant hormone that promotes programmed cell death, and exogenous ATP, which can block fumonisin B1-induced cell death, were used to treat Arabidopsis cell suspension cultures prior to isobaric-tagged relative and absolute quantitation analysis of secreted proteins. A total of 33 proteins, whose response to salicylic acid was suppressed by ATP, were identified as putative cell death-regulatory proteins. Among these was CYCLASE1, which was selected for further analysis using reverse genetics. Plants in which CYCLASE1 gene expression was knocked out by insertion of a transfer-DNA sequence manifested dramatically increased cell death when exposed to fumonisin B1 or a bacterial pathogen that triggers the defensive hypersensitive cell death. Although pathogen inoculation altered CYCLASE1 gene expression, multiplication of bacterial pathogens was indistinguishable between wild type and CYCLASE1 knockout plants. However, remarkably severe chlorosis symptoms developed on gene knockout plants in response to inoculation with either a virulent bacterial pathogen or a disabled mutant that is incapable of causing disease in wild type plants. These results show that CYCLASE1, which

  1. State Electricity Regulatory Policy and Distributed Resources: Distributed Resource Distribution Credit Pilot Programs--Revealing the Value to Consumers and Vendors

    Energy Technology Data Exchange (ETDEWEB)

    Moskovitz, D.; Harrington, C.; Shirley, W.; Cowart, R.; Sedano, R.; Weston, F.

    2002-10-01

    Designing and implementing credit-based pilot programs for distributed resources distribution is a low-cost, low-risk opportunity to find out how these resources can help defer or avoid costly electric power system (utility grid) distribution upgrades. This report describes implementation options for deaveraged distribution credits and distributed resource development zones. Developing workable programs implementing these policies can dramatically increase the deployment of distributed resources in ways that benefit distributed resource vendors, users, and distribution utilities. This report is one in the State Electricity Regulatory Policy and Distributed Resources series developed under contract to NREL (see Annual Technical Status Report of the Regulatory Assistance Project: September 2000-September 2001, NREL/SR-560-32733). Other titles in this series are: (1) Accommodating Distributed Resources in Wholesale Markets, NREL/SR-560-32497; (2) Distributed Resources and Electric System Re liability, NREL/SR-560-32498; (3) Distribution System Cost Methodologies for Distributed Generation, NREL/SR-560-32500; (4) Distribution System Cost Methodologies for Distributed Generation Appendices, NREL/SR-560-32501.

  2. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.

    Science.gov (United States)

    Lakhina, Vanisha; Arey, Rachel N; Kaletsky, Rachel; Kauffman, Amanda; Stein, Geneva; Keyes, William; Xu, Daniel; Murphy, Coleen T

    2015-01-21

    Induced CREB activity is a hallmark of long-term memory, but the full repertoire of CREB transcriptional targets required specifically for memory is not known in any system. To obtain a more complete picture of the mechanisms involved in memory, we combined memory training with genome-wide transcriptional analysis of C. elegans CREB mutants. This approach identified 757 significant CREB/memory-induced targets and confirmed the involvement of known memory genes from other organisms, but also suggested new mechanisms and novel components that may be conserved through mammals. CREB mediates distinct basal and memory transcriptional programs at least partially through spatial restriction of CREB activity: basal targets are regulated primarily in nonneuronal tissues, while memory targets are enriched for neuronal expression, emanating from CREB activity in AIM neurons. This suite of novel memory-associated genes will provide a platform for the discovery of orthologous mammalian long-term memory components. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. The Prevention Disaster Program of Flood in 2013 for the 4th Grade Students of Kawatanaka Primary School, Tokushima Prefecture, Japan and Underflow Channels Revealed in 2016

    Science.gov (United States)

    Kawamata, Sanae; Murata, Mamoru

    2017-12-01

    The Typhoon No. 18 caused flood on September 15, 2013 in the Kawata River basin, Yoshinogawa City, Tokushima Prefecture. The Kawata River is a raised river bed of 36.7 m with banks to 40.5 m above sea level. The heavy rain did not destroy the banks but made the river level 39.4 m high and then pressed the underflow channel. As the Kawatanaka primary school is located at 36.2 m height, it was not submerged although the underflow channel overbanked the adjacent playground. An educational program on the prevention and reduction for natural disaster, which consists of science, social studies and presentation, was conducted to 18 students of the 4th grade in the period of integrated study in the Kawatanaka primary school from September 17, 2013. On the first day, flow current markings from 625 holes, 30 cm to 1 mm in diameter, on the playground were observed. The flow currents showed direction from SE to NW. On the basis of their observations on the flow currents that water runs from high to low, the students considered the phenomena as a result of tilting of the ground. They conducted activity as their homework to confirm their hypothesis to know if there is any tilt in the ground. They took plastic bottle filled with water and reviled that the ground had 1 to 2 degrees’ tilt to the NW during the experiment. On the bases of the difference between E to W flow of the Kawata River and their SE to NW estimated current flow on the playground and the fact that the bank of the river was not destroyed, the students suggested that the heavy rain had pressed the underflow channels. The suggested channels were found on the playground, where new school buildings were constructed in 2016, by one of the students who studied the program in 2013.

  4. Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution.

    Directory of Open Access Journals (Sweden)

    Claire Burns

    2010-09-01

    Full Text Available Coprinopsis cinerea (also known as Coprinus cinereus is a multicellular basidiomycete mushroom particularly suited to the study of meiosis due to its synchronous meiotic development and prolonged prophase. We examined the 15-hour meiotic transcriptional program of C. cinerea, encompassing time points prior to haploid nuclear fusion though tetrad formation, using a 70-mer oligonucleotide microarray. As with other organisms, a large proportion (∼20% of genes are differentially regulated during this developmental process, with successive waves of transcription apparent in nine transcriptional clusters, including one enriched for meiotic functions. C. cinerea and the fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe diverged ∼500-900 million years ago, permitting a comparison of transcriptional programs across a broad evolutionary time scale. Previous studies of S. cerevisiae and S. pombe compared genes that were induced upon entry into meiosis; inclusion of C. cinerea data indicates that meiotic genes are more conserved in their patterns of induction across species than genes not known to be meiotic. In addition, we found that meiotic genes are significantly more conserved in their transcript profiles than genes not known to be meiotic, which indicates a remarkable conservation of the meiotic process across evolutionarily distant organisms. Overall, meiotic function genes are more conserved in both induction and transcript profile than genes not known to be meiotic. However, of 50 meiotic function genes that were co-induced in all three species, 41 transcript profiles were well-correlated in at least two of the three species, but only a single gene (rad50 exhibited coordinated induction and well-correlated transcript profiles in all three species, indicating that co-induction does not necessarily predict correlated expression or vice versa. Differences may reflect differences in meiotic mechanisms or new roles for paralogs

  5. Multiple incursions and putative species revealed using a mitochondrial and nuclear phylogenetic approach to the Trogoderma variabile (Coleoptera: Dermestidae) trapping program in Australia.

    Science.gov (United States)

    Castalanelli, M A; Mikac, K M; Baker, A M; Munyard, K; Grimm, M; Groth, D M

    2011-06-01

    The Warehouse beetle, Trogoderma variabile (Coleoptera: Dermestidae), is an internationally significant invasive pest of packed goods and stored grain. When it was first documented in Australia at Griffith, New South Wales, in 1977, an eradication campaign was initiated. After several years and considerable effort, the eradication campaign was abandoned. To monitor the presence and spread of T. variabile, surveys were carried out by government agencies in 1992 and 2002. When survey data was compared, it was concluded that the distribution of morphologically identified T. variabile had doubled in most Australian states. Here, we used samples from the 2002 survey to conduct a phylogenetic study using partial sequences of mitochondrial genes Cytochrome oxidase I and Cytochrome B, and the nuclear gene 18S, to examine the distribution and dispersal of T. variabile and detect the presence of misidentified species. Based on our molecular results, we show that only 47% of the samples analysed were T. variabile, and the remaining were a mixture of six putative species. In addition, T. variabile was found in only 78% of the trapping sites. We discuss the importance of correct diagnosis in relation to the eradication campaign.

  6. Differences in the relative timing of developmental events during oogenesis in lower dipterans (Nematocera) reveal the autonomy of follicular cells' differentiation program.

    Science.gov (United States)

    Mazurkiewicz-Kania, Marta; Jędrzejowska, Izabela; Kubrakiewicz, Janusz

    2012-01-01

    Although the ovaries of Nematocera are of the same meroistic-polytrophic type, they show significant differences in the activity of germ cells (oocytes, nurse cells) and their relative contribution to ribosome synthesis and storage during oogenesis. These different activities result in the different growth rate of the germ cells and may determine the life span of the nurse cells. Comparative analysis revealed that with reference to germ cell activity, two basic types of oogenesis in Nematocera can be distinguished. In the Tinearia type, the nurse cells grow considerably and are active until advanced stages of oogenesis, whereas the oocyte is transcriptionally inert. Conversely, in the Tipula type of oogenesis, the oocyte nucleus contains transcriptionally active multiple nucleoli, while nurse cells probably do not contribute to ribosome synthesis, remain relatively small and degenerate early in oogenesis. We studied and compared the process of somatic follicular cell differentiation in nematoceran species representing both types of oogenesis. Our observations indicate that morphogenesis of the follicular cells is at least partly independent of the nurse cell activity, while the execution of their differentiation does not require direct contacts between the follicular cells and the oocyte. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Sproglig Metode og Analyse

    DEFF Research Database (Denmark)

    le Fevre Jakobsen, Bjarne

    Publikationen indeholder øvematerialer, tekster, powerpointpræsentationer og handouts til undervisningsfaget Sproglig Metode og Analyse på BA og tilvalg i Dansk/Nordisk 2010-2011......Publikationen indeholder øvematerialer, tekster, powerpointpræsentationer og handouts til undervisningsfaget Sproglig Metode og Analyse på BA og tilvalg i Dansk/Nordisk 2010-2011...

  8. The kinetics of transcriptomic changes induced by cigarette smoke in rat lungs reveals a specific program of defense, inflammation, and circadian clock gene expression.

    Science.gov (United States)

    Gebel, Stephan; Gerstmayer, Bernhard; Kuhl, Peter; Borlak, Jürgen; Meurrens, Kris; Müller, Thomas

    2006-10-01

    Gene expression profiling in animal models exposed to cigarette mainstream smoke (CS) shapes up as a promising tool for investigating the molecular mechanisms involved in the onset and development of CS-related disease and may aid in the identification of disease candidate genes. Here we report on differential gene expression in lungs of rats exposed for 2, 7, and 13 weeks to 300 and 600 microg total particulate matter/l CS with sacrifice 2, 6, or 20 h after the last exposure. Regarding antioxidant and xenobiotic-metabolizing (phase I/II) enzymes, a stereotypic, mostly transient, expression pattern of differentially expressed genes was observed after each exposure period. The expression patterns were generally dose dependent for antioxidant and phase II genes and not dose dependent for phase I genes at the CS concentrations tested. However, with increasing length of exposure, there was a distinct, mostly sustained and dose-sensitive, expression of genes implicated in innate and adaptive immune responses, clearly pointing to an emerging inflammatory response. Notably, this inflammatory response included the expression of lung disease-related genes not yet linked to CS exposure, such as galectin-3, arginase 1, and chitinase, as well as genes encoding proteolytic enzymes. Finally, our experiments also revealed a CS exposure-dependent shift in the cyclical expression of genes involved in controlling the circadian rhythm. Altogether, these results provide further insight into the molecular mechanisms of CS-dependent disease onset and development and thus may also be useful for defining CS-specific molecular biomarkers of disease.

  9. More than a century of Grain for Green Program is expected to restore soil carbon stock on alpine grassland revealed by field {sup 13}C pulse labeling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qi; Chen, Dongdong; Zhao, Liang [Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai (China); Yang, Xue [Department of Education of Qinghai Province, Xining 810008, Qinghai (China); Xu, Shixiao [Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai (China); Zhao, Xinquan, E-mail: xqzhao@nwipb.cas.cn [Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai (China); Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 10041, Sichuan (China)

    2016-04-15

    Anthropogenic changes in land use/cover have altered the vegetation, soil, and carbon (C) cycling on the Qinghai–Tibetan Plateau (QTP) over the last ~ 50 years. As a result, the Grain for Green Program (GfGP) has been widely implemented over the last 10 years to mitigate the impacts of cultivation. To quantify the effects of the GfGP on C partitioning and turnover rates at the ecosystem scale, an in situ {sup 13}C pulse labeling experiment was conducted on natural and GfGP grasslands in an agro-pastoral ecotone in the Lake Qinghai region on the QTP. We found that there were significant differences in the C stocks of all the considered pools in both the natural and GfGP grasslands, with higher CO{sub 2} uptake rates in the GfGP grassland than that in the natural grassland. Partitioning of photoassimilate (% of recovered {sup 13}C) in C pools of both grasslands was similar 25 days after labeling, except in the roots of the 0–15 and 5–15 cm soil layer. Soil organic C (SOC) sequestration rate in the GfGP grassland was 11.59 ± 1.89 g C m{sup −2} yr{sup −1} significantly greater than that in the natural grassland. The results confirmed that the GfGP is an efficient approach for grassland restoration and C sequestration. However, it will take more than a century (119.19 ± 20.26 yr) to restore the SOC stock from the current cropland baseline level to the approximate level of natural grassland. We suggest that additional measures are needed in the selection of suitable plant species for vegetation restoration, and in reasonable grazing management. - Highlights: • Grain for Green Project initiated in 1999 converts cropland to grassland/shrubland. • Impact of Grain for Green on carbon cycling on Qinghai–Tibetan Plateau is unknown. • Effects on carbon partitioning and turnover were accessed by {sup 13}CO{sub 2} pulse labeling. • Different mass of {sup 13}C in excess, similar {sup 13}C partitioning are shown in grasslands. • Soil organic carbon of

  10. Supporting analyses and assessments

    Energy Technology Data Exchange (ETDEWEB)

    Ohi, J. [National Renewable Energy Lab., Golden, CO (United States)

    1995-09-01

    Supporting analysis and assessments can provide a sound analytic foundation and focus for program planning, evaluation, and coordination, particularly if issues of hydrogen production, distribution, storage, safety, and infrastructure can be analyzed in a comprehensive and systematic manner. The overall purpose of this activity is to coordinate all key analytic tasks-such as technology and market status, opportunities, and trends; environmental costs and benefits; and regulatory constraints and opportunities-within a long-term and systematic analytic foundation for program planning and evaluation. Within this context, the purpose of the project is to help develop and evaluate programmatic pathway options that incorporate near and mid-term strategies to achieve the long-term goals of the Hydrogen Program. In FY 95, NREL will develop a comprehensive effort with industry, state and local agencies, and other federal agencies to identify and evaluate programmatic pathway options to achieve the long-term goals of the Program. Activity to date is reported.

  11. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...

  12. Meta-analyses

    NARCIS (Netherlands)

    Hendriks, Maria A.; Luyten, Johannes W.; Scheerens, Jaap; Sleegers, P.J.C.; Scheerens, J

    2014-01-01

    In this chapter results of a research synthesis and quantitative meta-analyses of three facets of time effects in education are presented, namely time at school during regular lesson hours, homework, and extended learning time. The number of studies for these three facets of time that could be used

  13. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach...

  14. Report sensory analyses veal

    NARCIS (Netherlands)

    Veldman, M.; Schelvis-Smit, A.A.M.

    2005-01-01

    On behalf of a client of Animal Sciences Group, different varieties of veal were analyzed by both instrumental and sensory analyses. The sensory evaluation was performed with a sensory analytical panel in the period of 13th of May and 31st of May, 2005. The three varieties of veal were: young bull,

  15. Filmstil - teori og analyse

    DEFF Research Database (Denmark)

    Hansen, Lennard Højbjerg

    Filmstil påvirker på afgørende vis vores oplevelse af film. Men filmstil, måden, de levende billeder organiserer fortællingen på fylder noget mindre end filmens handling, når vi taler om film. Filmstil - teori og analyse er en rigt eksemplificeret præsentation, kritik og videreudvikling af...

  16. Morphometry and micromorphometry analyses

    African Journals Online (AJOL)

    MRT

    2013-08-14

    Aug 14, 2013 ... Studies on seed morphology with scanning electron microscope (SEM) have revealed taxonomically useful micro- characters. The present study was performed to study morphological and micromorphological features in seven Silene species and subspecies in the sect Auriculatae and Inflatae growing in ...

  17. Dropped object protection analyses

    OpenAIRE

    Nilsen, Ingve

    2014-01-01

    Master's thesis in Offshore structural engineering Impact from dropped object is a typical accident action (NOKSOK N-004, 2013). Hence, the DOP structure is to be analyzed in an accidental limit state (ALS) design practice, which means that a non-linear finite element analysis can be applied. The DOP structure will be based on a typical DOP structure. Several FEM analyses are performed for the DOP structure. Different shapes size and weights and various impact positions are used for si...

  18. A History of Rotorcraft Comprehensive Analyses

    Science.gov (United States)

    Johnson, Wayne

    2013-01-01

    A history of the development of rotorcraft comprehensive analyses is presented. Comprehensive analyses are digital computer programs that calculate the aeromechanical behavior of the rotor and aircraft, bringing together the most advanced models of the geometry, structure, dynamics, and aerodynamics available in rotary wing technology. The development of the major codes of the last five decades from industry, government, and universities is described. A number of common themes observed in this history are discussed.

  19. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  20. Evaluasi Program English Club

    OpenAIRE

    Kurniawan, Mirdan; Herpratiwi, Herpratiwi; Purnomo, Eddy

    2015-01-01

    The purposes of this study were to 1) reveal students' perceptions about instructional English club program 2) reveal the students' perceptions about instructional English fun day program 3) reveal perception of students about instructional English wall magazine program. From the results of the study it was concluded that 1) students' perceptions of the instructional English club program was less advantages for students, 2) students' perceptions of instructional English fun day program have ...

  1. Information system and geographic information system tools in the data analyses of the control program for visceral leishmaniases from 2006 to 2010 in the sanitary district of venda nova, belo horizonte, minas gerais, Brazil.

    Science.gov (United States)

    Saraiva, Lara; Leite, Camila Gonçalves; de Carvalho, Luiz Otávio Alves; Andrade Filho, José Dilermando; de Menezes, Fernanda Carvalho; Fiúza, Vanessa de Oliveira Pires

    2012-01-01

    The aim of this paper is to report a brief history of control actions for Visceral Leishmaniasis (VL) from 2006 to 2010 in the Sanitary District (DS) of Venda Nova, Belo Horizonte, Minas Gerais, Brazil, focusing on the use of information systems and Geographic Information System (GIS) tools. The analyses showed that the use of an automated database allied with geoprocessing tools may favor control measures of VL, especially with regard to the evaluation of control actions carried out. Descriptive analyses of control measures allowed to evaluating that the information system and GIS tools promoted greater efficiency in making decisions and planning activities. These analyses also pointed to the necessity of new approaches to the control of VL in large urban centers.

  2. Statistical Analyses of Digital Collections

    DEFF Research Database (Denmark)

    Frandsen, Tove Faber; Nicolaisen, Jeppe

    2016-01-01

    Using statistical methods to analyse digital material for patterns makes it possible to detect patterns in big data that we would otherwise not be able to detect. This paper seeks to exemplify this fact by statistically analysing a large corpus of references in systematic reviews. The aim...... of the analysis is to study the phenomenon of non-citation: Situations where just one (or some) document(s) are cited from a pool of otherwise equally citable documents. The study is based on more than 120,000 cited studies, and a total number of non-cited studies of more than 1.6 million. The number of cited...... 10 years. After 10 years the cited and non-cited studies tend to be more similar in terms of age. Separating the data set into different sub-disciplines reveals that the sub-disciplines vary in terms of age of cited vs. non-cited references. Some fields may be expanding and the number of published...

  3. Force-plate analyses of balance following a balance exercise program during acute post-operative phase in individuals with total hip and knee arthroplasty: A randomized clinical trial

    Directory of Open Access Journals (Sweden)

    Pankaj Jogi

    2016-11-01

    Full Text Available Objectives: Typical rehabilitation programs following total hip arthroplasty and total knee arthroplasty include joint range of motion and muscle-strengthening exercises. Balance and balance exercises following total hip arthroplasty and total knee arthroplasty have not received much attention. The purpose of this study was to determine whether an intervention of balance exercises added to a typical rehabilitation program positively affects patients’ balance. Methods: A total of 63 patients were provided with outpatient physical therapy at their home. Patients were randomly assigned to either typical (n = 33 or balance (n = 30 exercise group. The typical group completed seven typical surgery-specific joint range of motion and muscle-strengthening exercises, while the balance group completed the typical exercises plus three balance exercises. After 5 weeks of administering the rehabilitation program, patients’ balance was assessed on a force plate using 95% ellipse area of the center of pressure amplitude. Results: Patients in the balance group demonstrated significant reduction in the 95% ellipse area for the anterior and posterior lean standing conditions (p < 0.01. Conclusion: Balance exercises added to the typical outpatient physical therapy program resulted in significantly greater improvements in balance for participants with total hip arthroplasty or total knee arthroplasty, compared to the typical exercise program alone. Physical therapists might consider the use of balance exercises to improve balance in individuals in the acute post-operative phase following total hip arthroplasty or total knee arthroplasty.

  4. Persistent Monitoring of Urban Infrasound Phenomenology. Report 1: Modeling an Urban Environment for Acoustical Analyses using the 3-D Finite-Difference Time-Domain Program PSTOP3D

    Science.gov (United States)

    2015-08-01

    ER D C TR -1 5- 5 Remote Assessment of Critical Infrastructure Persistent Monitoring of Urban Infrasound Phenomenology Report 1...ERDC TR-15-5 August 2015 Persistent Monitoring of Urban Infrasound Phenomenology Report 1: Modeling an Urban Environment for Acoustical Analyses...From - To) 4. TITLE AND SUBTITLE Persistent Monitoring of Urban Infrasound Phenomenology ; Report 1: Modeling an Urban Environment for

  5. Chemical Analyses of Silicon Aerogel Samples

    CERN Document Server

    van der Werf, I; De Leo, R; Marrone, S

    2008-01-01

    After five years of operating, two Aerogel counters: A1 and A2, taking data in Hall A at Jefferson Lab, suffered a loss of performance. In this note possible causes of degradation have been studied. In particular, various chemical and physical analyses have been carried out on several Aerogel tiles and on adhesive tape in order to reveal the presence of contaminants.

  6. Chemical Analyses of Silicon Aerogel Samples

    Energy Technology Data Exchange (ETDEWEB)

    van der Werf, I.; Palmisano, F.; De Leo, Raffaele; Marrone, Stefano

    2008-04-01

    After five years of operating, two Aerogel counters: A1 and A2, taking data in Hall A at Jefferson Lab, suffered a loss of performance. In this note possible causes of degradation have been studied. In particular, various chemical and physical analyses have been carried out on several Aerogel tiles and on adhesive tape in order to reveal the presence of contaminants.

  7. Cosmetology: Task Analyses. Competency-Based Education.

    Science.gov (United States)

    Henrico County Public Schools, Glen Allen, VA. Virginia Vocational Curriculum Center.

    These task analyses are designed to be used in combination with the "Trade and Industrial Education Service Area Resource" in order to implement competency-based education in the cosmetology program in Virginia. The task analysis document contains the task inventory, suggested task sequence lists, and content outlines for the secondary…

  8. EEG analyses with SOBI.

    Energy Technology Data Exchange (ETDEWEB)

    Glickman, Matthew R.; Tang, Akaysha (University of New Mexico, Albuquerque, NM)

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  9. Analyse af elbilers forbrug

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Torp, Kristian

    2014-01-01

    Denne rapport undersøger GPS og CAN bus datagrundlaget opsamlet ved kørsel med elbiler og analysere på elbilers forbrug. Analyserne er baseret på godt 133 millioner GPS og CAN bus målinger opsamlet fra 164 elbiler (Citroen C-Zero, Mitsubishi iMiev og Peugeot Ion) i kalenderåret 2012....... For datagrundlaget kan det konstateres, at der er behov for væsentlige, men simple opstramninger for fremadrettet at gøre det nemmere at anvende GPS/CAN bus data fra elbiler i andre analyser. Brugen af elbiler er sammenlignet med brændstofbiler og konklusionen er, at elbiler generelt kører 10-15 km/t langsommere på...

  10. Inductive Temporal Logic Programming

    OpenAIRE

    Kolter, Robert

    2009-01-01

    We study the extension of techniques from Inductive Logic Programming (ILP) to temporal logic programming languages. Therefore we present two temporal logic programming languages and analyse the learnability of programs from these languages from finite sets of examples. In first order temporal logic the following topics are analysed: - How can we characterize the denotational semantics of programs? - Which proof techniques are best suited? - How complex is the learning task? In propositional ...

  11. Analyses of hydraulic performance of velocity caps

    DEFF Research Database (Denmark)

    Christensen, Erik Damgaard; Degn Eskesen, Mark Chr.; Buhrkall, Jeppe

    2014-01-01

    The hydraulic performance of a velocity cap has been investigated. Velocity caps are often used in connection with offshore intakes. CFD (computational fluid dynamics) examined the flow through the cap openings and further down into the intake pipes. This was combined with dimension analyses...... in order to analyse the effect of different layouts on the flow characteristics. In particular, flow configurations going all the way through the structure were revealed. A couple of suggestions to minimize the risk for flow through have been tested....

  12. Analysing qualitative research data using computer software.

    Science.gov (United States)

    McLafferty, Ella; Farley, Alistair H

    An increasing number of clinical nurses are choosing to undertake qualitative research. A number of computer software packages are available designed for the management and analysis of qualitative data. However, while it is claimed that the use of these programs is also increasing, this claim is not supported by a search of recent publications. This paper discusses the advantages and disadvantages of using computer software packages to manage and analyse qualitative data.

  13. Phylogenetic and molecular evolutionary analyses of gypsy group ...

    African Journals Online (AJOL)

    Gypsy group retrotransposons in the Egyptian cotton, Gossypium barbadense, was examined by phylogenetic and molecular evolutionary analyses. DNA sequences of gypsy group retrotransposons in two G. barbadense cultivars revealed that these sequences are heterogeneous and represent two distinct families.

  14. Time-resolved cell culture assay analyser (TReCCA Analyser) for the analysis of on-line data: data integration--sensor correction--time-resolved IC50 determination.

    Science.gov (United States)

    Lochead, Julia; Schessner, Julia; Werner, Tobias; Wölfl, Stefan

    2015-01-01

    Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal the dynamics of quality controlled experiments. However, they lead to the generation of large data sets, which can represent a complexity barrier to their use. We therefore developed the Time-Resolved Cell Culture Assay (TReCCA) Analyser program to perform standard cell assay analyses efficiently and make sophisticated in-depth analyses easily available. The functions of the program include data normalising and averaging, as well as smoothing and slope calculation, pin-pointing exact change time points. A time-resolved IC50/EC50 calculation provides a better understanding of drug toxicity over time and a more accurate drug to drug comparison. Finally the logarithmic sensor recalibration function, for sensors with an exponential calibration curve, homogenises the sensor output and enables the detection of low-scale changes. To illustrate the capabilities of the TReCCA Analyser, we performed on-line monitoring of dissolved oxygen in the culture media of the breast cancer cell line MCF-7 treated with different concentrations of the anti-cancer drug Cisplatin. The TReCCA Analyser is freely available at www.uni-heidelberg.de/fakultaeten/biowissenschaften/ipmb/biologie/woelfl/Research.html. By introducing the program, we hope to encourage more systematic use of time-resolved assays and lead researchers to fully exploit their data.

  15. Selection of interest and inflation rates for infrastructure investment analyses.

    Science.gov (United States)

    2014-12-01

    The South Dakota Department of Transportation (SDDOT) uses engineering economic analyses (EEA) to : support planning, design, and construction decision-making such as project programming and planning, : pavement type selection, and the occasional val...

  16. The MAFLA (Mississippi, Alabama, Florida) Study, Grain Size Analyses

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The MAFLA (Mississippi, Alabama, Florida) Study was funded by NOAA as part of the Outer Continental Shelf Program. Dr. L.J. Doyle produced grain size analyses in the...

  17. A Combination of Citation Analyses Can Reveal the Nature of a Journal’s Scholarly Communication, Its Influence in a Scientific Community, and the Geographic Location of Its Authors and Citers. A review of: Bonnevie‐Nebelong, Ellen. “Methods for Journal Evaluation: Journal Citation Identity, Journal Citation Image, and Internationalisation.” Scientometrics 66.2 (Jan. 2006: 411‐24.

    Directory of Open Access Journals (Sweden)

    Gaby Haddow

    2006-12-01

    Full Text Available Objective – To conduct a number of citation analyses of the Journal of Documentation (JDOC, comparing the results with analyses of the Journal of Information Science (JIS, and the Journal of the American Society of Information Science and Technology (JASIST to illustrate features of JDOC.Design – Bibliometric study.Setting – Library and information science journal literature.Sample – Citations given by and given to the JDOC were analysed and compared to those from the JASIST and the JIS. Author affiliation data were analysed from articles published in JDOC and from articles citing JDOC. The data were drawn from three time periods: 1975‐2003, 1980‐2003, and 1990‐2003.Methods – Journal Citation Identity was examined for the period 1990‐2003. The analysis involved calculating the number of different journals represented by citations given by a journal in a publishing year. The resulting citation/citee ratio is indicative of diversity and extent of scholarly sources used by a journal. Journal Citation Identity was also examined by calculating the number of journal self‐citations (in the period 1980 to 2003 as a proportion of the total number of citations given by the journal. A high rate of journal self‐citations suggests introspection or isolation from other journals in its field. The content of the three journals was examined for the period 1973‐2003 to determine the proportion of scientific content (i.e. articles, notes, reviews, and letters. Journal Citation Image was examined by calculating journal self‐citations as a proportion of the citations given by other journals to the sample journal. The result signifies the degree of a journal’s visibility in its field. A second aspect of Journal Citation Image was investigated using the New Journal Diffusion Factor (N JDF. The N JDF was carried out for each year between 1975 and 2003 and calculated the average number of different journals that cite an article in a sample

  18. On the reproducibility of meta-analyses : six practical recommendations

    NARCIS (Netherlands)

    Lakens, D.; Hilgard, J.; Staaks, J.

    2016-01-01

    Meta-analyses play an important role in cumulative science by combining information across multiple studies and attempting to provide effect size estimates corrected for publication bias. Research on the reproducibility of meta-analyses reveals that errors are common, and the percentage of effect

  19. Descriptive Analyses of Pediatric Food Refusal and Acceptance

    Science.gov (United States)

    Borrero, Carrie S. W.; Woods, Julia N.; Borrero, John C.; Masler, Elizabeth A.; Lesser, Aaron D.

    2010-01-01

    Functional analyses of inappropriate mealtime behavior typically include conditions to determine if the contingent delivery of attention, tangible items, or escape reinforce food refusal. In the current investigation, descriptive analyses were conducted for 25 children who had been admitted to a program for the assessment and treatment of food…

  20. A Formal Model to Analyse the Firewall Configuration Errors

    Directory of Open Access Journals (Sweden)

    T. T. Myo

    2015-01-01

    Full Text Available The firewall is widely known as a brandmauer (security-edge gateway. To provide the demanded security, the firewall has to be appropriately adjusted, i.e. be configured. Unfortunately, when configuring, even the skilled administrators may make mistakes, which result in decreasing level of a network security and network infiltration undesirable packages.The network can be exposed to various threats and attacks. One of the mechanisms used to ensure network security is the firewall.The firewall is a network component, which, using a security policy, controls packages passing through the borders of a secured network. The security policy represents the set of rules.Package filters work in the mode without inspection of a state: they investigate packages as the independent objects. Rules take the following form: (condition, action. The firewall analyses the entering traffic, based on the IP address of the sender and recipient, the port number of the sender and recipient, and the used protocol. When the package meets rule conditions, the action specified in the rule is carried out. It can be: allow, deny.The aim of this article is to develop tools to analyse a firewall configuration with inspection of states. The input data are the file with the set of rules. It is required to submit the analysis of a security policy in an informative graphic form as well as to reveal discrepancy available in rules. The article presents a security policy visualization algorithm and a program, which shows how the firewall rules act on all possible packages. To represent a result in an intelligible form a concept of the equivalence region is introduced.Our task is the program to display results of rules action on the packages in a convenient graphic form as well as to reveal contradictions between the rules. One of problems is the large number of measurements. As it was noted above, the following parameters are specified in the rule: Source IP address, appointment IP

  1. Measurement and Analysis of P2P IPTV Program Resource

    Directory of Open Access Journals (Sweden)

    Wenxian Wang

    2014-01-01

    Full Text Available With the rapid development of P2P technology, P2P IPTV applications have received more and more attention. And program resource distribution is very important to P2P IPTV applications. In order to collect IPTV program resources, a distributed multi-protocol crawler is proposed. And the crawler has collected more than 13 million pieces of information of IPTV programs from 2009 to 2012. In addition, the distribution of IPTV programs is independent and incompact, resulting in chaos of program names, which obstructs searching and organizing programs. Thus, we focus on characteristic analysis of program resources, including the distributions of length of program names, the entropy of the character types, and hierarchy depth of programs. These analyses reveal the disorderly naming conventions of P2P IPTV programs. The analysis results can help to purify and extract useful information from chaotic names for better retrieval and accelerate automatic sorting of program and establishment of IPTV repository. In order to represent popularity of programs and to predict user behavior and popularity of hot programs over a period, we also put forward an analytical model of hot programs.

  2. Revealing, Reinterpreting, Rewriting Mujeres

    Science.gov (United States)

    Preuss, Cara Lynne; Saavedra, Cinthya M.

    2014-01-01

    This paper reanalyzed research previously conducted with Spanish-speaking childcare providers who participated in an educational literacy program. The women in the program were generally framed as the deficient other--illiterate, immigrant women. The authors used a critical framework and Chicana/Latina feminist methodologies, namely "pláticas…

  3. Behavioral Outcomes of Parent-Child Interaction Therapy and Triple P-Positive Parenting Program: A Review and Meta-Analysis

    Science.gov (United States)

    Thomas, Rae; Zimmer-Gembeck, Melanie

    2007-01-01

    We conducted a review and meta-analyses of 24 studies to evaluate and compare the outcomes of two widely disseminated parenting interventions--Parent-Child Interaction Therapy and Triple P-Positive Parenting Program. Participants in all studies were caregivers and 3- to 12-year-old children. In general, our analyses revealed positive effects of…

  4. Inorganic Analyses in Water Quality Control Programs. Training Manual.

    Science.gov (United States)

    Kroner, Audrey; And Others

    This lecture/laboratory manual for a five-day course deals with the analysis of selected inorganic pollutants. The manual is an instructional aid for classroom presentations to those with little or no experience in the field, but having one year (or equivalent) of college level inorganic chemistry, one semester of college level quantitative…

  5. Organic Analyses in Water Quality Control Programs. Training Manual.

    Science.gov (United States)

    Office of Water Program Operations (EPA), Cincinnati, OH. National Training and Operational Technology Center.

    This document is a lecture/laboratory manual dealing with the analysis of selected organic pollutants. It is intended for use by those having little or no experience in the field, but having one year (or equivalent) of college organic chemistry, and having basic laboratory skills (volumetric glassware, titration, analytical and trip balances).…

  6. National Defense Stockpile Program. Phase 1. Development and Analyses

    Science.gov (United States)

    1990-03-01

    percent respectively for each year. Examples include appliances , furniture, jewelry, power tools and sporting equipment (NIPA categories 3, 5-16 and 18...8. Mattresses & Bedding 45. Telephone & Telegraph 9. Appliances 46. Domestic Services 10. China, Glassware & Utensils 47. Misc. Household Services 11...Jewelry & Watches 53. Misc. Transportation 17. Opthalmic & Orthopedic Goods 54. Rail Transportation 18. Books & Maps 55. Airline Transportation 19. Boats

  7. Conjoint-Analyse und Marktsegmentierung

    OpenAIRE

    Steiner, Winfried J.; Baumgartner, Bernhard

    2003-01-01

    Die Marktsegmentierung zählt neben der Neuproduktplanung und Preisgestaltung zu den wesentlichen Einsatzgebieten der Conjoint-Analyse. Neben traditionell eingesetzten zweistufigen Vorgehensweisen, bei denen Conjoint-Analyse und Segmentierung in zwei getrennten Schritten erfolgen, stehen heute mit Methoden wie der Clusterwise Regression oder Mixture-Modellen neuere Entwicklungen, die eine simultane Segmentierung und Präferenzschätzung ermöglichen, zur Verfügung. Der Beitrag gibt einen Überblic...

  8. Analyse des Organisations en Afrique

    African Journals Online (AJOL)

    de celle-ci pourtenter d'identifier et d'élucider les dynamiques sociales qui s'y déroulent, puis de les examiner en rapport avec les stratégies d'acteurs et le contexte général (l'environnement) dans lequel évolue cette organisation, ... Et son Analyse. L'analyse des organisations est une démarche ancienne dont les ...

  9. A Program Transformation for Backwards Analysis of Logic Programs

    DEFF Research Database (Denmark)

    Gallagher, John Patrick

    2003-01-01

    programs presented here is based on a transformation of the input program, which makes explicit the dependencies of the given program points on the initial goals. The transformation is derived from the resultants semantics of logic programs. The transformed program is then analysed using a standard...... framework and no special properties of the abstract domain....

  10. Pawnee Nation Energy Option Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Matlock, M.; Kersey, K.; Riding In, C.

    2009-07-21

    Pawnee Nation of Oklahoma Energy Option Analyses In 2003, the Pawnee Nation leadership identified the need for the tribe to comprehensively address its energy issues. During a strategic energy planning workshop a general framework was laid out and the Pawnee Nation Energy Task Force was created to work toward further development of the tribe’s energy vision. The overarching goals of the “first steps” project were to identify the most appropriate focus for its strategic energy initiatives going forward, and to provide information necessary to take the next steps in pursuit of the “best fit” energy options. Description of Activities Performed The research team reviewed existing data pertaining to the availability of biomass (focusing on woody biomass, agricultural biomass/bio-energy crops, and methane capture), solar, wind and hydropower resources on the Pawnee-owned lands. Using these data, combined with assumptions about costs and revenue streams, the research team performed preliminary feasibility assessments for each resource category. The research team also reviewed available funding resources and made recommendations to Pawnee Nation highlighting those resources with the greatest potential for financially-viable development, both in the near-term and over a longer time horizon. Findings and Recommendations Due to a lack of financial incentives for renewable energy, particularly at the state level, combined mediocre renewable energy resources, renewable energy development opportunities are limited for Pawnee Nation. However, near-term potential exists for development of solar hot water at the gym, and an exterior wood-fired boiler system at the tribe’s main administrative building. Pawnee Nation should also explore options for developing LFGTE resources in collaboration with the City of Pawnee. Significant potential may also exist for development of bio-energy resources within the next decade. Pawnee Nation representatives should closely monitor

  11. Behavioral program synthesis with genetic programming

    CERN Document Server

    Krawiec, Krzysztof

    2016-01-01

    Genetic programming (GP) is a popular heuristic methodology of program synthesis with origins in evolutionary computation. In this generate-and-test approach, candidate programs are iteratively produced and evaluated. The latter involves running programs on tests, where they exhibit complex behaviors reflected in changes of variables, registers, or memory. That behavior not only ultimately determines program output, but may also reveal its `hidden qualities' and important characteristics of the considered synthesis problem. However, the conventional GP is oblivious to most of that information and usually cares only about the number of tests passed by a program. This `evaluation bottleneck' leaves search algorithm underinformed about the actual and potential qualities of candidate programs. This book proposes behavioral program synthesis, a conceptual framework that opens GP to detailed information on program behavior in order to make program synthesis more efficient. Several existing and novel mechanisms subs...

  12. CHEMICAL ANALYSES OF SODIUM SYSTEMS FINAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    Greenhalgh, W. O.; Yunker, W. H.; Scott, F. A.

    1970-06-01

    BNWL-1407 summarizes information gained from the Chemical Analyses of Sodium Systems Program pursued by Battelle- Northwest over the period from July 1967 through June 1969. Tasks included feasibility studies for performing coulometric titration and polarographic determinations of oxygen in sodium, and the development of new separation techniques for sodium impurities and their subsequent analyses. The program was terminated ahead of schedule so firm conclusions were not obtained in all areas of the work. At least 40 coulometric titrations were carried out and special test cells were developed for coulometric application. Data indicated that polarographic measurements are theoretically feasible, but practical application of the method was not verified. An emission spectrographic procedure for trace metal impurities was developed and published. Trace metal analysis by a neutron activation technique was shown to be feasible; key to the success of the activation technique was the application of a new ion exchange resin which provided a sodium separation factor of 10{sup 11}. Preliminary studies on direct scavenging of trace metals produced no conclusive results.

  13. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences......The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well...

  14. Revealed preference analysis of noncooperative household consumption

    NARCIS (Netherlands)

    Cherchye, L.J.H.; Demuynck, T.; de Rock, B.

    2011-01-01

    We develop a revealed preference approach to analyse non-unitary household consumption behaviour that is not cooperative (or Pareto efficient). We derive global necessary and sufficient conditions for data consistency with the model. We show that the conditions can be verified by means of relatively

  15. Beskrivende analyse af mekaniske systemer

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Hansen, Claus Thorp

    Descriptive analysis is the activity, where a given product is analysed for obtaining insight into different aspects, leading to an explicit description of each of these aspects. This textbook is worked out for course 72101 Produktanalyse (Analysis of products) given at DTU.......Descriptive analysis is the activity, where a given product is analysed for obtaining insight into different aspects, leading to an explicit description of each of these aspects. This textbook is worked out for course 72101 Produktanalyse (Analysis of products) given at DTU....

  16. An extensible analysable system model

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, Rene Rydhof

    2008-01-01

    , this does not hold for real physical systems. Approaches such as threat modelling try to target the formalisation of the real-world domain, but still are far from the rigid techniques available in security research. Many currently available approaches to assurance of critical infrastructure security......Analysing real-world systems for vulnerabilities with respect to security and safety threats is a difficult undertaking, not least due to a lack of availability of formalisations for those systems. While both formalisations and analyses can be found for artificial systems such as software...