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Sample records for closest relatives reveal

  1. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds.

    Science.gov (United States)

    Suh, Alexander; Paus, Martin; Kiefmann, Martin; Churakov, Gennady; Franke, Franziska Anni; Brosius, Jürgen; Kriegs, Jan Ole; Schmitz, Jürgen

    2011-08-23

    The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free retroposon insertions to this controversy. Our study examined ~200,000 retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed. © 2011 Macmillan Publishers Limited. All rights reserved.

  2. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

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    Walter J. Müller

    2016-09-01

    Full Text Available Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.

  3. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01.

    Science.gov (United States)

    Müller, Walter J; Tlalajoe, Nokuthula; Cason, Errol D; Litthauer, Derek; Reva, Oleg; Brzuszkiewicz, Elzbieta; van Heerden, Esta

    2016-09-08

    Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain's genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin-Benson-Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3 (-) rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01. Copyright © 2016 Müller et al.

  4. Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principal Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

    Science.gov (United States)

    Müller, Walter J.; Tlalajoe, Nokuthula; Cason, Errol D.; Litthauer, Derek; Reva, Oleg; Brzuszkiewicz, Elzbieta; van Heerden, Esta

    2016-01-01

    Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01. PMID:27412985

  5. Morphological diversity in tenrecs (Afrosoricida, Tenrecidae: comparing tenrec skull diversity to their closest relatives

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    Sive Finlay

    2015-04-01

    Full Text Available It is important to quantify patterns of morphological diversity to enhance our understanding of variation in ecological and evolutionary traits. Here, we present a quantitative analysis of morphological diversity in a family of small mammals, the tenrecs (Afrosoricida, Tenrecidae. Tenrecs are often cited as an example of an exceptionally morphologically diverse group. However, this assumption has not been tested quantitatively. We use geometric morphometric analyses of skull shape to test whether tenrecs are more morphologically diverse than their closest relatives, the golden moles (Afrosoricida, Chrysochloridae. Tenrecs occupy a wider range of ecological niches than golden moles so we predict that they will be more morphologically diverse. Contrary to our expectations, we find that tenrec skulls are only more morphologically diverse than golden moles when measured in lateral view. Furthermore, similarities among the species-rich Microgale tenrec genus appear to mask higher morphological diversity in the rest of the family. These results reveal new insights into the morphological diversity of tenrecs and highlight the importance of using quantitative methods to test qualitative assumptions about patterns of morphological diversity.

  6. Tunicates and not cephalochordates are the closest living relatives of vertebrates.

    Science.gov (United States)

    Delsuc, Frédéric; Brinkmann, Henner; Chourrout, Daniel; Philippe, Hervé

    2006-02-23

    Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.

  7. Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives

    OpenAIRE

    Gama, R.; Aguirre Gutierrez, J; Stech, M

    2017-01-01

    Abstract The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended I...

  8. Interspecific scaling patterns of talar articular surfaces within primates and their closest living relatives.

    Science.gov (United States)

    Yapuncich, Gabriel S; Boyer, Doug M

    2014-02-01

    The articular facets of interosseous joints must transmit forces while maintaining relatively low stresses. To prevent overloading, joints that transmit higher forces should therefore have larger facet areas. The relative contributions of body mass and muscle-induced forces to joint stress are unclear, but generate opposing hypotheses. If mass-induced forces dominate, facet area should scale with positive allometry to body mass. Alternatively, muscle-induced forces should cause facets to scale isometrically with body mass. Within primates, both scaling patterns have been reported for articular surfaces of the femoral and humeral heads, but more distal elements are less well studied. Additionally, examination of complex articular surfaces has largely been limited to linear measurements, so that 'true area' remains poorly assessed. To re-assess these scaling relationships, we examine the relationship between body size and articular surface areas of the talus. Area measurements were taken from microCT scan-generated surfaces of all talar facets from a comprehensive sample of extant euarchontan taxa (primates, treeshrews, and colugos). Log-transformed data were regressed on literature-derived log-body mass using reduced major axis and phylogenetic least squares regressions. We examine the scaling patterns of muscle mass and physiological cross-sectional area (PCSA) to body mass, as these relationships may complicate each model. Finally, we examine the scaling pattern of hindlimb muscle PCSA to talar articular surface area, a direct test of the effect of mass-induced forces on joint surfaces. Among most groups, there is an overall trend toward positive allometry for articular surfaces. The ectal (= posterior calcaneal) facet scales with positive allometry among all groups except 'sundatherians', strepsirrhines, galagids, and lorisids. The medial tibial facet scales isometrically among all groups except lemuroids. Scaling coefficients are not correlated with sample size

  9. Interspecific scaling patterns of talar articular surfaces within primates and their closest living relatives

    Science.gov (United States)

    Yapuncich, Gabriel S; Boyer, Doug M

    2014-01-01

    The articular facets of interosseous joints must transmit forces while maintaining relatively low stresses. To prevent overloading, joints that transmit higher forces should therefore have larger facet areas. The relative contributions of body mass and muscle-induced forces to joint stress are unclear, but generate opposing hypotheses. If mass-induced forces dominate, facet area should scale with positive allometry to body mass. Alternatively, muscle-induced forces should cause facets to scale isometrically with body mass. Within primates, both scaling patterns have been reported for articular surfaces of the femoral and humeral heads, but more distal elements are less well studied. Additionally, examination of complex articular surfaces has largely been limited to linear measurements, so that ‘true area' remains poorly assessed. To re-assess these scaling relationships, we examine the relationship between body size and articular surface areas of the talus. Area measurements were taken from microCT scan-generated surfaces of all talar facets from a comprehensive sample of extant euarchontan taxa (primates, treeshrews, and colugos). Log-transformed data were regressed on literature-derived log-body mass using reduced major axis and phylogenetic least squares regressions. We examine the scaling patterns of muscle mass and physiological cross-sectional area (PCSA) to body mass, as these relationships may complicate each model. Finally, we examine the scaling pattern of hindlimb muscle PCSA to talar articular surface area, a direct test of the effect of mass-induced forces on joint surfaces. Among most groups, there is an overall trend toward positive allometry for articular surfaces. The ectal (= posterior calcaneal) facet scales with positive allometry among all groups except ‘sundatherians', strepsirrhines, galagids, and lorisids. The medial tibial facet scales isometrically among all groups except lemuroids. Scaling coefficients are not correlated with sample

  10. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives.

    Science.gov (United States)

    Howard-Azzeh, Mohammad; Shamseer, Larissa; Schellhorn, Herb E; Gupta, Radhey S

    2014-11-01

    cyanobacteria are uniquely shared by two smaller clades of cyanobacteria, which form the successive outgroups of the clade comprising of the heterocystous cyanobacteria in the protein trees. Based upon their close relationship to the heterocystous cyanobacteria, the members of these clades are indicated to be the closest relatives of the heterocysts-forming cyanobacteria.

  11. Evidence for functional diversity between the voltage-gated proton channel Hv1 and its closest related protein HVRP1.

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    Iris H Kim

    Full Text Available The Hv1 channel and voltage-sensitive phosphatases share with voltage-gated sodium, potassium, and calcium channels the ability to detect changes in membrane potential through voltage-sensing domains (VSDs. However, they lack the pore domain typical of these other channels. NaV, KV, and CaV proteins can be found in neurons and muscles, where they play important roles in electrical excitability. In contrast, VSD-containing proteins lacking a pore domain are found in non-excitable cells and are not involved in neuronal signaling. Here, we report the identification of HVRP1, a protein related to the Hv1 channel (from which the name Hv1 Related Protein 1 is derived, which we find to be expressed primarily in the central nervous system, and particularly in the cerebellum. Within the cerebellar tissue, HVRP1 is specifically expressed in granule neurons, as determined by in situ hybridization and immunohistochemistry. Analysis of subcellular distribution via electron microscopy and immunogold labeling reveals that the protein localizes on the post-synaptic side of contacts between glutamatergic mossy fibers and the granule cells. We also find that, despite the similarities in amino acid sequence and structural organization between Hv1 and HVRP1, the two proteins have distinct functional properties. The high conservation of HVRP1 in vertebrates and its cellular and subcellular localizations suggest an important function in the nervous system.

  12. The other "closest living relative". How bonobos (Pan paniscus) challenge traditional assumptions about females, dominance, intra- and intersexual interactions, and hominid evolution.

    Science.gov (United States)

    Parish, A R; De Waal, F B

    2000-04-01

    Chimpanzee (Pan troglodytes) societies are typically characterized as physically aggressive, male-bonded and male-dominated. Their close relatives, the bonobos (Pan paniscus), differ in startling and significant ways. For instance, female bonobos bond with one another, form coalitions, and dominate males. A pattern of reluctance to consider, let alone acknowledge, female dominance in bonobos exists, however. Because both species are equally "man's" closest relative, the bonobo social system complicates models of human evolution that have historically been based upon referents that are male and chimpanzee-like. The bonobo evidence suggests that models of human evolution must be reformulated such that they also accommodate: real and meaningful female bonds; the possibility of systematic female dominance over males; female mating strategies which encompass extra-group paternities; hunting and meat distribution by females; the importance of the sharing of plant foods; affinitive inter-community interactions; males that do not stalk and attack and are not territorial; and flexible social relationships in which philopatry does not necessarily predict bonding pattern.

  13. Linguistic analysis of face-to-face interviews with patients with an explicit request for euthanasia, their closest relatives, and their attending physicians: the use of modal verbs in Dutch.

    Science.gov (United States)

    Dieltjens, Sylvain M; Heynderickx, Priscilla C; Dees, Marianne K; Vissers, Kris C

    2014-04-01

    The literature, field research, and daily practice stress the need for adequate communication in palliative care. Although language is of the utmost importance in communication, linguistic analysis of end-of-life discussions is scarce. Our aim is 2-fold: We want to determine what the use of 4 significant Dutch modal verbs expressing volition, obligation, possibility, and permission reveals about the concept of unbearable suffering and about physicians' communicative style. We quantitatively (TextStat) and qualitatively (bottom-up approach) analyzed the use of the modal verbs in 15 interviews, with patients requesting euthanasia or physician-assisted suicide, their physicians, and their closest relatives. An essential element of unbearable suffering is the patient's incapacity to perform certain tasks. Further, the physician's preference for particular modal verbs reveals whether his attitude toward patients is more or less patronizing and more or less appreciative. Linguistic analysis can help medical professionals to better understand their communicative skills, styles, and approach to patients in end-of-life situations. We have shown how linguistic analysis can contribute to a better understanding of physician-patient interaction. Moreover, we have illustrated the usefulness of interdisciplinary research in the medical domain. © 2013 World Institute of Pain.

  14. Divergence between the Highly Virulent Zoonotic Pathogen Helicobacter heilmannii and Its Closest Relative, the Low-Virulence “Helicobacter ailurogastricus” sp. nov.

    Science.gov (United States)

    Joosten, Myrthe; Lindén, Sara; Rossi, Mirko; Skoog, Emma; Padra, Médea; Peters, Fanny; Perkins, Tim; Vandamme, Peter; Van Nieuwerburgh, Filip; D'Herde, Katharina; Van den Broeck, Wim; Flahou, Bram; Deforce, Dieter; Ducatelle, Richard; Marshall, Barry; Haesebrouck, Freddy

    2015-01-01

    Helicobacter heilmannii naturally colonizes the stomachs of dogs and cats and has been associated with gastric disorders in humans. Nine feline Helicobacter strains, classified as H. heilmannii based on ureAB and 16S rRNA gene sequences, were divided into a highly virulent and a low-virulence group. The genomes of these strains were sequenced to investigate their phylogenetic relationships, to define their gene content and diversity, and to determine if the differences in pathogenicity were associated with the presence or absence of potential virulence genes. The capacities of these helicobacters to bind to the gastric mucosa were investigated as well. Our analyses revealed that the low-virulence strains do not belong to the species H. heilmannii but to a novel, closely related species for which we propose the name Helicobacter ailurogastricus. Several homologs of H. pylori virulence factors, such as IceA1, HrgA, and jhp0562-like glycosyltransferase, are present in H. heilmannii but absent in H. ailurogastricus. Both species contain a VacA-like autotransporter, for which the passenger domain is remarkably larger in H. ailurogastricus than in H. heilmannii. In addition, H. ailurogastricus shows clear differences in binding to the gastric mucosa compared to H. heilmannii. These findings highlight the low-virulence character of this novel Helicobacter species. PMID:26527212

  15. A hybrid metaheuristic for closest string problem.

    Science.gov (United States)

    Mousavi, Sayyed Rasoul

    2011-01-01

    The Closest String Problem (CSP) is an optimisation problem, which is to obtain a string with the minimum distance from a number of given strings. In this paper, a new metaheuristic algorithm is investigated for the problem, whose main feature is relatively high speed in obtaining good solutions, which is essential when the input size is large. The proposed algorithm is compared with four recent algorithms suggested for the problem, outperforming them in more than 98% of the cases. It is also remarkably faster than all of them, running within 1 s in most of the experimental cases.

  16. Identification of the genes required for the culture of Liberibacter crescens, the closest cultured relative of the uncultured Liberibacter plant pathogens

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    Kin-Kwan eLai

    2016-04-01

    Full Text Available Here Tn5 random transposon mutagenesis was used to identify the essential elements for culturing Liberibacter crescens BT-1 that can serve as antimicrobial targets for the closely related pathogens of citrus, Candidatus Liberibacter asiaticus (Las and tomato and potato, Candidatus Liberibacter solanacearum (Lso. In order to gain insight on the virulence, metabolism, and culturability of the pathogens within the genus Liberibacter, a mini-Tn5 transposon derivative system consisting of a gene specifying resistance to kanamycin, flanked by a 19-base-pair terminal repeat sequence of Tn5, was used for the genome-wide mutagenesis of L. crescens BT-1 and created an insertion mutant library. By analyzing the location of insertions using Sanger and Illumina Mi-Seq sequencing, 314 genes are proposed as essential for the culture of L. crescens BT-1 on BM-7 medium. Of those genes, 76 are not present in the uncultured Liberibacter pathogens and, as a result, suggest molecules necessary for the culturing these pathogens. Those molecules include the aromatic amino acids, several vitamins, histidine, cysteine, lipopolysaccharides, and fatty acids. In addition, the 238 essential genes of L. crescens in common with L. asiaticus are potential targets for the development of therapeutics against the disease.

  17. Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives.

    Science.gov (United States)

    Johannesson, Hanna; Vidal, Pilar; Guarro, Josep; Herr, Roger A; Cole, Garry T; Taylor, John W

    2004-06-01

    In this study, we investigate the possibility of selection acting on the proline-rich antigen (PRA) gene in natural populations of the two human pathogens, Coccidioides immitis and Coccidioides posadasii, and three of their close relatives, Chrysosporium lucknowense, Chrysosporium queenslandicum, and Uncinocarpus reesii. We addressed the following questions: Is diversifying selection acting on PRA in the pathogenic species as a result of avoidance of the host's immune system, and has adaptation to a pathogenic life style lead to positive directional selection and increased rate of evolution in PRA between the species? For these purposes, we amplified and sequenced from 40 individuals belonging to the five species, the entire coding region of the PRA gene, as well as partial sequences from the coding region of each of the three housekeeping genes glyderaldehyde-3-phosphate dehydrogenase, glutamine synthetase A, and hexokinase A. We used likelihood-based methods to compare models of different types of selective pressure among codons to analyze the mode of evolution of the genes and found that the PRA gene evolves under positive selection, but the investigated parts of the housekeeping genes evolve primarily under purifying selection. We found a very low level of intraspecific variability and no evidence of diversifying selection, suggesting that the increased rate of evolution in the PRA gene is not a result of avoidance of the host's immune system. Neither did likelihood-based analyses suggest that selection was stronger on the branch separating pathogenic and nonpathogenic species. Instead, we suggest that positive selection act on PRA as a consequence of spore cell-wall morphogenesis unique to each species.

  18. Variation in reproductive outcomes of women with histories of bulimia nervosa, anorexia nervosa, or eating disorder not otherwise specified relative to the general population and closest-aged sisters.

    Science.gov (United States)

    Tabler, Jennifer; Utz, Rebecca L; Smith, Ken R; Hanson, Heidi A; Geist, Claudia

    2018-02-01

    This study seeks to examine the long-term reproductive consequences of eating disorders (ED), to assess variation in reproductive outcomes by ED type, and to examine reproductive differences between women with previous ED diagnosis and their discordant sisters. Using a sample of women with previous ED diagnosis generated by the Utah Population Database, this study compares the fecundity (parity) and age at first birth of women by ED subtype (bulimia nervosa [BN], anorexia nervosa [AN], and ED not otherwise specified [EDNOS]) (n = 1,579). We also employed general population match case-control, and discordant sibling pair analyses, to estimate the magnitude of association between EDs and reproductive outcomes. Women previously diagnosed with AN or EDNOS experienced delayed first birth (HRR = 0.33, HRR = 0.34, respectively) and lower parity (IRR = 0.19, IRR = 0.22, respectively) relative to BN (p < .05), the general population (p < .05), and closest-aged sisters (p < .05). Women previously diagnosed with BN experienced more moderate reductions and delays to their reproduction, and had similar reproductive outcomes as their discordant sisters. Clinicians should consider ED type and family fertility histories when addressing the long-term reproductive health needs of women with prior AN, BN, or EDNOS diagnosis. Women previously diagnosed with AN or EDNOS likely experience the greatest reductions and delays in reproduction across their lifespan. Reproductive health screenings may be especially critical for the wellbeing of women with a history of AN or EDNOS. © 2018 Wiley Periodicals, Inc.

  19. Self-perceived symptoms and care needs of patients with severe to very severe chronic obstructive pulmonary disease, congestive heart failure or chronic renal failure and its consequences for their closest relatives: the research protocol

    Directory of Open Access Journals (Sweden)

    Schols Jos MGA

    2008-05-01

    Full Text Available Abstract Background Recent research shows that the prevalence of patients with very severe chronic obstructive pulmonary disease (COPD, congestive heart failure (CHF and chronic renal failure (CRF continues to rise over the next years. Scientific studies concerning self-perceived symptoms and care needs in patients with severe to very severe COPD, CHF and CRF are scarce. Consequently, it will be difficult to develop an optimal patient-centred palliative care program for patients with end-stage COPD, CHF or CRF. The present study has been designed to assess the symptoms, care needs, end-of-life care treatment preferences and communication needs of patients with severe to very severe COPD, CHF or CRF. Additionally, family distress and care giving burden of relatives of these patients will be assessed. Methods/design A cross-sectional comparative and prospective longitudinal study in patients with end-stage COPD, CHF or CRF has been designed. Patients will be recruited by their treating physician specialist. Patients and their closest relatives will be visited at baseline and every 4 months after baseline for a period of 12 months. The following outcomes will be assessed during home visits: self-perceived symptoms and care needs; daily physical functioning; general health status; end-of-life care treatment preferences; end-of-life care communication and care-giver burden of family caregivers. Additionally, end-of-life care communication and prognosis of survival will be assessed with the physician primarily responsible for the management of the chronic organ failure. Finally, if patients decease during the study period, the baseline preferences with regard to life-sustaining treatments will be compared with the real end-of-life care. Discussion To date, the symptoms, care needs, caregiver burden, end-of-life care treatment preferences and communication needs of patients with very severe COPD, CHF or CRF remain unknown. The present study will

  20. Asteroid Ida - Limb at Closest Approach

    Science.gov (United States)

    1994-01-01

    The Galileo imaging system captured this picture of the limb of the asteroid 243 Ida about 46 seconds after its closest approach on August 28, 1993, from a range of only 2480 kilometers. It is the highest-resolution image of an asteroid's surface ever captured and shows detail at a scale of about 25 meters per pixel. This image is one frame of a mosaic of 15 frames shuttered near Galileo's closest approach to Ida. Since the exact location of Ida in space was not well-known prior to the Galileo flyby, this mosaic was estimated to have only about a 50 percent chance of capturing Ida. Fortunately, this single frame did successfully image a part of the sunlit side of Ida. The area seen in this frame shows some of the same territory seen in a slightly lower resolution full disk mosaic of Ida returned from the spacecraft in September, 1993, but from a different perspective. Prominent in this view is a 2 kilometer deep 'valley' seen in profile on the limb. This limb profile and the stereoscopic effect between this image and the full disk mosaic will permit detailed refinement of Ida's shape in this region. This high resolution view shows many small craters and some grooves on the surface of Ida, which give clues to understanding the history of this heavily impacted object. The Galileo project, whose primary mission is the exploration of the Jupiter system in 1995-97, is managed for NASA's Office of Space Science by the Jet Propulsion Laboratory.

  1. Anticipatory looks reveal expectations about discourse relations.

    Science.gov (United States)

    Rohde, Hannah; Horton, William S

    2014-12-01

    Previous research provides evidence for expectation-driven processing within sentences at phonological, lexical, and syntactic levels of linguistic structure. Less well-established is whether comprehenders also anticipate pragmatic relationships between sentences. To address this, we evaluate a unit of discourse structure that comprehenders must infer to hold between sentences in order for a discourse to make sense-the intersentential coherence relation. In a novel eyetracking paradigm, we trained participants to associate particular spatial locations with particular coherence relations. Experiment 1 shows that the subset of listeners who successfully acquired the location∼relation mappings during training subsequently looked to these locations during testing in response to a coherence-signaling intersentential connective. Experiment 2 finds that listeners' looks during sentences containing coherence-biasing verbs reveal expectations about upcoming sentence types. This work extends existing research on prediction beyond sentence-internal structure and provides a new methodology for examining the cues that comprehenders use to establish relationships at the discourse level. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Calculus on Surfaces with General Closest Point Functions

    KAUST Repository

    März, Thomas

    2012-01-01

    The closest point method for solving partial differential equations (PDEs) posed on surfaces was recently introduced by Ruuth and Merriman [J. Comput. Phys., 227 (2008), pp. 1943- 1961] and successfully applied to a variety of surface PDEs. In this paper we study the theoretical foundations of this method. The main idea is that surface differentials of a surface function can be replaced with Cartesian differentials of its closest point extension, i.e., its composition with a closest point function. We introduce a general class of these closest point functions (a subset of differentiable retractions), show that these are exactly the functions necessary to satisfy the above idea, and give a geometric characterization of this class. Finally, we construct some closest point functions and demonstrate their effectiveness numerically on surface PDEs. © 2012 Society for Industrial and Applied Mathematics.

  3. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives.

    Science.gov (United States)

    Naushad, Sohail; Adeolu, Mobolaji; Wong, Shirley; Sohail, Misbah; Schellhorn, Herbert E; Gupta, Radhey S

    2015-02-01

    The current taxonomy of the order Xanthomonadales is highly problematic and no comprehensive phylogenomic studies have been completed that include the most divergent members within the order. In this work, we have completed a phylogenomic analysis of a wide range of genomes, five of which were sequenced for the first time for this work, representing the vast majority of the diversity within the order Xanthomonadales. Using comparative genomic techniques, we have identified a large number of conserved signature inserts/deletions (CSIs) that are specifically found in different groups of related organisms, at different taxonomic levels, within the order. Our phylogenetic analyses do not support a monophyletic grouping of the members of the order Xanthomonadales and no CSIs were identified which are uniquely shared by all sequenced species within this order. However, our work has identified 10 CSIs which are specific to all members of the family Xanthomonadaceae and an additional 10 and 11 CSIs that are specific to one of two phylogenetically well-defined clades within the family Xanthomonadaceae. On the basis of the identified CSIs and the results of phylogenomic analyses, we propose a new taxonomic framework for the order Xanthomonadales. In this proposal, the families Algiphilaceae and Solimonadaceae (Nevskiaceae), which do not branch with the other members of the order Xanthomonadales, are transferred into the order Nevskiales ord. nov. The remaining members of the order Xanthomonadales are divided into two families: the family Xanthomonadaceae, containing the genus Xanthomonas and its closest relatives, and a new family, Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Additionally, we have also emended descriptions of the order Lysobacterales, the family Lysobacteraceae, and the family Nevskiaceae to indicate that they are earlier synonyms of the order Xanthomonadales, the family Xanthomonadaceae, and the family

  4. ESA's Integral detects closest cosmic gamma-ray burst

    Science.gov (United States)

    2004-08-01

    5 August 2004 A gamma-ray burst detected by ESA's Integral gamma-ray observatory on 3 December 2003 has been thoroughly studied for months by an armada of space and ground-based observatories. Astronomers have now concluded that this event, called GRB 031203, is the closest cosmic gamma-ray burst on record, but also the faintest. This also suggests that an entire population of sub-energetic gamma-ray bursts has so far gone unnoticed... Gamma ray burst model hi-res Size hi-res: 22 KB Credits: CXC/M. Weiss Artist impression of a low-energy gamma-ray burst This illustration describes a model for a gamma-ray burst, like the one detected by Integral on 3 December 2003 (GRB 031203). A jet of high-energy particles from a rapidly rotating black hole interacts with surrounding matter. Observations with Integral on 3 December 2003 and data on its afterglow, collected afterwards with XMM-Newton, Chandra and the Very Large Array telescope, show that GRB 031203 radiated only a fraction of the energy of normal gamma-ray bursts. Like supernovae, gamma-ray bursts are thought to be produced by the collapse of the core of a massive star. However, while the process leading to supernovae is relatively well understood, astronomers still do not know what happens when a core collapses to form a black hole. The discovery of 'under-energetic' gamma-ray bursts, like GRB 031203, should provide valuable clues as to links between supernovae, black holes and gamma-ray bursts. Lo-res JPG (22 Kb) Hi-res TIFF (5800 Kb) Cosmic gamma-ray bursts (GRBs) are flashes of gamma rays that can last from less than a second to a few minutes and occur at random positions in the sky. A large fraction of them is thought to result when a black hole is created from a dying star in a distant galaxy. Astronomers believe that a hot disc surrounding the black hole, made of gas and matter falling onto it, somehow emits an energetic beam parallel to the axis of rotation. According to the simplest picture, all GRBs

  5. Rosetta performs ESA's closest-ever Earth fly-by

    Science.gov (United States)

    2005-03-01

    The passage through the Earth-Moon system allowed ground controllers to test Rosetta's 'asteroid fly-by mode' (AFM) using the Moon as a 'fake' asteroid, rehearsing the fly-bys of asteroids Steins and Lutetia due in 2008 and 2010 respectively. The AFM test started at 23:01 GMT and ran for nine minutes during which the two onboard navigation cameras successfully tracked the Moon, allowing Rosetta's attitude to be automatically adjusted. Before and after closest approach, the navigation cameras also acquired a series of images of the Moon and Earth; these data will be downloaded early today for ground processing and are expected to be available by 8 March. In addition, other onboard instruments were switched on, including ALICE (ultraviolet imaging spectrometer), VIRTIS (visible and infrared mapping spectrometer) and MIRO (microwave instrument for the Rosetta orbiter), for calibration and general testing using the Earth and Moon as targets. The fly-by manoeuvre swung the three-tonne spacecraft around our planet and out towards Mars, where it will make a fly-by on 26 February 2007. Rosetta will return to Earth again in a series of four planet fly-bys (three times with Earth, once with Mars) before reaching Comet 67P/Churyumov-Gerasimenko in 2014, when it will enter orbit and deliver a lander, Philae, onto the surface. The fly-bys are necessary to accelerate the spacecraft so as to eventually match the velocity of the target comet. They are a fuel-saving way to boost speed using planetary gravity. Yesterday's fly-by came one year and two days after launch and highlights the valuable opportunities for instrument calibration and data gathering available during the mission's multi-year voyage. In just three months, on 4 July, Rosetta will be in a good position to observe and gather data during NASA's spectacular Deep Impact event, when the Deep Impact probe will hurl a 380 kg projectile into Comet Tempel 1, revealing data on the comet's internal structure. Certain of

  6. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

    National Research Council Canada - National Science Library

    Mitchell, Kieren J; Llamas, Bastien; Soubrier, Julien; Rawlence, Nicolas J; Worthy, Trevor H; Wood, Jamie; Lee, Michael S Y; Cooper, Alan

    2014-01-01

    ...) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant...

  7. Why the closest ambulance cannot be dispatched in an urban emergency medical services system.

    Science.gov (United States)

    Dean, Stephen F

    2008-01-01

    Response time performance is related to increased survival for a relatively small group of patients with critical emergencies. Effectively utilizing current resources is a challenge for all emergency medical services (EMS) systems for reasons of cost-effectiveness and safety. The objective of this study was to identify opportunities for improving ambulance response-time performance in an urban EMS system using fixed deployment. This was a qualitative and quantitative case study which consisted of structured interviews with policy makers, managers, and workers in a fire department EMS division, as well as analysis of dispatch data and observation of dispatch operations. The current computer-aided dispatch (CAD) system does not identify the closest ambulance to the emergency, and therefore, dispatchers must guess which unit is closer when units are not within their stations or "first due" areas. There is no means to track how often dispatchers guess correctly or how often the closest ambulance actually is dispatched to the emergency. Temporal and geographic patterns were identified. Opportunities also were identified to improve response time performance through the use of dynamic deployment and peak-load staffing. The results suggest that there were opportunities for improving ambulance response times by implementing strategies such as peak-load staffing and dynamic deployment. However, the most important improvement would be the implementation of a policy to send the closest ambulance to the emergency. More research is needed to identify how prevalent the failure to send the closest ambulance is within EMS systems that use fixed-deployment response strategies and computer-aided dispatch systems that are incapable of tracking unit locations outside of their stations.

  8. Solving variational problems and partial differential equations that map between manifolds via the closest point method

    Science.gov (United States)

    King, Nathan D.; Ruuth, Steven J.

    2017-05-01

    Maps from a source manifold M to a target manifold N appear in liquid crystals, color image enhancement, texture mapping, brain mapping, and many other areas. A numerical framework to solve variational problems and partial differential equations (PDEs) that map between manifolds is introduced within this paper. Our approach, the closest point method for manifold mapping, reduces the problem of solving a constrained PDE between manifolds M and N to the simpler problems of solving a PDE on M and projecting to the closest points on N. In our approach, an embedding PDE is formulated in the embedding space using closest point representations of M and N. This enables the use of standard Cartesian numerics for general manifolds that are open or closed, with or without orientation, and of any codimension. An algorithm is presented for the important example of harmonic maps and generalized to a broader class of PDEs, which includes p-harmonic maps. Improved efficiency and robustness are observed in convergence studies relative to the level set embedding methods. Harmonic and p-harmonic maps are computed for a variety of numerical examples. In these examples, we denoise texture maps, diffuse random maps between general manifolds, and enhance color images.

  9. A modified iterative closest point algorithm for noisy data

    Science.gov (United States)

    Tihonkih, Dmitrii; Makovetskii, Artyom; Voronin, Aleksei

    2017-09-01

    The problem of aligning of 3D point data is the known registration task. The most popular registration algorithm is the Iterative Closest Point (ICP) algorithm. The traditional ICP algorithm is a fast and accurate approach for rigid registration between two point clouds but it is unable to handle affine case. Recently, extension of the ICP algorithm for composition of scaling, rotation, and translation is proposed. A generalized ICP version for an arbitrary affine transformation is also suggested. In this paper, a new iterative algorithm for registration of point clouds based on the point-to-plane ICP algorithm with affine transformations is proposed. At each iteration, a closed-form solution to the affine transformation is derived. This approach allows us to get a precise solution for transformations such as rotation, translation, and scaling. With the help of computer simulation, the proposed algorithm is compared with common registration algorithms.

  10. 3D Visual SLAM Based on Multiple Iterative Closest Point

    Directory of Open Access Journals (Sweden)

    Chunguang Li

    2015-01-01

    Full Text Available With the development of novel RGB-D visual sensors, data association has been a basic problem in 3D Visual Simultaneous Localization and Mapping (VSLAM. To solve the problem, a VSLAM algorithm based on Multiple Iterative Closest Point (MICP is presented. By using both RGB and depth information obtained from RGB-D camera, 3D models of indoor environment can be reconstructed, which provide extensive knowledge for mobile robots to accomplish tasks such as VSLAM and Human-Robot Interaction. Due to the limited views of RGB-D camera, additional information about the camera pose is needed. In this paper, the motion of the RGB-D camera is estimated by a motion capture system after a calibration process. Based on the estimated pose, the MICP algorithm is used to improve the alignment. A Kinect mobile robot which is running Robot Operating System and the motion capture system has been used for experiments. Experiment results show that not only the proposed VSLAM algorithm achieved good accuracy and reliability, but also the 3D map can be generated in real time.

  11. Schemas reveal spatial relations to a patient with simultanagnosia.

    Science.gov (United States)

    Kranjec, Alexander; Ianni, Geena; Chatterjee, Anjan

    2013-01-01

    Maps, graphs, and diagrams use simplified graphic forms, like lines and blobs, to represent basic spatial relations, like boundaries and enclosures. A schema is an iconic representation where perceptual detail has been abstracted away from reality in order to provide a more flexible structure for cognition. Unlike truly symbolic representations of spatial relations (i.e., prepositions) a schema preserves some analog spatial qualities of the relation it stands in for. We tested the efficacy of schemas in facilitating the perception and comprehension of spatial relations in a patient with bilateral occipitoparietal damage and resulting simultanagnosia. Patient E.E. performed six matching tasks involving WORDS (in, on, above, below), photographic PICTURES of objects, and/or SCHEMAS depicting the same spatial relations. E.E. was instructed to match a single spatial relation to a corresponding image from an array of four choices. On the two tasks that did not include matching to or from schemas, E.E. performed at chance levels. On tasks with schemas, performance was significantly better, indicating that schematic representations make spatial relations visible in a manner that symbols and complex images do not. The results provide general insight as to how schemas facilitate spatial reasoning when used in graphic depictions, and how such theoretically intermediate representational structures could serve to link perceptual and verbal representations of spatial relations in the brain. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Palaeoseismicity in relation to basin tectonics as revealed from soft ...

    Indian Academy of Sciences (India)

    Although such soft-sediment deformation structures maybe formed by various processes, in the present area the association of these structures, their relation to the adjacent sedimentary rocks and the tectonic and depositional setting of the formation suggest that these structures are seismogenic. Movements along the basin ...

  13. Markerless registration for intracerebral hemorrhage surgical system using weighted Iterative Closest Point (ICP).

    Science.gov (United States)

    Shin, Sangkyun; Lee, Deukhee; Kim, Youngjun; Park, Sehyung

    2012-01-01

    It is required to use a stereotactic frame on a patient's crainial surface to access an intracerebral hematoma in conventional ICH (Intracerebral Hemorrhage) removal surgery. Since ICH using a stereotactic frame is an invasive procedure and also takes a long time, we attempt to develop a robotic ICH removal procedure with a markerless registration system using an optical 3-D scanner. Preoperative planning is performed using a patient's CT (Computed Tomography) images, which include the patient's 3-D geometrical information on the hematoma and internal structures of brain. To register the preplanned data and the intraoperative patient's data, the patient's facial surface is scanned by an optical 3-D scanner on the bed in the operating room. The intraoperatively scanned facial surface is registered to the pose of the patient's preoperative facial surface. The conventional ICP (Iterative Closest Point) algorithm can be used for the registration. In this paper, we propose a weighted ICP in order to improve the accuracy of the registration results. We investigated facial regions that can be used as anatomical landmarks. The facial regions for the landmarks in the preoperative 3-D model are weighted for more accurate registration. We increase weights at the relatively undeformed facial regions, and decrease weights at the other regions. As a result, more accurate and robust registration can be achieved from the preoperative data even with local facial shape changes.

  14. The Closest Point Method and Multigrid Solvers for Elliptic Equations on Surfaces

    KAUST Repository

    Chen, Yujia

    2015-01-01

    © 2015 Society for Industrial and Applied Mathematics. Elliptic partial differential equations are important from both application and analysis points of view. In this paper we apply the closest point method to solve elliptic equations on general curved surfaces. Based on the closest point representation of the underlying surface, we formulate an embedding equation for the surface elliptic problem, then discretize it using standard finite differences and interpolation schemes on banded but uniform Cartesian grids. We prove the convergence of the difference scheme for the Poisson\\'s equation on a smooth closed curve. In order to solve the resulting large sparse linear systems, we propose a specific geometric multigrid method in the setting of the closest point method. Convergence studies in both the accuracy of the difference scheme and the speed of the multigrid algorithm show that our approaches are effective.

  15. Efficient Verifiable Range and Closest Point Queries in Zero-Knowledge

    Directory of Open Access Journals (Sweden)

    Ghosh Esha

    2016-10-01

    Full Text Available We present an efficient method for answering one-dimensional range and closest-point queries in a verifiable and privacy-preserving manner. We consider a model where a data owner outsources a dataset of key-value pairs to a server, who answers range and closest-point queries issued by a client and provides proofs of the answers. The client verifies the correctness of the answers while learning nothing about the dataset besides the answers to the current and previous queries. Our work yields for the first time a zero-knowledge privacy assurance to authenticated range and closest-point queries. Previous work leaked the size of the dataset and used an inefficient proof protocol. Our construction is based on hierarchical identity-based encryption. We prove its security and analyze its efficiency both theoretically and with experiments on synthetic and real data (Enron email and Boston taxi datasets.

  16. Haptic Distal Spatial Perception Mediated by Strings: Point of Closest Approach and Bypass Distance

    Science.gov (United States)

    Cabe, Patrick A.; Hofman, L. Leigh

    2012-01-01

    Four experiments examined haptic perception of two distal spatial properties in a bypass event. A hook suspended a string held taut between the participant's finger and a weight. Moving their fingers laterally beneath the hook, participants estimated the finger's point of closest approach (PCA) to the hook and bypass distance (BPD; i.e., hook…

  17. The closest vector problem in tensored root lattices of type A and in their duals

    NARCIS (Netherlands)

    L. Ducas (Léo); W.P.J. van Woerden (Wessel)

    2017-01-01

    textabstractIn this work we consider the closest vector problem (CVP)—a problem also known as maximum-likelihood decoding—in the tensor of two root lattices of type A ((Formula presented.)), as well as in their duals ((Formula presented.)). This problem is mainly motivated by lattice based

  18. The Curvature-Augmented Closest Point method with vesicle inextensibility application

    Science.gov (United States)

    Vogl, Christopher J.

    2017-09-01

    The Closest Point method, initially developed by Ruuth and Merriman, allows for the numerical solution of surface partial differential equations without the need for a parameterization of the surface itself. Surface quantities are embedded into the surrounding domain by assigning each value at a given spatial location to the corresponding value at the closest point on the surface. This embedding allows for surface derivatives to be replaced by their Cartesian counterparts (e.g. ∇s = ∇). This equivalence is only valid on the surface, and thus, interpolation is used to enforce what is known as the side condition away from the surface. To improve upon the method, this work derives an operator embedding that incorporates curvature information, making it valid in a neighborhood of the surface. With this, direct enforcement of the side condition is no longer needed. Comparisons in R2 and R3 show that the resulting Curvature-Augmented Closest Point method has better accuracy and requires less memory, through increased matrix sparsity, than the Closest Point method, while maintaining similar matrix condition numbers. To demonstrate the utility of the method in a physical application, simulations of inextensible, bi-lipid vesicles evolving toward equilibrium shapes are also included.

  19. The Curvature-Augmented Closest Point method with vesicle inextensibility application

    Energy Technology Data Exchange (ETDEWEB)

    Vogl, Christopher J.

    2017-09-01

    The Closest Point method, initially developed by Ruuth and Merriman, allows for the numerical solution of surface partial differential equations without the need for a parameterization of the surface itself. Surface quantities are embedded into the surrounding domain by assigning each value at a given spatial location to the corresponding value at the closest point on the surface. This embedding allows for surface derivatives to be replaced by their Cartesian counterparts (e.g. ∇s=∇). This equivalence is only valid on the surface, and thus, interpolation is used to enforce what is known as the side condition away from the surface. To improve upon the method, this work derives an operator embedding that incorporates curvature information, making it valid in a neighborhood of the surface. With this, direct enforcement of the side condition is no longer needed. Comparisons in R2 and R3 show that the resulting Curvature-Augmented Closest Point method has better accuracy and requires less memory, through increased matrix sparsity, than the Closest Point method, while maintaining similar matrix condition numbers. To demonstrate the utility of the method in a physical application, simulations of inextensible, bi-lipid vesicles evolving toward equilibrium shapes are also included.

  20. Integration Over Curves and Surfaces Defined by the Closest Point Mapping

    Science.gov (United States)

    2015-04-01

    3 Numerical simulations In this section we investigate the convergence of our numerical integration using simple Riemann sum over uniform Cartesian...be considered integration of functions defined on suitable hypercubes, periodically extended. In such settings, simple Riemann sums on Cartesian grids... Integration over curves and surfaces defined by the closest point mapping Catherine Kublik∗ and Richard Tsai† Abstract We propose a new formulation

  1. Event-related potentials reveal the relations between feature representations at different levels of abstraction.

    Science.gov (United States)

    Hannah, Samuel D; Shedden, Judith M; Brooks, Lee R; Grundy, John G

    2016-11-01

    In this paper, we use behavioural methods and event-related potentials (ERPs) to explore the relations between informational and instantiated features, as well as the relation between feature abstraction and rule type. Participants are trained to categorize two species of fictitious animals and then identify perceptually novel exemplars. Critically, two groups are given a perfectly predictive counting rule that, according to Hannah and Brooks (2009. Featuring familiarity: How a familiar feature instantiation influences categorization. Canadian Journal of Experimental Psychology/Revue Canadienne de Psychologie Expérimentale, 63, 263-275. Retrieved from http://doi.org/10.1037/a0017919), should orient them to using abstract informational features when categorizing the novel transfer items. A third group is taught a feature list rule, which should orient them to using detailed instantiated features. One counting-rule group were taught their rule before any exposure to the actual stimuli, and the other immediately after training, having learned the instantiations first. The feature-list group were also taught their rule after training. The ERP results suggest that at test, the two counting-rule groups processed items differently, despite their identical rule. This not only supports the distinction that informational and instantiated features are qualitatively different feature representations, but also implies that rules can readily operate over concrete inputs, in contradiction to traditional approaches that assume that rules necessarily act on abstract inputs.

  2. Altruistic Behavior among Twins Willingness to Fight and Self-Sacrifice for their Closest Relatives.

    Science.gov (United States)

    Tornero, Encarnación; Sánchez-Romera, Juan F; Morosoli, José J; Vázquez, Alexandra; Gómez, Ángel; Ordoñana, Juan R

    2017-10-28

    According to kin selection theory, indirect reproductive advantages may induce individuals to care for others with whom they share genes by common descent, and the amount of care, including self-sacrifice, will increase with the proportion of genes shared. Twins represent a natural situation in which this hypothesis can be tested. Twin pairs experience the same early environment because they were born and raised at the same time and in the same family but their genetic relatedness differs depending on zygosity. We compared the degree of willingness to fight and sacrifice for the co-twin among monozygotic (MZ) and dizygotic (DZ) pairs in a sample of 1443 same-sex and opposite-sex twins. We also analyzed the effect of the subject's gender and that of the co-twin on those altruistic behaviors. Results partly supported the postulated explanation. MZ twins (who share nearly their entire genome) were significantly more likely than DZ twins (who on average share half of their segregating genes) to self-sacrifice for their co-twins, but zygosity did not affect willingness to fight for him/her. The genders of the subject and of the co-twin, not genetic relatedness, were the best predictors of aggressive altruistic intentions.

  3. Efficient and accurate nearest neighbor and closest pair search in high-dimensional space

    KAUST Repository

    Tao, Yufei

    2010-07-01

    Nearest Neighbor (NN) search in high-dimensional space is an important problem in many applications. From the database perspective, a good solution needs to have two properties: (i) it can be easily incorporated in a relational database, and (ii) its query cost should increase sublinearly with the dataset size, regardless of the data and query distributions. Locality-Sensitive Hashing (LSH) is a well-known methodology fulfilling both requirements, but its current implementations either incur expensive space and query cost, or abandon its theoretical guarantee on the quality of query results. Motivated by this, we improve LSH by proposing an access method called the Locality-Sensitive B-tree (LSB-tree) to enable fast, accurate, high-dimensional NN search in relational databases. The combination of several LSB-trees forms a LSB-forest that has strong quality guarantees, but improves dramatically the efficiency of the previous LSH implementation having the same guarantees. In practice, the LSB-tree itself is also an effective index which consumes linear space, supports efficient updates, and provides accurate query results. In our experiments, the LSB-tree was faster than: (i) iDistance (a famous technique for exact NN search) by two orders ofmagnitude, and (ii) MedRank (a recent approximate method with nontrivial quality guarantees) by one order of magnitude, and meanwhile returned much better results. As a second step, we extend our LSB technique to solve another classic problem, called Closest Pair (CP) search, in high-dimensional space. The long-term challenge for this problem has been to achieve subquadratic running time at very high dimensionalities, which fails most of the existing solutions. We show that, using a LSB-forest, CP search can be accomplished in (worst-case) time significantly lower than the quadratic complexity, yet still ensuring very good quality. In practice, accurate answers can be found using just two LSB-trees, thus giving a substantial

  4. Effect of denture fabrication and wear on closest speaking space and interocclusal distance during deglutition.

    Science.gov (United States)

    de Souza, Raphael Freitas; Marra, Julie; Pero, Ana Carolina; Compagnoni, Marco Antonio

    2007-06-01

    The accuracy of assessing maxillomandibular relationships for trial bases and dentures using phonetic and swallowing methods has not been compared to that observed with definitive prostheses. Thus, there is no evidence to prove whether measurements obtained through such methods remain the same after adaptation to dentures. This study investigated changes in the closest speaking space, interocclusal rest space, and interocclusal distance during deglutition in edentulous patients during and after complete denture treatment. Eighteen edentulous subjects participated in this study and measurements were performed after 7 intervals of time: (1) with occlusion rims and record bases following creation of the maxillomandibular relationship record, (2) with trial dentures, (3) at insertion of definitive complete dentures, (4) 1 week, (5) 2 weeks, (6) 1 month, and (7) 3 months after insertion. Recordings of interocclusal distances were made with a mandibular kinesiograph. Closest speaking space was measured during the pronunciation of the word 'seis'. The distance between postural rest position and centric occlusion, or interocclusal rest space, was measured using a kinesiograph. Interocclusal distance during deglutition was tested by recording the closest mandibular position recorded during swallowing of 20 mL of water. Data were analyzed using repeated-measure ANOVA, followed by the Student-Newman-Keuls test (alpha=.05). A significant (Pdeglutition among the time periods evaluated. The presence of occlusion rims can influence mandibular position during pronunciation of the /s/ sound. The arrangement of artificial teeth changes the closest speaking space. However, rest position and deglutition were not affected, either during denture fabrication or short-term use.

  5. The Closest Alligator to the Boat: Mexico’s Drug-Fueled Violence

    Science.gov (United States)

    2011-01-28

    outside stimulus. This plays into why cartels are able to so freely recruit new members into their ranks. Machismo , a learned response and a real...part of Hispanic culture, is one of the overriding forces driving the Latin American male psyche. Machismo , directly translated from Spanish...closest English word to machismo is macho which seems to be an out of vogue word in 2010 America. In America, it is acceptable to be in touch with

  6. Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves

    OpenAIRE

    Feng, Dan; Wang, Yanwei; Lu, Tiegang; Zhang, Zhiguo; Han, Xiao

    2017-01-01

    Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related ...

  7. Social support from the closest person and sleep quality in later life: Evidence from a British birth cohort study.

    Science.gov (United States)

    Stafford, Mai; Bendayan, Rebecca; Tymoszuk, Ula; Kuh, Diana

    2017-07-01

    Supportive social relationships have been found to be related to fewer sleep problems and better sleep quality. We examined associations between positive and negative support from the nominated close person across 15years of follow-up with sleep quality in older age. MRC National Survey of Health and Development study members reported sleep quality at age 68 (n=2446). Cumulative exposure to and changes in positive and negative support were derived from data at age 53, 60-64 and 68years. Pittsburgh Sleep Quality Index scores were regressed on social support measures adjusted for i) gender only then additionally ii) education, marital status, number in household, limiting illness, body mass index, caregiving, iii) and affective symptoms. Greater exposure to positive support and lower exposure to negative support over 15years were independently associated with better sleep quality at age 68. Sleep quality was poorer for those who experienced declining positive support or increasing negative support. Those who nominated their spouse/partner as their closest person at age 53 but not at age 68 had poorer sleep quality than those who nominated their spouse on both occasions. These associations were not explained by the covariates, including affective symptoms. Based on repeat data on support from the closest person, this study finds a link between declining social relationship quality and poor sleep quality. Whilst acknowledging that the association may be bi-directional, the study suggests that interventions to improve older people's social relationships may have benefits for sleep. Copyright © 2017. Published by Elsevier Inc.

  8. Hubble Space Telescope astrometry of the closest brown dwarf binary system -- I. Overview and improved orbit

    OpenAIRE

    Bedin, L. R.; Pourbaix, D.; Apai, D.; Burgasser, A. J.; Buenzli, E.; Boffin, H.~M.~J.; Libralato, M.

    2017-01-01

    Located at ~2pc, the L7.5+T0.5 dwarfs system WISE J104915.57-531906.1 (Luhman16AB) is the third closest system known to Earth, making it a key benchmark for detailed investigation of brown dwarf atmospheric properties, thermal evolution, multiplicity, and planet-hosting frequency. In the first study of this series -- based on a multi-cycle Hubble Space Telescope (HST) program -- we provide an overview of the project and present improved estimates of positions, proper motions, annual parallax,...

  9. Is the closest facility the one actually used? An assessment of travel time estimation based on mammography facilities.

    Science.gov (United States)

    Alford-Teaster, Jennifer; Lange, Jane M; Hubbard, Rebecca A; Lee, Christoph I; Haas, Jennifer S; Shi, Xun; Carlos, Heather A; Henderson, Louise; Hill, Deirdre; Tosteson, Anna N A; Onega, Tracy

    2016-02-18

    Characterizing geographic access depends on a broad range of methods available to researchers and the healthcare context to which the method is applied. Globally, travel time is one frequently used measure of geographic access with known limitations associated with data availability. Specifically, due to lack of available utilization data, many travel time studies assume that patients use the closest facility. To examine this assumption, an example using mammography screening data, which is considered a geographically abundant health care service in the United States, is explored. This work makes an important methodological contribution to measuring access--which is a critical component of health care planning and equity almost everywhere. We analyzed one mammogram from each of 646,553 women participating in the US based Breast Cancer Surveillance Consortium for years 2005-2012. We geocoded each record to street level address data in order to calculate travel time to the closest and to the actually used mammography facility. Travel time between the closest and the actual facility used was explored by woman-level and facility characteristics. Only 35% of women in the study population used their closest facility, but nearly three-quarters of women not using their closest facility used a facility within 5 min of the closest facility. Individuals that by-passed the closest facility tended to live in an urban core, within higher income neighborhoods, or in areas where the average travel times to work was longer. Those living in small towns or isolated rural areas had longer closer and actual median drive times. Since the majority of US women accessed a facility within a few minutes of their closest facility this suggests that distance to the closest facility may serve as an adequate proxy for utilization studies of geographically abundant services like mammography in areas where the transportation networks are well established.

  10. Event-related brain potentials reveal correlates of the transformation of stimulus functions through derived relations in healthy humans.

    Science.gov (United States)

    O'Regan, L M; Farina, F R; Hussey, I; Roche, R A P

    2015-03-02

    This research aimed to explore the neural correlates of relational learning by recording high-density EEG during a behavioural task involving derivation levels of varying complexity. A total of 15 participants (5 male; age range 18-23 years; mean age=20.0 years) completed contextual cue training, relational learning, function training and a derivation task while 128-channel event-related potentials (ERPs) were recorded from the scalp (Background). Differences in response latencies were observed between the two derived (symmetry and equivalence) and directly trained relations, with longest latencies found for equivalence and shortest for the directly trained relations. This pattern failed to reach statistical significance. Importantly, ERPs revealed an early P3a positivity (from 230 to 350ms) over right posterior scalp sites. Significantly larger mean amplitudes were found at three channels (P6, E115 and E121) for the equivalence relations compared to the two other types (Results). We believe this may constitute a first demonstration of differences in brain electrophysiology in the transformation of stimulus functions through derived relations of hierarchical levels of complexity (Conclusions). Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Selection effects in identifying magnetic clouds and the importance of the closest approach parameter

    Directory of Open Access Journals (Sweden)

    R. P. Lepping

    2010-08-01

    Full Text Available This study is motivated by the unusually low number of magnetic clouds (MCs that are strictly identified within interplanetary coronal mass ejections (ICMEs, as observed at 1 AU; this is usually estimated to be around 30% or lower. But a looser definition of MCs may significantly increase this percentage. Another motivation is the unexpected shape of the occurrence distribution of the observers' "closest approach distances" (measured from a MC's axis, and called CA which drops off somewhat rapidly as |CA| (in % of MC radius approaches 100%, based on earlier studies. We suggest, for various geometrical and physical reasons, that the |CA|-distribution should be somewhere between a uniform one and the one actually observed, and therefore the 30% estimate should be higher. So we ask, When there is a failure to identify a MC within an ICME, is it occasionally due to a large |CA| passage, making MC identification more difficult, i.e., is it due to an event selection effect? In attempting to answer this question we examine WIND data to obtain an accurate distribution of the number of MCs vs. |CA| distance, whether the event is ICME-related or not, where initially a large number of cases (N=98 are considered. This gives a frequence distribution that is far from uniform, confirming earlier studies. This along with the fact that there are many ICME identification-parameters that do not depend on |CA| suggest that, indeed an MC event selection effect may explain at least part of the low ratio of (No. MCs/(No. ICMEs. We also show that there is an acceptable geometrical and physical consistency in the relationships for both average "normalized" magnetic field intensity change and field direction change vs. |CA| within a MC, suggesting that our estimates of |CA|, BO (magnetic field intensity on the axis, and choice of a proper "cloud coordinate" system (all needed in the analysis are acceptably accurate. Therefore, the MC fitting model (Lepping et al., 1990

  12. Computational Analysis of Distance Operators for the Iterative Closest Point Algorithm.

    Directory of Open Access Journals (Sweden)

    Higinio Mora

    Full Text Available The Iterative Closest Point (ICP algorithm is currently one of the most popular methods for rigid registration so that it has become the standard in the Robotics and Computer Vision communities. Many applications take advantage of it to align 2D/3D surfaces due to its popularity and simplicity. Nevertheless, some of its phases present a high computational cost thus rendering impossible some of its applications. In this work, it is proposed an efficient approach for the matching phase of the Iterative Closest Point algorithm. This stage is the main bottleneck of that method so that any efficiency improvement has a great positive impact on the performance of the algorithm. The proposal consists in using low computational cost point-to-point distance metrics instead of classic Euclidean one. The candidates analysed are the Chebyshev and Manhattan distance metrics due to their simpler formulation. The experiments carried out have validated the performance, robustness and quality of the proposal. Different experimental cases and configurations have been set up including a heterogeneous set of 3D figures, several scenarios with partial data and random noise. The results prove that an average speed up of 14% can be obtained while preserving the convergence properties of the algorithm and the quality of the final results.

  13. Nonrigid iterative closest points for registration of 3D biomedical surfaces

    Science.gov (United States)

    Liang, Luming; Wei, Mingqiang; Szymczak, Andrzej; Petrella, Anthony; Xie, Haoran; Qin, Jing; Wang, Jun; Wang, Fu Lee

    2018-01-01

    Advanced 3D optical and laser scanners bring new challenges to computer graphics. We present a novel nonrigid surface registration algorithm based on Iterative Closest Point (ICP) method with multiple correspondences. Our method, called the Nonrigid Iterative Closest Points (NICPs), can be applied to surfaces of arbitrary topology. It does not impose any restrictions on the deformation, e.g. rigidity or articulation. Finally, it does not require parametrization of input meshes. Our method is based on an objective function that combines distance and regularization terms. Unlike the standard ICP, the distance term is determined based on multiple two-way correspondences rather than single one-way correspondences between surfaces. A Laplacian-based regularization term is proposed to take full advantage of multiple two-way correspondences. This term regularizes the surface movement by enforcing vertices to move coherently with their 1-ring neighbors. The proposed method achieves good performances when no global pose differences or significant amount of bending exists in the models, for example, families of similar shapes, like human femur and vertebrae models.

  14. Cold climate during the closest Stage 11 analog to recent Millennia

    Science.gov (United States)

    Ruddiman, William F.

    2005-05-01

    The early part of marine isotopic Stage 11 near 400,000 years ago provides the closest analog to Holocene insolation levels of any interglaciation during the era of strong 100,000-year climatic cycles. The CH 4 concentration measured in Vostok ice fell to ˜450 ppb, and CO 2 values to ˜250 ppm. These natural decreases contrast with the increases in recent millennia and support the early anthropogenic hypothesis of major gas emissions from late-Holocene farming. During the same interval, δD values fell from typical interglacial to nearly glacial values, indicating a major cooling in Antarctica early in Stage 11. Other evidence suggests that new ice was accumulating during the closest insolation analog to the present day: a major increase in δ18O atm at Vostok, a similar increase in marine δ18O values, and re-initiation of ice rafting in the Nordic Sea. The evidence permits extended (>20,000 year) intervals of Stage 11 interglacial warmth in the Antarctic and North Atlantic, yet it also requires that this warmth ended and a new glacial era began when insolation was most similar to recent millennia. The Holocene CO 2 anomaly was produced only in part by direct anthropogenic emissions; over half of the anomaly resulted from the failure of CO 2 values to fall as they had during previous interglaciations because of natural responses, including a sea-ice advance in the Antarctic and ice-sheet growth in the northern hemisphere.

  15. Novel method for rail wear inspection based on the sparse iterative closest point method

    Science.gov (United States)

    Yi, Bing; Yang, Yue; Yi, Qian; Dai, Wanlin; Li, Xiongbing

    2017-12-01

    As trains become progressively faster, it is becoming imperative to automatically and precisely inspect the rail profile of high-speed railways to ensure their safety and reliability. To realize this, a new method based on the sparse iterative closest point method is proposed in this study. Moreover, the noncontact method is mainly used for convenience and practicality. First, a line laser-based measurement system is constructed, and the position of the line laser is calculated to ensure that both the top and sides of the rail are in range of the line laser. Then, the measured data of the rail profile are separated into a baseline part and worn part. The baseline is involved in registering the measured data and reference profile by the sparse iterative closest point method. The worn part is then transformed by the same matrix of the baseline part. Finally, the Hausdorff distance is introduced to measure the distance between the wear model and reference model. The experimental results demonstrate the effectiveness and efficiency of the proposed method.

  16. Near-infrared colors of asteroid 2012 DA14 at its closest approach to Earth: Observations with the Nishiharima Infrared Camera (NIC)

    Science.gov (United States)

    Takahashi, Jun; Urakawa, Seitaro; Terai, Tsuyoshi; Hanayama, Hidekazu; Arai, Akira; Honda, Satoshi; Takagi, Yuhei; Itoh, Yoichi; Zenno, Takahiro; Ishiguro, Masateru

    2014-06-01

    We present the results of our JHKs photometry of asteroid 2012 DA14 at its closest approach to Earth on 2013 February 15. Possible spectral changes associated with resurfacing by planetary encounters are of great interest. The Earth flyby of 2012 DA14 provided a rare opportunity to investigate this effect. Our observations were conducted using the Nishiharima Infrared Camera (NIC) attached to the 2.0 m Nayuta telescope at the Nishi-Harima Astronomical Observatory. Despite the extraordinarily fast sky motion of up to near 50″ s-1, the telescope successfully tracked the asteroid. The NIC achievement of three-band simultaneous observations allowed us to reliably deduce the colors of this fast-moving object. The derived near-infrared relative reflectances are flat, which is consistent with the classification of the asteroid as L-type. The J - H and H - Ks colors at 0.5-1 hr after the closest approach are compared with those observed by de León (2013, A&A, 555, L2) at ˜ 10 hr after the closest time. We did not detect color changes significantly exceeding the photometric errors, which are ˜ 0.1 mag. This project has demonstrated the potential of the NIC as a three-band simultaneous imager, especially for observations of rapidly time-variable phenomena.

  17. Comparative Transcriptome Analysis Reveals Related Regulatory Mechanisms of Androgenic Gland in Eriocheir sinensis

    Directory of Open Access Journals (Sweden)

    Chunpeng Fu

    2017-01-01

    Full Text Available Chinese mitten crab (Eriocheir sinensis is one of the most commercially important aquaculture species in China. The androgenic gland (AG of crustaceans plays pivotal roles in the regulation of male differentiation and in maintaining the male sexual characteristics. In order to reveal related mechanisms in AG, we compared transcriptomes of AG between proliferation and secretion phase. A total of 72,000 unigenes and 4,027 differentially expressed genes were obtained. Gene ontology enrichment analysis indicated that biological processes and metabolic pathways related to protein synthesis and secretion such as transcription, translation, and signal transduction were significantly enriched. Critical genes such as IAG, SXL, TRA-2, SRY, FTZ-F1, FOXL2, and FEM-1 were identified and potentially involved in maintaining the testis development and spermatogenesis. Ribosomes pathway revealed the cause of insulin-like androgenic gland hormone secretion increase. Three insulin-like receptors were thought to be associated with growth and spermatogenesis. In the neuroactive ligand-receptor interaction pathway, the expression of octopamine receptor, 5-HT receptor 1, and melatonin receptor was significantly changed, which revealed the key regulation mechanism of aggressive and mating behavior of males. Comparative transcriptome analysis provided new insights into the genome-wide molecular mechanisms of AG development and the regulatory mechanisms of male development.

  18. Effect of the destructive disagreement belief on relationship satisfaction with a romantic partner or closest friend.

    Science.gov (United States)

    Cramer, Duncan

    2004-03-01

    This study tested the rational-emotive-behaviour theory hypothesis that, when imagining having a serious disagreement with one's romantic partner or closest friend, imagining believing the rational belief that disagreement is not destructive will lead to less dissatisfaction with either relationship than imagining endorsing the irrational belief that disagreement is destructive. The influence of demand characteristics on such an effect was assessed with two counter-demand control conditions. Undergraduates (106 women and 44 men) were assigned randomly to one of five conditions in a pretest/posttest design. The belief appeared to be effectively manipulated. Post-test relationship satisfaction was significantly higher in the rational condition than in the control or irrational condition. These results were not affected by the counter-demand instructions and suggest that this rational belief may reduce relationship dissatisfaction during disagreements.

  19. Perturbations to Saturn's F-ring strands at their closest approach to Prometheus

    Science.gov (United States)

    Giuliatti, Winter S.M.; Murray, C.D.; Gordon, M.

    2000-01-01

    The strange morphology of the F ring of Saturn is thought to be caused by the perturbing effects of two close satellites, Prometheus and Pandora. The F ring and the satellites also experience periodic close encounters as a result of differential precession arising from Saturn's oblateness. Using the orbits of the F-ring strands derived by Murray et al. (1997, Icarus 129, 304-316) the behaviour of the ring particles at their closest approach to Prometheus is analysed using numerical simulations. The results show that a gap and a wave are formed in the ring at each encounter with the satellite. However, the gap is expected to have a short lifetime due to keplerian shear. ?? 2000 Elsevier Science Ltd. All rights reserved.

  20. Hubble Space Telescope astrometry of the closest brown dwarf binary system - I. Overview and improved orbit★

    Science.gov (United States)

    Bedin, L. R.; Pourbaix, D.; Apai, D.; Burgasser, A. J.; Buenzli, E.; Boffin, H. M. J.; Libralato, M.

    2017-09-01

    Located at 2 pc, the L7.5+T0.5 dwarfs system WISE J104915.57-531906.1 (Luhman 16 AB) is the third closest system known to Earth, making it a key benchmark for detailed investigation of brown dwarf atmospheric properties, thermal evolution, multiplicity, and planet-hosting frequency. In the first study of this series - based on a multicycle Hubble Space Telescope (HST) program - we provide an overview of the project and present improved estimates of positions, proper motions, annual parallax, mass ratio, and the current best assessment of the orbital parameters of the A-B pair. Our HST observations encompass the apparent periastron of the binary at 220.5 ± 0.2 mas at epoch 2016.402. Although our data seem to be inconsistent with recent ground-based astrometric measurements, we also exclude the presence of third bodies down to Neptune masses and periods longer than a year.

  1. Solving eigenvalue problems on curved surfaces using the Closest Point Method

    KAUST Repository

    Macdonald, Colin B.

    2011-06-01

    Eigenvalue problems are fundamental to mathematics and science. We present a simple algorithm for determining eigenvalues and eigenfunctions of the Laplace-Beltrami operator on rather general curved surfaces. Our algorithm, which is based on the Closest Point Method, relies on an embedding of the surface in a higher-dimensional space, where standard Cartesian finite difference and interpolation schemes can be easily applied. We show that there is a one-to-one correspondence between a problem defined in the embedding space and the original surface problem. For open surfaces, we present a simple way to impose Dirichlet and Neumann boundary conditions while maintaining second-order accuracy. Convergence studies and a series of examples demonstrate the effectiveness and generality of our approach. © 2011 Elsevier Inc.

  2. Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves.

    Science.gov (United States)

    Feng, Dan; Wang, Yanwei; Lu, Tiegang; Zhang, Zhiguo; Han, Xiao

    2017-01-01

    Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

  3. Novel gene function revealed by mouse mutagenesis screens for models of age-related disease

    Science.gov (United States)

    Potter, Paul K.; Bowl, Michael R.; Jeyarajan, Prashanthini; Wisby, Laura; Blease, Andrew; Goldsworthy, Michelle E.; Simon, Michelle M.; Greenaway, Simon; Michel, Vincent; Barnard, Alun; Aguilar, Carlos; Agnew, Thomas; Banks, Gareth; Blake, Andrew; Chessum, Lauren; Dorning, Joanne; Falcone, Sara; Goosey, Laurence; Harris, Shelley; Haynes, Andy; Heise, Ines; Hillier, Rosie; Hough, Tertius; Hoslin, Angela; Hutchison, Marie; King, Ruairidh; Kumar, Saumya; Lad, Heena V.; Law, Gemma; MacLaren, Robert E.; Morse, Susan; Nicol, Thomas; Parker, Andrew; Pickford, Karen; Sethi, Siddharth; Starbuck, Becky; Stelma, Femke; Cheeseman, Michael; Cross, Sally H.; Foster, Russell G.; Jackson, Ian J.; Peirson, Stuart N.; Thakker, Rajesh V.; Vincent, Tonia; Scudamore, Cheryl; Wells, Sara; El-Amraoui, Aziz; Petit, Christine; Acevedo-Arozena, Abraham; Nolan, Patrick M.; Cox, Roger; Mallon, Anne-Marie; Brown, Steve D. M.

    2016-01-01

    Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss. PMID:27534441

  4. Delay discounting task in pigs reveals response strategies related to dopamine metabolite.

    Science.gov (United States)

    Melotti, Luca; Thomsen, Liat Romme; Toscano, Michael J; Mendl, Michael; Held, Suzanne

    2013-08-15

    We developed a novel delay discounting task to investigate outcome impulsivity in pigs. As impulsivity can affect aggression, and might also relate to proactive and reactive coping styles, eight proactive (HR) and eight reactive (LR) pigs identified in a manual restraint test ("Backtest", after Bolhuis et al., 2003) were weaned and mixed in four pens of four unfamiliar pigs, so that each pen had two HR and two LR pigs, and aggression was scored in the 9h after mixing. In the delay discounting task, each pig chose between two levers, one always delivering a small immediate reward, the other a large delayed reward with daily increasing delays, impulsive individuals being the ones discounting the value of the large reward quicker. Two novel strategies emerged: some pigs gradually switched their preference towards the small reward ('Switchers') as predicted, but others persistently preferred the large reward until they stopped making choices ('Omitters'). Outcome impulsivity itself was unrelated to these strategies, to urinary serotonin metabolite (5-HIAA) or dopamine metabolite (HVA) levels, aggression at weaning, or coping style. However, HVA was relatively higher in Omitters than Switchers, and positively correlated with behavioural measures of indecisiveness and frustration during choosing. The delay discounting task thus revealed two response strategies that seemed to be related to the activity of the dopamine system and might indicate a difference in execution, rather than outcome, impulsivity. © 2013.

  5. Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species

    Science.gov (United States)

    Claußen, Maike; Lingner, Thomas; Pommerenke, Claudia; Opitz, Lennart; Salinas, Gabriela; Pieler, Tomas

    2015-01-01

    RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery. PMID:26337391

  6. Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.

    Science.gov (United States)

    Vandroemme, Joachim; Cottyn, Bart; Baeyen, Steve; De Vos, Paul; Maes, Martine

    2013-11-25

    Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content. The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xanthomonas, and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones. The draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.

  7. The Debye light scattering equation’s scaling relation reveals the purity of synthetic dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, Hui-Yu; Chen, Hsiao-Ping [National Chung Cheng University, Department of Chemistry and Biochemistry (China); Tang, Yi-Hsuan [Kaohsiung Medical University, Department of Medicinal and Applied Chemistry (China); Chen, Hui-Ting [Kaohsiung Medical University, Department of Fragrance and Cosmetic Science (China); Kao, Chai-Lin, E-mail: clkao@kmu.edu.tw [Kaohsiung Medical University, Department of Medicinal and Applied Chemistry (China); Wang, Shau-Chun, E-mail: chescw@ccu.edu.tw [National Chung Cheng University, Department of Chemistry and Biochemistry (China)

    2016-03-15

    Spherical dendrimer structures cannot be structurally modeled using conventional polymer models of random coil or rod-like configurations during the calibration of the static light scattering (LS) detectors used to determine the molecular weight (M.W.) of a dendrimer or directly assess the purity of a synthetic compound. In this paper, we used the Debye equation-based scaling relation, which predicts that the static LS intensity per unit concentration is linearly proportional to the M.W. of a synthetic dendrimer in a dilute solution, as a tool to examine the purity of high-generational compounds and to monitor the progress of dendrimer preparations. Without using expensive equipment, such as nuclear magnetic resonance or mass spectrometry, this method only required an affordable flow injection set-up with an LS detector. Solutions of the purified dendrimers, including the poly(amidoamine) (PAMAM) dendrimer and its fourth to seventh generation pyridine derivatives with size range of 5–9 nm, were used to establish the scaling relation with high linearity. The use of artificially impure mixtures of six or seven generations revealed significant deviations from linearity. The raw synthesized products of the pyridine-modified PAMAM dendrimer, which included incompletely reacted dendrimers, were also examined to gauge the reaction progress. As a reaction toward a particular generational derivative of the PAMAM dendrimers proceeded over time, deviations from the linear scaling relation decreased. The difference between the polydispersity index of the incompletely converted products and that of the pure compounds was only about 0.01. The use of the Debye equation-based scaling relation, therefore, is much more useful than the polydispersity index for monitoring conversion processes toward an indicated functionality number in a given preparation.Graphical abstract.

  8. The Debye light scattering equation's scaling relation reveals the purity of synthetic dendrimers

    Science.gov (United States)

    Tseng, Hui-Yu; Chen, Hsiao-Ping; Tang, Yi-Hsuan; Chen, Hui-Ting; Kao, Chai-Lin; Wang, Shau-Chun

    2016-03-01

    Spherical dendrimer structures cannot be structurally modeled using conventional polymer models of random coil or rod-like configurations during the calibration of the static light scattering (LS) detectors used to determine the molecular weight (M.W.) of a dendrimer or directly assess the purity of a synthetic compound. In this paper, we used the Debye equation-based scaling relation, which predicts that the static LS intensity per unit concentration is linearly proportional to the M.W. of a synthetic dendrimer in a dilute solution, as a tool to examine the purity of high-generational compounds and to monitor the progress of dendrimer preparations. Without using expensive equipment, such as nuclear magnetic resonance or mass spectrometry, this method only required an affordable flow injection set-up with an LS detector. Solutions of the purified dendrimers, including the poly(amidoamine) (PAMAM) dendrimer and its fourth to seventh generation pyridine derivatives with size range of 5-9 nm, were used to establish the scaling relation with high linearity. The use of artificially impure mixtures of six or seven generations revealed significant deviations from linearity. The raw synthesized products of the pyridine-modified PAMAM dendrimer, which included incompletely reacted dendrimers, were also examined to gauge the reaction progress. As a reaction toward a particular generational derivative of the PAMAM dendrimers proceeded over time, deviations from the linear scaling relation decreased. The difference between the polydispersity index of the incompletely converted products and that of the pure compounds was only about 0.01. The use of the Debye equation-based scaling relation, therefore, is much more useful than the polydispersity index for monitoring conversion processes toward an indicated functionality number in a given preparation.

  9. Gamma radioactivity in the Iberian marine environment closest to the NEA dumping site

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, P.I.; Vidal-Quadras, A.; Font, J.L.; Oliva, M.

    1988-01-01

    The distributions of caesium-137 and some naturally occurring gamma-emitters in a range of environmental samples, collected along the north-west Iberian coastline during April 1984, are presented. Samples, including surface waters, algae, sediments and fish, have been analyzed to establish accurate baselines for that region of the continental shelf closest to the NEA dumping site. Results indicate that caesium-137 levels were a factor of three lower than those typical of waters off the west coast of Ireland and are consistent with those expected from global fallout prior to the Chernobyl accident. The mean caesium-137 concentration in sea water at six well-separated stations near the coast was 3.85 +- 0.19 Bq m/sup -3/, whilst caesium-137 levels in widely consumed species of fish were in the range 1.1-6.2 Bq kg/sup -1/ (dry wt). It is estimated that caesium-137, through one year's ingestion of fish and shellfish, generates a collective dose equivalent commitment to the adult Galician population of 0.78 man-Sv, which is approximately 3% of the total annual collective dose equivalent from non-medical sources of radiation.

  10. Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle

    Science.gov (United States)

    2011-01-01

    Background Campylobacter jejuni and Campylobacter coli are human intestinal pathogens of global importance. Zoonotic transmission from livestock animals or animal-derived food is the likely cause for most of these infections. However, little is known about their general and host-specific mechanisms of colonization, or virulence and pathogenicity factors. In certain hosts, Campylobacter species colonize persistently and do not cause disease, while they cause acute intestinal disease in humans. Results Here, we investigate putative host-specificity using phenotypic characterization and genome-wide analysis of genetically closely related C. jejuni strains from different sources. A collection of 473 fresh Campylobacter isolates from Germany was assembled between 2006 and 2010 and characterized using MLST. A subset of closely related C. jejuni strains of the highly prevalent sequence type ST-21 was selected from different hosts and isolation sources. PCR typing of strain-variable genes provided evidence that some genes differed between these strains. Furthermore, phenotypic variation of these strains was tested using the following criteria: metabolic variation, protein expression patterns, and eukaryotic cell interaction. The results demonstrated remarkable phenotypic diversity within the ST-21 group, which however did not correlate with isolation source. Whole genome sequencing was performed for five ST-21 strains from chicken, human, bovine, and food sources, in order to gain insight into ST-21 genome diversity. The comparisons showed extensive genomic diversity, primarily due to recombination and gain of phage-related genes. By contrast, no genomic features associated with isolation source or host were identified. Conclusions The genome information and phenotypic data obtained in vitro and in a chicken infection model provided little evidence of fixed adaptation to a specific host. Instead, the dominant C. jejuni ST-21 appeared to be characterized by phenotypic

  11. Successful syllable detection in aphasia despite processing impairments as revealed by event-related potentials

    Directory of Open Access Journals (Sweden)

    Becker Frank

    2007-01-01

    Full Text Available Abstract Background The role of impaired sound and speech sound processing for auditory language comprehension deficits in aphasia is unclear. No electrophysiological studies of attended speech sound processing in aphasia have been performed for stimuli that are discriminable even for patients with severe auditory comprehension deficits. Methods Event-related brain potentials (ERPs were used to study speech sound processing in a syllable detection task in aphasia. In an oddball paradigm, the participants had to detect the infrequent target syllable /ta:/ amongst the frequent standard syllable /ba:/. 10 subjects with moderate and 10 subjects with severe auditory comprehension impairment were compared to 11 healthy controls. Results N1 amplitude was reduced indicating impaired primary stimulus analysis; N1 reduction was a predictor for auditory comprehension impairment. N2 attenuation suggests reduced attended stimulus classification and discrimination. However, all aphasic patients were able to discriminate the stimuli almost without errors, and processes related to the target identification (P3 were not significantly reduced. The aphasic subjects might have discriminated the stimuli by purely auditory differences, while the ERP results reveal a reduction of language-related processing which however did not prevent performing the task. Topographic differences between aphasic subgroups and controls indicate compensatory changes in activation. Conclusion Stimulus processing in early time windows (N1, N2 is altered in aphasics with adverse consequences for auditory comprehension of complex language material, while allowing performance of simpler tasks (syllable detection. Compensational patterns of speech sound processing may be activated in syllable detection, but may not be functional in more complex tasks. The degree to which compensational processes can be activated probably varies depending on factors as lesion site, time after injury, and

  12. Change Detection from differential airborne LiDAR using a weighted Anisotropic Iterative Closest Point Algorithm

    Science.gov (United States)

    Zhang, X.; Kusari, A.; Glennie, C. L.; Oskin, M. E.; Hinojosa-Corona, A.; Borsa, A. A.; Arrowsmith, R.

    2013-12-01

    Differential LiDAR (Light Detection and Ranging) from repeated surveys has recently emerged as an effective tool to measure three-dimensional (3D) change for applications such as quantifying slip and spatially distributed warping associated with earthquake ruptures, and examining the spatial distribution of beach erosion after hurricane impact. Currently, the primary method for determining 3D change is through the use of the iterative closest point (ICP) algorithm and its variants. However, all current studies using ICP have assumed that all LiDAR points in the compared point clouds have uniform accuracy. This assumption is simplistic given that the error for each LiDAR point is variable, and dependent upon highly variable factors such as target range, angle of incidence, and aircraft trajectory accuracy. Therefore, to rigorously determine spatial change, it would be ideal to model the random error for every LiDAR observation in the differential point cloud, and use these error estimates as apriori weights in the ICP algorithm. To test this approach, we implemented a rigorous LiDAR observation error propagation method to generate estimated random error for each point in a LiDAR point cloud, and then determine 3D displacements between two point clouds using an anistropic weighted ICP algorithm. The algorithm was evaluated by qualitatively and quantitatively comparing post earthquake slip estimates from the 2010 El Mayor-Cucapah Earthquake between a uniform weight and anistropically weighted ICP algorithm, using pre-event LiDAR collected in 2006 by Instituto Nacional de Estadística y Geografía (INEGI), and post-event LiDAR collected by The National Center for Airborne Laser Mapping (NCALM).

  13. The edge-driven dual-bootstrap iterative closest point algorithm for multimodal retinal image registration

    Science.gov (United States)

    Tsai, Chia-Ling; Li, Chun-Yi; Yang, Gehua

    2008-03-01

    Red-free (RF) fundus retinal images and fluorescein angiogram (FA) sequence are often captured from an eye for diagnosis and treatment of abnormalities of the retina. With the aid of multimodal image registration, physicians can combine information to make accurate surgical planning and quantitative judgment of the progression of a disease. The goal of our work is to jointly align the RF images with the FA sequence of the same eye in a common reference space. Our work is inspired by Generalized Dual-Bootstrap Iterative Closest Point (GDB-ICP), which is a fully-automatic, feature-based method using structural similarity. GDB-ICP rank-orders Lowe keypoint matches and refines the transformation computed from each keypoint match in succession. Albeit GDB-ICP has been shown robust to image pairs with illumination difference, the performance is not satisfactory for multimodal and some FA pairs which exhibit substantial non-linear illumination changes. Our algorithm, named Edge-Driven DBICP, modifies generation of keypoint matches for initialization by extracting the Lowe keypoints from the gradient magnitude image, and enriching the keypoint descriptor with global-shape context using the edge points. Our dataset consists of 61 randomly selected pathological sequences, each on average having two RF and 13 FA images. There are total of 4985 image pairs, out of which 1323 are multimodal pairs. Edge-Driven DBICP successfully registered 93% of all pairs, and 82% multimodal pairs, whereas GDB-ICP registered 80% and 40%, respectively. Regarding registration of the whole image sequence in a common reference space, Edge-Driven DBICP succeeded in 60 sequences, which is 26% improvement over GDB-ICP.

  14. RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion.

    Science.gov (United States)

    Liu, Qianchun; Wen, Changlong; Zhao, Hong; Zhang, Liying; Wang, Jian; Wang, Yongqin

    2014-01-01

    The waxy cuticle plays a very important role in plant resistance to various biotic and abiotic stresses and is an important characteristic of Welsh onions. Two different types of biangan Welsh onions (BG) were selected for this study: BG, a wild-type covered by wax, which forms a continuous lipid membrane on its epidermal cells, and GLBG, a glossy mutant of BG whose epidermal cells are not covered by wax. To elucidate the waxy cuticle-related gene expression changes, we used RNA-Seq to compare these two Welsh onion varieties with distinct differences in cuticular wax. The de novo assembly yielded 42,881 putative unigenes, 25.41% of which are longer than 1,000 bp. Among the high-quality unique sequences, 22,289 (52.0%) had at least one significant match to an existing gene model. A total of 798 genes, representing 1.86% of the total putative unigenes, were differentially expressed between these two Welsh onion varieties. The expression patterns of four important unigenes that are related to waxy cuticle biosynthesis were confirmed by RT-qPCR and COG class annotation, which demonstrated that these genes play an important role in defense mechanisms and lipid transport and metabolism. To our knowledge, this study is the first exploration of the Welsh onion waxy cuticle. These results may help to reveal the molecular mechanisms underlying the waxy cuticle and will be useful for waxy gene cloning, genetics and breeding as well as phylogenetic and evolutionary studies of the Welsh onion.

  15. Genome-wide comparison of cowpox viruses reveals a new clade related to Variola virus.

    Directory of Open Access Journals (Sweden)

    Piotr Wojtek Dabrowski

    Full Text Available Zoonotic infections caused by several orthopoxviruses (OPV like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages.

  16. Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

    Directory of Open Access Journals (Sweden)

    Patrizia Pezzoli

    Full Text Available Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

  17. Structural genomics reveals EVE as a new ASCH/PUA-related domain.

    Science.gov (United States)

    Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A; Kennedy, Michael A; Cort, John R; Belachew, Adam; Hunt, John F; Tong, Liang; Montelione, Gaetano T; Rost, Burkhard

    2009-05-15

    We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.

  18. Prohibitin-2 gene reveals sex-related differences in the salmon louse Caligus rogercresseyi.

    Science.gov (United States)

    Farlora, Rodolfo; Nuñez-Acuña, Gustavo; Gallardo-Escárate, Cristian

    2015-06-10

    Prohibitins are evolutionarily conserved proteins present in multiple cellular compartments, and are involved in diverse cellular processes, including steroid hormone transcription and gametogenesis. In the present study, we report for the first time the characterization of the prohibitin-2 (Phb2) gene in the sea lice Caligus rogercresseyi. The CrPhb2 cDNA showed a total length of 1406 bp, which contained a predicted open reading frame (ORF) of 894 base pairs (bp) encoding for 298 amino acids. Multiple sequence alignments of prohibitin proteins from other arthropods revealed a high degree of amino acid sequence conservation. In silico Illumina read counts and RT-qPCR analyses showed a sex-dependent differential expression, with mRNA levels exhibiting a 1.7-fold (RT-qPCR) increase in adult females compared with adult males. A total of nine single nucleotide polymorphisms (SNPs) were identified, three were located in the 5' UTR of the Phb2 messenger and six in the ORF, but no mutations associated with sex were found. These results contribute to expand the present knowledge of the reproduction-related genes in C. rogercresseyi, and may be useful in future experiments aimed at controlling the impacts of sea lice in fish farming. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

    Science.gov (United States)

    Pezzoli, Patrizia; Antfolk, Jan; Santtila, Pekka

    2017-01-01

    Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

  20. Structural genomics reveals EVE as a new ASCH/PUA-related domain

    Science.gov (United States)

    Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

    2014-01-01

    Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354

  1. Genomic history of the origin and domestication of common bean unveils its closest sister species.

    Science.gov (United States)

    Rendón-Anaya, Martha; Montero-Vargas, Josaphat M; Saburido-Álvarez, Soledad; Vlasova, Anna; Capella-Gutierrez, Salvador; Ordaz-Ortiz, José Juan; Aguilar, O Mario; Vianello-Brondani, Rosana P; Santalla, Marta; Delaye, Luis; Gabaldón, Toni; Gepts, Paul; Winkler, Robert; Guigó, Roderic; Delgado-Salinas, Alfonso; Herrera-Estrella, Alfredo

    2017-03-29

    Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

  2. Comparative Transcriptomics Reveals Jasmonic Acid-Associated Metabolism Related to Cotton Fiber Initiation.

    Directory of Open Access Journals (Sweden)

    Liman Wang

    Full Text Available Analysis of mutants and gene expression patterns provides a powerful approach for investigating genes involved in key stages of plant fiber development. In this study, lintless-fuzzless XinWX and linted-fuzzless XinFLM with a single genetic locus difference for lint were used to identify differentially expressed genes. Scanning electron microscopy showed fiber initiation in XinFLM at 0 days post anthesis (DPA. Fiber transcriptional profiling of the lines at three initiation developmental stages (-1, 0, 1 DPA was performed using an oligonucleotide microarray. Loop comparisons of the differentially expressed genes within and between the lines was carried out, and functional classification and enrichment analysis showed that gene expression patterns during fiber initiation were heavily associated with hormone metabolism, transcription factor regulation, lipid transport, and asparagine biosynthetic processes, as previously reported. Further, four members of the allene-oxide cyclase (AOC family that function in jasmonate biosynthesis were parallel up-regulation in fiber initiation, especially at -1 DPA, compared to other tissues and organs in linted-fuzzed TM-1. Real time-quantitative PCR (RT-qPCR analysis in different fiber mutant lines revealed that AOCs were up-regulated higher at -1 DPA in lintless-fuzzless than that in linted-fuzzless and linted-fuzzed materials, and transcription of the AOCs was increased under jasmonic acid (JA treatment. Expression analysis of JA biosynthesis-associated genes between XinWX and XinFLM showed that they were up-regulated during fiber initiation in the fuzzless-lintless mutant. Taken together, jasmonic acid-associated metabolism was related to cotton fiber initiation. Parallel up-regulation of AOCs expression may be important for normal fiber initiation development, while overproduction of AOCs might disrupt normal fiber development.

  3. Comparative Transcriptomics Reveals Jasmonic Acid-Associated Metabolism Related to Cotton Fiber Initiation.

    Science.gov (United States)

    Wang, Liman; Zhu, Youmin; Hu, Wenjing; Zhang, Xueying; Cai, Caiping; Guo, Wangzhen

    2015-01-01

    Analysis of mutants and gene expression patterns provides a powerful approach for investigating genes involved in key stages of plant fiber development. In this study, lintless-fuzzless XinWX and linted-fuzzless XinFLM with a single genetic locus difference for lint were used to identify differentially expressed genes. Scanning electron microscopy showed fiber initiation in XinFLM at 0 days post anthesis (DPA). Fiber transcriptional profiling of the lines at three initiation developmental stages (-1, 0, 1 DPA) was performed using an oligonucleotide microarray. Loop comparisons of the differentially expressed genes within and between the lines was carried out, and functional classification and enrichment analysis showed that gene expression patterns during fiber initiation were heavily associated with hormone metabolism, transcription factor regulation, lipid transport, and asparagine biosynthetic processes, as previously reported. Further, four members of the allene-oxide cyclase (AOC) family that function in jasmonate biosynthesis were parallel up-regulation in fiber initiation, especially at -1 DPA, compared to other tissues and organs in linted-fuzzed TM-1. Real time-quantitative PCR (RT-qPCR) analysis in different fiber mutant lines revealed that AOCs were up-regulated higher at -1 DPA in lintless-fuzzless than that in linted-fuzzless and linted-fuzzed materials, and transcription of the AOCs was increased under jasmonic acid (JA) treatment. Expression analysis of JA biosynthesis-associated genes between XinWX and XinFLM showed that they were up-regulated during fiber initiation in the fuzzless-lintless mutant. Taken together, jasmonic acid-associated metabolism was related to cotton fiber initiation. Parallel up-regulation of AOCs expression may be important for normal fiber initiation development, while overproduction of AOCs might disrupt normal fiber development.

  4. Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely RelatedIlexSpecies.

    Science.gov (United States)

    Wen, Lingling; Yun, Xiaoyun; Zheng, Xiasheng; Xu, Hui; Zhan, Ruoting; Chen, Weiwen; Xu, Yaping; Chen, Ye; Zhang, Jie

    2017-01-01

    Native to Southern China, Ilex pubescens and Ilex asprella are frequently used in traditional Chinese medicine. Both of them produce a large variety of ursane-type triterpenoid saponins, which have been demonstrated to have different pharmacological effects. However, little is known about their biosynthesis. In this study, transcriptomic analysis of I. pubescens and comparison with its closely related specie I. asprella were carried out to identify potential genes involved in triterpenoid saponin biosynthesis. Through RNA sequencing (RNA-seq) and de novo transcriptome assembly of I. pubescens , a total of 68,688 UniGene clusters are obtained, of which 32,184 (46.86%) are successfully annotated by comparison with the sequences in major public databases (NCBI, Swiss-Prot, and KEGG). It includes 128 UniGenes related to triterpenoid backbone biosynthesis, 11 OSCs (oxidosqualene cyclases), 233 CYPs (cytochrome P450), and 269 UGTs (UDP-glycosyltransferases). By homology-based blast and phylogenetic analysis with well-characterized genes involved in triterpenoid saponin biosynthesis, 5 OSC s, 14 CYP s, and 1 UGT are further proposed as the most promising candidate genes. Transcriptomic comparison between two Ilex species using blastp and OrthoMCL method reveals high sequence similarity. All OSC s and UGT s as well as most CYP s are classified as orthologous genes, while only 5 CYP s in I. pubescens and 3 CYP s in I. asprella are species-specific. One of OSC candidates, named as IpAS 1, was successfully cloned and expressed in Saccharomyces cerevisiae INV Sc 1. Analysis of the yeast extract by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) shows IpAS 1 is a mixed amyrin synthase, producing α-amyrin and β-amyrin at ratio of 5:1, which is similar to its ortholog IaAS 1 from I. asprella . This study is the first exploration to profile the transcriptome of I. pubescens , the generated data and gene models will facilitate further molecular studies on

  5. Comparative and functional triatomine genomics reveals reductions and expansions in insecticide resistance-related gene families.

    Directory of Open Access Journals (Sweden)

    Lucila Traverso

    2017-02-01

    Full Text Available Triatomine insects are vectors of Trypanosoma cruzi, a protozoan parasite that is the causative agent of Chagas' disease. This is a neglected disease affecting approximately 8 million people in Latin America. The existence of diverse pyrethroid resistant populations of at least two species demonstrates the potential of triatomines to develop high levels of insecticide resistance. Therefore, the incorporation of strategies for resistance management is a main concern for vector control programs. Three enzymatic superfamilies are thought to mediate xenobiotic detoxification and resistance: Glutathione Transferases (GSTs, Cytochromes P450 (CYPs and Carboxyl/Cholinesterases (CCEs. Improving our knowledge of key triatomine detoxification enzymes will strengthen our understanding of insecticide resistance processes in vectors of Chagas' disease.The discovery and description of detoxification gene superfamilies in normalized transcriptomes of three triatomine species: Triatoma dimidiata, Triatoma infestans and Triatoma pallidipennis is presented. Furthermore, a comparative analysis of these superfamilies among the triatomine transcriptomes and the genome of Rhodnius prolixus, also a triatomine vector of Chagas' disease, and other well-studied insect genomes was performed. The expression pattern of detoxification genes in R. prolixus transcriptomes from key organs was analyzed. The comparisons reveal gene expansions in Sigma class GSTs, CYP3 in CYP superfamily and clade E in CCE superfamily. Moreover, several CYP families identified in these triatomines have not yet been described in other insects. Conversely, several groups of insecticide resistance related enzymes within each enzyme superfamily are reduced or lacking in triatomines. Furthermore, our qRT-PCR results showed an increase in the expression of a CYP4 gene in a T. infestans population resistant to pyrethroids. These results could point to an involvement of metabolic detoxification mechanisms

  6. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses

    Directory of Open Access Journals (Sweden)

    Xiaodong Zai

    2017-11-01

    Full Text Available Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular

  7. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

    Science.gov (United States)

    Zai, Xiaodong; Yang, Qiaoling; Yin, Ying; Li, Ruihua; Qian, Mengying; Zhao, Taoran; Li, Yaohui; Zhang, Jun; Fu, Ling; Xu, Junjie; Chen, Wei

    2017-01-01

    Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic

  8. Monitoring studies should consider temporal variability to reveal relations between cyanobacterial abundance and environmental variables

    Directory of Open Access Journals (Sweden)

    JULIANA WOJCIECHOWSKI

    2015-09-01

    Full Text Available One of the main goals of monitoring cyanobacteria blooms in aquatic environments is to reveal the relationship between cyanobacterial abundance and environmental variables. Studies typically correlate data that were simultaneously sampled. However, samplings occur sparsely over time and may not reveal the short-term responses of cyanobacterial abundance to environmental changes. In this study, we tested the hypothesis that stronger cyanobacteria x environment relationships in monitoring are found when the temporal variability of sampling points is incorporated in the statistical analyses. To this end, we investigated relationships between cyanobacteria and seven environmental variables that were sampled twice yearly for three years across 11 reservoirs, and data from an intensive monitoring in one of these reservoirs. Poor correlations were obtained when correlating data simultaneously sampled. In fact, the 'highly recurrent' role of phosphorus in cyanobacteria blooms is not properly observed in all sampling periods. On the other hand, the strongest correlation values for the total phosphorus x cyanobacteria relationship were observed when we used the variation of sampling points. We have also shown that environment variables better explain cyanobacteria when a time lag is considered. We conclude that, in cyanobacteria monitoring, the best approach to reveal determinants of cyanobacteria blooms is to consider environmental variability.

  9. Event related potentials reveal differences between morphological (prefixes) and phonological (syllables) processing of words.

    Science.gov (United States)

    Domínguez, Alberto; Alija, Maira; Cuetos, Fernando; de Vega, Mauel

    2006-11-06

    Behavioral measures in visual priming tasks show opposite effects for syllables and morphemes, which indicate that they are processed by two independent systems. We used event related potentials (ERPs) to explore two priming situations in Spanish: prefix related words (reacción-REFORMA [reaction-reform]), in which prime and target words shared a first syllable that was also a prefix, and syllable related words (regalo-REFORMA [gift-reform.]), in which the shared first syllable was a pseudoprefix in the prime word. Prefix related pairs, unlike syllable related pairs, evoked a very early positivity in reaction to the target (at 150-250ms window), suggesting that the prefix information is immediately available, at a prelexical stage. By contrast, syllable related pairs showed a larger N400 effect. This late negativity may be caused by lateral inhibition among lexical candidates activated in the lexicon by the prime's first syllable.

  10. Google and Women's Health-Related Issues: What Does the Search Engine Data Reveal?

    Science.gov (United States)

    Baazeem, Mazin; Abenhaim, Haim

    2014-01-01

    Identifying the gaps in public knowledge of women's health related issues has always been difficult. With the increasing number of Internet users in the United States, we sought to use the Internet as a tool to help us identify such gaps and to estimate women's most prevalent health concerns by examining commonly searched health-related keywords in Google search engine. We collected a large pool of possible search keywords from two independent practicing obstetrician/gynecologists and classified them into five main categories (obstetrics, gynecology, infertility, urogynecology/menopause and oncology), and measured the monthly average search volume within the United States for each keyword with all its possible combinations using Google AdWords tool. We found that pregnancy related keywords were less frequently searched in general compared to other categories with an average of 145,400 hits per month for the top twenty keywords. Among the most common pregnancy-related keywords was "pregnancy and sex' while pregnancy-related diseases were uncommonly searched. HPV alone was searched 305,400 times per month. Of the cancers affecting women, breast cancer was the most commonly searched with an average of 247,190 times per month, followed by cervical cancer then ovarian cancer. The commonly searched keywords are often issues that are not discussed in our daily practice as well as in public health messages. The search volume is relatively related to disease prevalence with the exception of ovarian cancer which could signify a public fear.

  11. Dependency Network Analysis (DEPNA) Reveals Context Related Influence of Brain Network Nodes.

    Science.gov (United States)

    Jacob, Yael; Winetraub, Yonatan; Raz, Gal; Ben-Simon, Eti; Okon-Singer, Hadas; Rosenberg-Katz, Keren; Hendler, Talma; Ben-Jacob, Eshel

    2016-06-07

    Communication between and within brain regions is essential for information processing within functional networks. The current methods to determine the influence of one region on another are either based on temporal resolution, or require a predefined model for the connectivity direction. However these requirements are not always achieved, especially in fMRI studies, which have poor temporal resolution. We thus propose a new graph theory approach that focuses on the correlation influence between selected brain regions, entitled Dependency Network Analysis (DEPNA). Partial correlations are used to quantify the level of influence of each node during task performance. As a proof of concept, we conducted the DEPNA on simulated datasets and on two empirical motor and working memory fMRI tasks. The simulations revealed that the DEPNA correctly captures the network's hierarchy of influence. Applying DEPNA to the functional tasks reveals the dynamics between specific nodes as would be expected from prior knowledge. To conclude, we demonstrate that DEPNA can capture the most influencing nodes in the network, as they emerge during specific cognitive processes. This ability opens a new horizon for example in delineating critical nodes for specific clinical interventions.

  12. International Baccalaureate as a Litmus Test Revealing Conflicting Values and Power Relations in the Israeli Education System

    Science.gov (United States)

    Yemini, Miri; Dvir, Yuval

    2016-01-01

    This study comprises a comprehensive attempt to reveal the power relations and conflicting interests within the local-global nexus of the Israeli public education system. The perceptions of different stakeholders were explored, in regard to the implementation of the International Baccalaureate Diploma Program as an example of a globally oriented…

  13. Google and Women’s Health-Related Issues: What Does the Search Engine Data Reveal?

    Science.gov (United States)

    Baazeem, Mazin

    2014-01-01

    Objectives Identifying the gaps in public knowledge of women’s health related issues has always been difficult. With the increasing number of Internet users in the United States, we sought to use the Internet as a tool to help us identify such gaps and to estimate women’s most prevalent health concerns by examining commonly searched health-related keywords in Google search engine. Methods We collected a large pool of possible search keywords from two independent practicing obstetrician/gynecologists and classified them into five main categories (obstetrics, gynecology, infertility, urogynecology/menopause and oncology), and measured the monthly average search volume within the United States for each keyword with all its possible combinations using Google AdWords tool. Results We found that pregnancy related keywords were less frequently searched in general compared to other categories with an average of 145,400 hits per month for the top twenty keywords. Among the most common pregnancy-related keywords was “pregnancy and sex’ while pregnancy-related diseases were uncommonly searched. HPV alone was searched 305,400 times per month. Of the cancers affecting women, breast cancer was the most commonly searched with an average of 247,190 times per month, followed by cervical cancer then ovarian cancer. Conclusion The commonly searched keywords are often issues that are not discussed in our daily practice as well as in public health messages. The search volume is relatively related to disease prevalence with the exception of ovarian cancer which could signify a public fear. PMID:25422723

  14. RNA-Seq analysis reveals new evidence for inflammation-related changes in aged kidney

    Science.gov (United States)

    Park, Daeui; Kim, Byoung-Chul; Kim, Chul-Hong; Choi, Yeon Ja; Jeong, Hyoung Oh; Kim, Mi Eun; Lee, Jun Sik; Park, Min Hi; Chung, Ki Wung; Kim, Dae Hyun; Lee, Jaewon; Im, Dong-Soon; Yoon, Seokjoo; Lee, Sunghoon; Yu, Byung Pal; Bhak, Jong; Chung, Hae Young

    2016-01-01

    Age-related dysregulated inflammation plays an essential role as a major risk factor underlying the pathophysiological aging process. To better understand how inflammatory processes are related to aging at the molecular level, we sequenced the transcriptome of young and aged rat kidney using RNA-Seq to detect known genes, novel genes, and alternative splicing events that are differentially expressed. By comparing young (6 months of age) and old (25 months of age) rats, we detected 722 up-regulated genes and 111 down-regulated genes. In the aged rats, we found 32 novel genes and 107 alternatively spliced genes. Notably, 6.6% of the up-regulated genes were related to inflammation (P inflammation-related pathways such as cytokines (P = 4.4 × 10−16), which were found up-regulated in the aged rats. Furthermore, an up-regulated inflammatory gene analysis identified the involvement of transcription factors, such as STAT4, EGR1, and FOSL1, which regulate cancer as well as inflammation in aging processes. Thus, RNA changes in these pathways support their involvement in the pro-inflammatory status during aging. We propose that whole RNA-Seq is a useful tool to identify novel genes and alternative splicing events by documenting broadly implicated inflammation-related genes involved in aging processes. PMID:27153548

  15. Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion

    Directory of Open Access Journals (Sweden)

    Joshua Thomas Cooper

    2016-05-01

    Full Text Available Dinoflagellates are a major component of marine phytoplankton and many species are recognized for their ability to produce harmful algal blooms (HABs. Scrippsiella trochoidea is a non-toxic, marine dinoflagellate that can be found in both cold and tropic waters where it is known to produce red tide events. Little is known about the genomic makeup of S. trochoidea and a transcriptome study was conducted to shed light on the biochemical and physiological adaptations related to nutrient depletion. Cultures were grown under N and P limiting conditions and transcriptomes were generated via RNAseq technology. De novo assembly reconstructed 107,415 putative transcripts of which only 41% could be annotated. No significant transcriptomic response was observed in response to initial P depletion, however, a strong transcriptional response to N depletion was detected. Among the down-regulated pathways were those for glutamine/glutamate metabolism as well as urea and nitrate/nitrite transporters. Transcripts for ammonia transporters displayed both up- and down-regulation, perhaps related to a shift to higher affinity transporters. Genes for the utilization of DON compounds were up-regulated. These included transcripts for amino acids transporters, polyamine oxidase, and extracellular proteinase and peptidases. N depletion also triggered down regulation of transcripts related to the production of Photosystems I & II and related proteins. These data are consistent with a metabolic strategy that conserves N, while maximizing sustained metabolism by emphasizing the relative contribution of organic N sources. Surprisingly, the transcriptome also contained transcripts potentially related to secondary metabolite production, including a homolog to the Short Isoform Saxitoxin gene (sxtA from Alexandrium fundyense, which was significantly up-regulated under N-depletion. A total of 113 unique hits to Sxt genes, covering 17 of the 34 genes found in C. raciborskii were

  16. Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis

    NARCIS (Netherlands)

    Lai, Xuelei; Wichers, Harry J.; Soler-Lopez, Montserrat; Dijkstra, Bauke W.

    2017-01-01

    Tyrosinase-related protein 1 (TYRP1) is one of three tyrosinase-like glycoenzymes in human melanocytes that are key to the production of melanin, the compound responsible for the pigmentation of skin, eye, and hair. Difficulties with producing these enzymes in pure form have hampered the

  17. Atypical Brain Responses to Reward Cues in Autism as Revealed by Event-Related Potentials

    Science.gov (United States)

    Kohls, Gregor; Peltzer, Judith; Schulte-Ruther, Martin; Kamp-Becker, Inge; Remschmidt, Helmut; Herpertz-Dahlmann, Beate; Konrad, Kerstin

    2011-01-01

    Social motivation deficit theories suggest that children with autism do not properly anticipate and appreciate the pleasure of social stimuli. In this study, we investigated event-related brain potentials evoked by cues that triggered social versus monetary reward anticipation in children with autism. Children with autism showed attenuated P3…

  18. PR Perceptions: A Master's Thesis Reveals How Campus Pros View Public Relations--And Their Presidents.

    Science.gov (United States)

    Shoemaker, Donna

    1993-01-01

    A survey of 254 college public relations (PR) officers that focused on their relationships with their presidents is reported, and results are compared with an earlier survey of presidents. Differences in the two groups' perceptions of the PR officer's role in policy formation, lines of authority, and title are highlighted. (MSE)

  19. Inflammation-related alterations of lipids after spinal cord injury revealed by Raman spectroscopy

    Science.gov (United States)

    Tamosaityte, Sandra; Galli, Roberta; Uckermann, Ortrud; Sitoci-Ficici, Kerim H.; Koch, Maria; Later, Robert; Schackert, Gabriele; Koch, Edmund; Steiner, Gerald; Kirsch, Matthias

    2016-06-01

    Spinal cord injury (SCI) triggers several lipid alterations in nervous tissue. It is characterized by extensive demyelination and the inflammatory response leads to accumulation of activated microglia/macrophages, which often transform into foam cells by accumulation of lipid droplets after engulfment of the damaged myelin sheaths. Using an experimental rat model, Raman microspectroscopy was applied to retrieve the modifications of the lipid distribution following SCI. Coherent anti-Stokes Raman scattering (CARS) and endogenous two-photon fluorescence (TPEF) microscopies were used for the detection of lipid-laden inflammatory cells. The Raman mapping of CH2 deformation mode intensity at 1440 cm-1 retrieved the lipid-depleted injury core. Preserved white matter and inflammatory regions with myelin fragmentation and foam cells were localized by specifically addressing the distribution of esterified lipids, i.e., by mapping the intensity of the carbonyl Raman band at 1743 cm-1, and were in agreement with CARS/TPEF microscopy. Principal component analysis revealed that the inflammatory regions are notably rich in saturated fatty acids. Therefore, Raman spectroscopy enabled to specifically detect inflammation after SCI and myelin degradation products.

  20. Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family

    Directory of Open Access Journals (Sweden)

    Nordlund Henri R

    2005-03-01

    Full Text Available Abstract Background A chicken egg contains several biotin-binding proteins (BBPs, whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs and genes available in the NCBI database and chicken genome database using the reported N-terminal amino acid sequences of chicken egg-yolk BBPs as search strings. Results Two separate hits showing significant homology for these N-terminal sequences were discovered. For one of these hits, the chromosomal location in the immediate proximity of the avidin gene family was found. Both of these hits encode proteins having high sequence similarity with avidin suggesting that chicken BBPs are paralogous to avidin family. In particular, almost all residues corresponding to biotin binding in avidin are conserved in these putative BBP proteins. One of the found DNA sequences, however, seems to encode a carboxy-terminal extension not present in avidin. Conclusion We describe here the predicted properties of the putative BBP genes and proteins. Our present observations link BBP genes together with avidin gene family and shed more light on the genetic arrangement and variability of this family. In addition, comparative modelling revealed the potential structural elements important for the functional and structural properties of the putative BBP proteins.

  1. Attentional Selection Accompanied by Eye Vergence as Revealed by Event-Related Brain Potentials.

    Science.gov (United States)

    Sole Puig, Maria; Pallarés, Josep Marco; Perez Zapata, Laura; Puigcerver, Laura; Cañete, Josep; Supèr, Hans

    2016-01-01

    Neural mechanisms of attention allow selective sensory information processing. Top-down deployment of visual-spatial attention is conveyed by cortical feedback connections from frontal regions to lower sensory areas modulating late stimulus responses. A recent study reported the occurrence of small eye vergence during orienting top-down attention. Here we assessed a possible link between vergence and attention by comparing visual event related potentials (vERPs) to a cue stimulus that induced attention to shift towards the target location to the vERPs to a no-cue stimulus that did not trigger orienting attention. The results replicate the findings of eye vergence responses during orienting attention and show that the strength and time of eye vergence coincide with the onset and strength of the vERPs when subjects oriented attention. Our findings therefore support the idea that eye vergence relates to and possibly has a role in attentional selection.

  2. Attentional Selection Accompanied by Eye Vergence as Revealed by Event-Related Brain Potentials.

    Directory of Open Access Journals (Sweden)

    Maria Sole Puig

    Full Text Available Neural mechanisms of attention allow selective sensory information processing. Top-down deployment of visual-spatial attention is conveyed by cortical feedback connections from frontal regions to lower sensory areas modulating late stimulus responses. A recent study reported the occurrence of small eye vergence during orienting top-down attention. Here we assessed a possible link between vergence and attention by comparing visual event related potentials (vERPs to a cue stimulus that induced attention to shift towards the target location to the vERPs to a no-cue stimulus that did not trigger orienting attention. The results replicate the findings of eye vergence responses during orienting attention and show that the strength and time of eye vergence coincide with the onset and strength of the vERPs when subjects oriented attention. Our findings therefore support the idea that eye vergence relates to and possibly has a role in attentional selection.

  3. Genomic profiling reveals Pitx2 controls expression of mature extraocular muscle contraction-related genes.

    Science.gov (United States)

    Zhou, Yuefang; Gong, Bendi; Kaminski, Henry J

    2012-04-18

    To assess the influence of the Pitx2 transcription factor on the global gene expression profile of extraocular muscle (EOM) of mice. Mice with a conditional knockout of Pitx2, designated Pitx2(Δflox/Δflox) and their control littermates Pitx2(flox/flox), were used. RNA was isolated from EOM obtained at 3, 6, and 12 weeks of age and processed for microarray-based profiling. Pairwise comparisons were performed between mice of the same age and differentially expressed gene lists were generated. Select genes from the profile were validated using real-time quantitative polymerase chain reaction and protein immunoblot. Ultrastructural analysis was performed to evaluate EOM sarcomeric structure. The number of differentially expressed genes was relatively small. Eleven upregulated and 23 downregulated transcripts were identified common to all three age groups in the Pitx2-deficient extraocular muscle compared with littermate controls. These fell into a range of categories including muscle-specific structural genes, transcription factors, and ion channels. The differentially expressed genes were primarily related to muscle contraction. We verified by protein and ultrastructural analysis that myomesin 2 was expressed in the Pitx2-deficient mice, and this was associated with development of M lines evident in their orbital region. The global transcript expression analysis uncovered that Pitx2 primarily regulates a relatively select number of genes associated with muscle contraction. Pitx2 loss led to the development of M line structures, a feature more typical of other skeletal muscle.

  4. Error-related negativity in the skilled brain of pianists reveals motor simulation.

    Science.gov (United States)

    Proverbio, Alice Mado; Cozzi, Matteo; Orlandi, Andrea; Carminati, Manuel

    2017-03-27

    Evidences have been provided of a crucial role of multimodal audio-visuomotor processing in subserving the musical ability. In this paper we investigated whether musical audiovisual stimulation might trigger the activation of motor information in the brain of professional pianists, due to the presence of permanent gestures/sound associations. At this aim EEG was recorded in 24 pianists and naive participants engaged in the detection of rare targets while watching hundreds of video clips showing a pair of hands in the act of playing, along with a compatible or incompatible piano soundtrack. Hands size and apparent distance allowed self-ownership and agency illusions, and therefore motor simulation. Event-related potentials (ERPs) and relative source reconstruction showed the presence of an Error-related negativity (ERN) to incongruent trials at anterior frontal scalp sites, only in pianists, with no difference in naïve participants. ERN was mostly explained by an anterior cingulate cortex (ACC) source. Other sources included "hands" IT regions, the superior temporal gyrus (STG) involved in conjoined auditory and visuomotor processing, SMA and cerebellum (representing and controlling motor subroutines), and regions involved in body parts representation (somatosensory cortex, uncus, cuneus and precuneus). The findings demonstrate that instrument-specific audiovisual stimulation is able to trigger error shooting and correction neural responses via motor resonance and mirroring, being a possible aid in learning and rehabilitation. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  5. Immediate relativity: EEG reveals early engagement of comparison in social information processing.

    Science.gov (United States)

    Ohmann, Katharina; Stahl, Jutta; Mussweiler, Thomas; Kedia, Gayannée

    2016-11-01

    A wide array of social decisions relies on social comparisons. As such, these decisions require fast access to relative information. Therefore, we expect that signatures of the comparative process should be observable in electrophysiological components at an early stage of information processing. However, to date, little is known about the neural time course of social target comparisons. Therefore, we tested this hypothesis in 2 electroencephalography (EEG) studies using a social distance effect paradigm. The distance effect capitalizes on the fact that stimuli close on a certain dimension take longer to compare than stimuli clearly differing on this dimension. Here, we manipulated the distance of face characteristics regarding their levels of attractiveness (Study 1) and trustworthiness (Study 2), 2 essential social dimensions. In both studies, size comparisons served as a nonsocial control condition. In Study 1, distance related effects were apparent 170 ms (vertex positive potential, VPP) and 200 ms (N2) after stimulus onset for attractiveness comparisons. In Study 2, trustworthiness comparisons took effect already after 100 ms (N1) and likewise carried over to an event-related N2. Remarkably, we observed a similar temporal pattern for social (attractiveness, trustworthiness) and nonsocial (size) dimensions. These results speak in favor of an early encoding of comparative information and emphasize the primary role of comparison in social information processing. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  6. Space base laser torque applied on LEO satellites of various geometries at satellite’s closest approach

    OpenAIRE

    Khalifa, N.S.

    2013-01-01

    In light of using laser power in space applications, the motivation of this paper is to use a space based solar pumped laser to produce a torque on LEO satellites of various shapes. It is assumed that there is a space station that fires laser beam toward the satellite so the beam spreading due to diffraction is considered to be the dominant effect on the laser beam propagation. The laser torque is calculated at the point of closest approach between the space station and some sun synchronous l...

  7. Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum.

    Science.gov (United States)

    Li, Huie; Fu, Yaru; Sun, Hao; Zhang, Yanfu; Lan, Xiaozhong

    2017-03-06

    Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum, as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.

  8. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

    Science.gov (United States)

    Bredeson, Jessen V; Lyons, Jessica B; Prochnik, Simon E; Wu, G Albert; Ha, Cindy M; Edsinger-Gonzales, Eric; Grimwood, Jane; Schmutz, Jeremy; Rabbi, Ismail Y; Egesi, Chiedozie; Nauluvula, Poasa; Lebot, Vincent; Ndunguru, Joseph; Mkamilo, Geoffrey; Bart, Rebecca S; Setter, Tim L; Gleadow, Roslyn M; Kulakow, Peter; Ferguson, Morag E; Rounsley, Steve; Rokhsar, Daniel S

    2016-05-01

    Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

  9. Second language syntactic processing revealed through event-related potentials: an empirical review.

    Science.gov (United States)

    Caffarra, Sendy; Molinaro, Nicola; Davidson, Doug; Carreiras, Manuel

    2015-04-01

    Learning a second language (L2) can be crucial in the present globalized society. However, reaching the level of L1 performance of native speakers is still a challenge for many. Distinct factors could account for the persistent gap observed between natives' and non-natives' syntactic abilities: L1-L2 differences, AoA, proficiency, L2 immersion duration, L2 training duration. Although different theoretical approaches described the role of these several factors, not all studies using on-line measures have investigated them comprehensively and consistently. The present work reviews available ERP studies on L2 syntactic analysis in order to establish the relative weight of each factor on the time course of L2 processing. Logistic regression analyses were performed on the presence or absence of ERP effects reported in response to L2 syntactic violations, including all the influential factors as categorical independent variables. The results showed that immersion duration has an influence on the ERP correlates linked to early mechanisms of syntactic processing, while the global proficiency level has an impact on the ERP correlates related to late, language-monitoring activity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Quantitative proteomics reveals EVA1A-related proteins involved in neuronal differentiation.

    Science.gov (United States)

    Zhong, Lijun; Zhou, Juntuo; Chen, Xi; Liu, Jiao; Liu, Zhen; Chen, Yingyu; Bai, Yun

    2017-03-01

    EVA1A is an autophagy-related protein, which plays an important role in embryonic neurogenesis. In this study, we found that loss of EVA1A could decrease neural differentiation in the brain of adult Eva1a-/- mice. To determine the mechanism underlying this phenotype, we performed label-free quantitative proteomics and bioinformatics analysis using the brains of Eva1a-/- and wild-type mice. We identified 11 proteins that were up-regulated and 17 that were down-regulated in the brains of the knockout mice compared to the wild-type counterparts. Bioinformatics analysis indicated that biological processes, including ATP synthesis, oxidative phosphorylation, and the TCA cycle, are involved in the EVA1A regulatory network. In addition, gene set enrichment analysis showed that neurodegenerative diseases, such as Alzheimer's disease and Huntington's disease, were strongly associated with Eva1a knockout. Western blot experiments showed changes in the expression of nicotinamide nucleotide transhydrogenase, an important mitochondrial enzyme involved in the TCA cycle, in the brains of Eva1a knockout mice. Our study provides valuable information on the molecular functions and regulatory network of the Eva1a gene, as well as new perspectives on the relationship between autography-related proteins and neural differentiation. © 2017 Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. The molecular signature of AML mesenchymal stromal cells reveals candidate genes related to the leukemogenic process.

    Science.gov (United States)

    Binato, Renata; de Almeida Oliveira, Nathalia Correa; Du Rocher, Barbara; Abdelhay, Eliana

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Comparative proteomic analysis reveals mite (Varroa destructor) resistance-related proteins in Eastern honeybees (Apis cerana).

    Science.gov (United States)

    Ji, T; Shen, F; Liu, Z; Yin, L; Shen, J; Liang, Q; Luo, Y X

    2015-08-21

    The mite (Varroa destructor) has become the greatest threat to apiculture worldwide. As the original host of the mite, Apis cerana can effectively resist the mite. An increased understanding of the resistance mechanisms of Eastern honeybees against V. destructor may help researchers to protect other species against these parasites. In this study, the proteomes of 4 Apis cerana colonies were analyzed using an isobaric tag for relative and absolute quantitation technology. We determined the differences in gene and protein expression between susceptible and resistant colonies that were either unchallenged or challenged by V. destructor. The results showed that a total of 1532 proteins were identified. Gene Ontology enrichment analysis suggested that the transcription factors and basic metabolic and respiratory processes were efficient and feasible factors controlling this resistance, and 12 differentially expressed proteins were identified in Venn analysis. The results were validated by quantitative polymerase chain reaction. This study may provide insight into the genetic mechanisms underlying the resistance of honeybee to mites.

  13. Event-related potentials reveal increased distraction by salient global objects in older adults

    DEFF Research Database (Denmark)

    Wiegand, Iris; Finke, Kathrin; Töllner, Thomas

    search. Older participants detected target stimuli slower and less accurate than younger participants did. ERPs indicated that the general performance decline originated at multiple stages within the information-processing stream, from sensory coding to spatial allocation of attention: The P1......Age-related changes in visual functions influence how older individuals perceive and react upon objects in their environment. In particular, older individuals might be more distracted by highly salient, irrelevant information. Kanizsa figures induce a ‘global precedence’ effect, which reflects...... was decreased, the N1 was enhanced, and the posterior contralateral negativity (PCN) was decreased and delayed in older age. We further found a stronger a global precedence effect in the older group. This was associated with age differences in short-latency ERPs: The younger group showed a more pronounced P1...

  14. Small RNA sequencing reveals metastasis-related microRNAs in lung adenocarcinoma

    DEFF Research Database (Denmark)

    Daugaard, Iben; Venø, Morten T; Yan, Yan

    2017-01-01

    The majority of lung cancer deaths are caused by metastatic disease. MicroRNAs (miRNAs) are posttranscriptional regulators of gene expression and miRNA dysregulation can contribute to metastatic progression. Here, small RNA sequencing was used to profile the miRNA and piwi-interacting RNA (piRNA......) transcriptomes in relation to lung cancer metastasis. RNA-seq was performed using RNA extracted from formalin-fixed paraffin embedded (FFPE) lung adenocarcinomas (LAC) and brain metastases from 8 patients, and LACs from 8 patients without detectable metastatic disease. Impact on miRNA and piRNA transcriptomes...... was subtle with 9 miRNAs and 8 piRNAs demonstrating differential expression between metastasizing and non-metastasizing LACs. For piRNAs, decreased expression of piR-57125 was the most significantly associated with distant metastasis. Validation by RT-qPCR in a LAC cohort comprising 52 patients confirmed...

  15. Preserved reward outcome processing in ASD as revealed by event-related potentials

    Directory of Open Access Journals (Sweden)

    McPartland James C

    2012-07-01

    Full Text Available Abstract Background Problems with reward system function have been posited as a primary difficulty in autism spectrum disorders. The current study examined an electrophysiological marker of feedback monitoring, the feedback-related negativity (FRN, during a monetary reward task. The study advanced prior understanding by focusing exclusively on a developmental sample, applying rigorous diagnostic characterization and introducing an experimental paradigm providing more subtly different feedback valence (reward versus non-reward instead of reward versus loss. Methods Twenty-six children with autism spectrum disorder and 28 typically developing peers matched on age and full-scale IQ played a guessing game resulting in monetary gain (“win” or neutral outcome (“draw”. ERP components marking early visual processing (N1, P2 and feedback appraisal (FRN were contrasted between groups in each condition, and their relationships to behavioral measures of social function and dysfunction, social anxiety, and autism symptomatology were explored. Results FRN was observed on draw trials relative to win trials. Consistent with prior research, children with ASD exhibited a FRN to suboptimal outcomes that was comparable to typical peers. ERP parameters were unrelated to behavioral measures. Conclusions Results of the current study indicate typical patterns of feedback monitoring in the context of monetary reward in ASD. The study extends prior findings of normative feedback monitoring to a sample composed exclusively of children and demonstrates that, as in typical development, individuals with autism exhibit a FRN to suboptimal outcomes, irrespective of neutral or negative valence. Results do not support a pervasive problem with reward system function in ASD, instead suggesting any dysfunction lies in more specific domains, such as social perception, or in response to particular feedback-monitoring contexts, such as self-evaluation of one’s errors.

  16. Phase noise reveals early category-specific modulation of the event-related potentials

    Directory of Open Access Journals (Sweden)

    Kornél eNémeth

    2014-04-01

    Full Text Available Previous studies have found that the amplitude of the early event-related potential (ERP components evoked by faces, such as N170 and P2, changes systematically as a function of noise added to the stimuli. This change has been linked to an increased perceptual processing demand and to enhanced difficulty in perceptual decision making about faces. However, to date it has not yet been tested whether noise manipulation affects the neural correlates of decisions about face and non-face stimuli similarly. To this end, we measured the event-related potentials for faces and cars at three different phase noise levels. Subjects performed the same two-alternative age-discrimination task on stimuli chosen from young-old morphing continua that were created from faces as well as cars and were calibrated to lead to similar performances at each noise-level. Adding phase noise to the stimuli reduced performance and enhanced response latency for the two categories to the same extent. Parallel to that, phase noise reduced the amplitude and prolonged the latency of the face-specific N170 component. The amplitude of the P1 showed category-specific noise dependence: it was enhanced over the right hemisphere for cars and over the left hemisphere for faces as a result of adding phase noise to the stimuli, but remained stable across noise levels for cars over the left and for faces over the right hemisphere. Moreover, noise modulation altered the category-selectivity of the N170, while the P2 ERP component, typically associated with task decision difficulty, was larger for the more noisy stimuli regardless of stimulus category. Our results suggest that the category-specificity of noise-induced modulations of ERP responses starts at around 100 ms post-stimulus.

  17. Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection.

    Science.gov (United States)

    Martinez, Diego A; Oliver, Brian G; Gräser, Yvonne; Goldberg, Jonathan M; Li, Wenjun; Martinez-Rossi, Nilce M; Monod, Michel; Shelest, Ekaterina; Barton, Richard C; Birch, Elizabeth; Brakhage, Axel A; Chen, Zehua; Gurr, Sarah J; Heiman, David; Heitman, Joseph; Kosti, Idit; Rossi, Antonio; Saif, Sakina; Samalova, Marketa; Saunders, Charles W; Shea, Terrance; Summerbell, Richard C; Xu, Jun; Young, Sarah; Zeng, Qiandong; Birren, Bruce W; Cuomo, Christina A; White, Theodore C

    2012-01-01

    The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response.

  18. Expression profiling of CD34+ hematopoietic stem/ progenitor cells reveals distinct subtypes of therapy-related acute myeloid leukemia

    OpenAIRE

    Qian, Zhijian; Fernald, Anthony A.; Godley, Lucy A.; Larson, Richard A.; Le Beau, Michelle M.

    2002-01-01

    One of the most serious consequences of cytotoxic cancer therapy is the development of therapy-related acute myeloid leukemia (t-AML), a neoplastic disorder arising from a multipotential hematopoietic stem cell. To gain insights into the molecular basis of this disease, we performed gene expression profiling of CD34+ hematopoietic progenitor cells from t-AML patients. Our analysis revealed that there are distinct subtypes of t-AML that have a characteristic gene expression pattern. Common to ...

  19. Habitat use of bats in relation to wind turbines revealed by GPS tracking

    Science.gov (United States)

    Roeleke, Manuel; Blohm, Torsten; Kramer-Schadt, Stephanie; Yovel, Yossi; Voigt, Christian C.

    2016-07-01

    Worldwide, many countries aim at countering global climate change by promoting renewable energy. Yet, recent studies highlight that so-called green energy, such as wind energy, may come at environmental costs, for example when wind turbines kill birds and bats. Using miniaturized GPS loggers, we studied how an open-space foraging bat with high collision risk with wind turbines, the common noctule Nyctalus noctula (Schreber, 1774), interacts with wind turbines. We compared actual flight trajectories to correlated random walks to identify habitat variables explaining the movements of bats. Both sexes preferred wetlands but used conventionally managed cropland less than expected based on availability. During midsummer, females traversed the land on relatively long flight paths and repeatedly came close to wind turbines. Their flight heights above ground suggested a high risk of colliding with wind turbines. In contrast, males recorded in early summer commuted straight between roosts and foraging areas and overall flew lower than the operating range of most turbine blades, suggesting a lower collision risk. Flight heights of bats suggest that during summer the risk of collision with wind turbines was high for most studied bats at the majority of currently installed wind turbines. For siting of wind parks, preferred bat habitats and commuting routes should be identified and avoided.

  20. Fluorescent nanodiamond tracking reveals intraneuronal transport abnormalities induced by brain-disease-related genetic risk factors

    Science.gov (United States)

    Haziza, Simon; Mohan, Nitin; Loe-Mie, Yann; Lepagnol-Bestel, Aude-Marie; Massou, Sophie; Adam, Marie-Pierre; Le, Xuan Loc; Viard, Julia; Plancon, Christine; Daudin, Rachel; Koebel, Pascale; Dorard, Emilie; Rose, Christiane; Hsieh, Feng-Jen; Wu, Chih-Che; Potier, Brigitte; Herault, Yann; Sala, Carlo; Corvin, Aiden; Allinquant, Bernadette; Chang, Huan-Cheng; Treussart, François; Simonneau, Michel

    2017-05-01

    Brain diseases such as autism and Alzheimer's disease (each inflicting >1% of the world population) involve a large network of genes displaying subtle changes in their expression. Abnormalities in intraneuronal transport have been linked to genetic risk factors found in patients, suggesting the relevance of measuring this key biological process. However, current techniques are not sensitive enough to detect minor abnormalities. Here we report a sensitive method to measure the changes in intraneuronal transport induced by brain-disease-related genetic risk factors using fluorescent nanodiamonds (FNDs). We show that the high brightness, photostability and absence of cytotoxicity allow FNDs to be tracked inside the branches of dissociated neurons with a spatial resolution of 12 nm and a temporal resolution of 50 ms. As proof of principle, we applied the FND tracking assay on two transgenic mouse lines that mimic the slight changes in protein concentration (∼30%) found in the brains of patients. In both cases, we show that the FND assay is sufficiently sensitive to detect these changes.

  1. Superconducting gravimeters reveal unprecedented details of changes related to volcanic processes

    Science.gov (United States)

    Carbone, Daniele; Greco, Filippo; Cannavò, Flavio

    2017-04-01

    Continuous gravity measurements have been successfully carried out at a number of volcanoes around the world using spring gravimeters. Nevertheless, these instruments do not provide reliable measurements when used in continuous mode for weeks or more, because they are influenced by environmental factors and are subject to instrumental drift. Accordingly, most studies of continuous gravity at active volcanoes have focused on the analysis of changes over time-scales of minutes to a few days. An alternative to spring gravimeters for continuous measurements is given by superconducting gravimeters (SGs) that feature a much higher precision and stability than spring gravimeters. However, even the most portable SGs (e.g., the iGrav® by GWR) are not ideal for installation in the vicinity of active volcanic structures. Indeed, they require AC power at the installation site and some kind of hut or vault to house the instrumentation. At Mt. Etna, the installation of a mini-array of three SGs (distances of 3.5 to 15.5 km from the active craters) was begun in September 2014. To our knowledge, these are the first SGs ever installed on an active volcano. Signals from these instruments show hydrologically-induced components superimposed on small (a few microGal) gravity changes that are related to volcanic processes. Such changes, occurring over periods of minutes to weeks, would not be observable by spring gravimeters due to their intrinsic limitations regarding precision and long-term stability.

  2. Near-infrared spectroscopy can reveal increases in brain activity related to animal-assisted therapy.

    Science.gov (United States)

    Morita, Yuka; Ebara, Fumio; Morita, Yoshimitsu; Horikawa, Etsuo

    2017-08-01

    [Purpose] Previous studies have indicated that animal-assisted therapy can promote recovery of psychological, social, and physiological function in mental disorders. This study was designed as a pilot evaluation of the use of near-infrared spectroscopy to objectively identify changes in brain activity that could mediate the effect of animal-assisted therapy. [Subjects and Methods] The participants were 20 healthy students (10 males and 10 females; age 19-21 years) of the Faculty of Agriculture, Saga University. Participants were shown a picture of a Tokara goat or shack (control) while prefrontal cortical oxygenated haemoglobin levels (representing neural activity) were measured by near-infrared spectroscopy. [Results] The prefrontal cortical near-infrared spectroscopy signal was significantly higher during viewing of the animal picture than during a rest condition or during viewing of the control picture. [Conclusion] Our results suggest that near-infrared spectroscopy can be used to objectively identify brain activity changes during human mentation regarding animals; furthermore, these preliminary results suggest the efficacy of animal-assisted therapy could be related to increased activation of the prefrontal cortex.

  3. Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding.

    Science.gov (United States)

    Laurila, Kirsti; Lähdesmäki, Harri

    2009-01-01

    Detailed knowledge of the mechanisms of transcriptional regulation is essential in understanding the gene expression in its entirety. Transcription is regulated, among other things, by transcription factors that bind to DNA and can enhance or repress the transcription process. If a transcription factor fails to bind to DNA or binds to a wrong DNA region that can cause severe effects to the gene expression, to the cell and even to the individual. The problems in transcription factor binding can be caused by alterations in DNA structure which often occurs when parts of the DNA strands are mutated. An increasing number of the identified disease-related mutations occur in gene regulatory sequences. These regulatory mutations can disrupt transcription factor binding sites or create new ones. We have studied effects of mutations on transcription factor binding affinity computationally. We have compared our results with experimentally verified cases where a mutation in a gene regulatory region either creates a new transcription factor binding site or deletes a previously existing one. We have investigated the statistical properties of the changes on transcription factor binding affinity according to the mutation type. Our analysis shows that the probability of a loss of a transcription factor binding site and a creation of a new one varies remarkably by the mutation type. Our results demonstrate that computational analysis provides valuable information about the effect of mutations on transcription factor binding sites. The analysis results also give a useful test set for in vitro studies of regulatory mutation effects.

  4. Network-based analysis reveals functional connectivity related to internet addiction tendency

    Directory of Open Access Journals (Sweden)

    Tanya eWen

    2016-02-01

    Full Text Available IntroductionPreoccupation and compulsive use of the internet can have negative psychological effects, such that it is increasingly being recognized as a mental disorder. The present study employed network-based statistics to explore how whole-brain functional connections at rest is related to the extent of individual’s level of internet addiction, indexed by a self-rated questionnaire. We identified two topologically significant networks, one with connections that are positively correlated with internet addiction tendency, and one with connections negatively correlated with internet addiction tendency. The two networks are interconnected mostly at frontal regions, which might reflect alterations in the frontal region for different aspects of cognitive control (i.e., for control of internet usage and gaming skills. Next, we categorized the brain into several large regional subgroupings, and found that the majority of proportions of connections in the two networks correspond to the cerebellar model of addiction which encompasses the four-circuit model. Lastly, we observed that the brain regions with the most inter-regional connections associated with internet addiction tendency replicate those often seen in addiction literature, and is corroborated by our meta-analysis of internet addiction studies. This research provides a better understanding of large-scale networks involved in internet addiction tendency and shows that pre-clinical levels of internet addiction are associated with similar regions and connections as clinical cases of addiction.

  5. Jumping Stand Apparatus Reveals Rapidly Specific Age-Related Cognitive Impairments in Mouse Lemur Primates.

    Directory of Open Access Journals (Sweden)

    Jean-Luc Picq

    Full Text Available The mouse lemur (Microcebus murinus is a promising primate model for investigating normal and pathological cerebral aging. The locomotor behavior of this arboreal primate is characterized by jumps to and from trunks and branches. Many reports indicate insufficient adaptation of the mouse lemur to experimental devices used to evaluate its cognition, which is an impediment to the efficient use of this animal in research. In order to develop cognitive testing methods appropriate to the behavioral and biological traits of this species, we adapted the Lashley jumping stand apparatus, initially designed for rats, to the mouse lemur. We used this jumping stand apparatus to compare performances of young (n = 12 and aged (n = 8 adults in acquisition and long-term retention of visual discriminations. All mouse lemurs completed the tasks and only 25 trials, on average, were needed to master the first discrimination problem with no age-related differences. A month later, all mouse lemurs made progress for acquiring the second discrimination problem but only the young group reached immediately the criterion in the retention test of the first discrimination problem. This study shows that the jumping stand apparatus allows rapid and efficient evaluation of cognition in mouse lemurs and demonstrates that about half of the old mouse lemurs display a specific deficit in long-term retention but not in acquisition of visual discrimination.

  6. Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information.

    Science.gov (United States)

    Li, Xiao; Dunn, Jessilyn; Salins, Denis; Zhou, Gao; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Perelman, Dalia; Colbert, Elizabeth; Runge, Ryan; Rego, Shannon; Sonecha, Ria; Datta, Somalee; McLaughlin, Tracey; Snyder, Michael P

    2017-01-01

    A new wave of portable biosensors allows frequent measurement of health-related physiology. We investigated the use of these devices to monitor human physiological changes during various activities and their role in managing health and diagnosing and analyzing disease. By recording over 250,000 daily measurements for up to 43 individuals, we found personalized circadian differences in physiological parameters, replicating previous physiological findings. Interestingly, we found striking changes in particular environments, such as airline flights (decreased peripheral capillary oxygen saturation [SpO2] and increased radiation exposure). These events are associated with physiological macro-phenotypes such as fatigue, providing a strong association between reduced pressure/oxygen and fatigue on high-altitude flights. Importantly, we combined biosensor information with frequent medical measurements and made two important observations: First, wearable devices were useful in identification of early signs of Lyme disease and inflammatory responses; we used this information to develop a personalized, activity-based normalization framework to identify abnormal physiological signals from longitudinal data for facile disease detection. Second, wearables distinguish physiological differences between insulin-sensitive and -resistant individuals. Overall, these results indicate that portable biosensors provide useful information for monitoring personal activities and physiology and are likely to play an important role in managing health and enabling affordable health care access to groups traditionally limited by socioeconomic class or remote geography.

  7. Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

    KAUST Repository

    Matsuda, Shayle B.

    2017-03-01

    Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

  8. Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.

    Science.gov (United States)

    Kevorkian, Richard; Bird, Jordan T; Shumaker, Alexander; Lloyd, Karen G

    2018-01-01

    The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae , which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio , Desulfobacter , and Desulfobacterium , increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates

  9. The sound-induced flash illusion reveals dissociable age-related effects in multisensory integration

    Directory of Open Access Journals (Sweden)

    David P. Mcgovern

    2014-09-01

    Full Text Available While ageing can lead to significant declines in perceptual and cognitive function, the effects of age on multisensory integration, the process in which the brain combines information across the senses, are less clear. Recent reports suggest that older adults are susceptible to the sound-induced flash illusion (Shams et al., 2000 across a much wider range of temporal asynchronies than younger adults (Setti et al., 2011. To assess whether this cost for multisensory integration is a general phenomenon of combining asynchronous audiovisual input, we compared the time courses of two variants of the sound-induced flash illusion in young and older adults: the fission illusion, where one flash accompanied by two beeps appears as two flashes, and the fusion illusion, where two flashes accompanied by one beep appears as one flash. Twenty-five younger (18-30 years and older (65+ years adults were required to report whether they perceived one or two flashes, whilst ignoring irrelevant auditory beeps, in bimodal trials where auditory and visual stimuli were separated by one of six stimulus onset asynchronies (SOAs. There was a marked difference in the pattern of results for the two variants of the illusion. In conditions known to produce the fission illusion, older adults were significantly more susceptible to the illusion at longer SOAs compared to younger participants. In contrast, the performance of the younger and older groups was almost identical in conditions known to produce the fusion illusion. This surprising difference between sound-induced fission and fusion in older adults suggests dissociable age-related effects in multisensory integration, consistent with the idea that these illusions are mediated by distinct neural mechanisms.

  10. Good vibrations? Vibrotactile self-stimulation reveals anticipation of body-related action effects in motor control.

    Science.gov (United States)

    Pfister, Roland; Janczyk, Markus; Gressmann, Marcel; Fournier, Lisa R; Kunde, Wilfried

    2014-03-01

    Previous research suggests that motor actions are intentionally generated by recollecting their sensory consequences. Whereas this has been shown to apply to visual or auditory consequences in the environment, surprisingly little is known about the contribution of immediate, body-related consequences, such as proprioceptive and tactile reafferences. Here, we report evidence for a contribution of vibrotactile reafferences to action selection by using a response-effect compatibility paradigm. More precisely, anticipating actions to cause spatially incompatible vibrations delayed responding to a small but reliable degree. Whereas this observation suggests functional equivalence of body-related and environment-related reafferences to action control, the future application of the described experimental procedure might reveal functional peculiarities of specific types of sensory consequences in action control.

  11. Clean, Logistically Light Access to Explore the Closest Places on Earth to Europa and Enceladus

    Science.gov (United States)

    Winebrenner, D. P.; Elam, W. T.; Kintner, P. M. S.; Tyler, S.; Selker, J. S.

    2016-12-01

    At present, the logistical costs of ice drilling to depths of kilometers severely limit sampling and measurements beneath ice sheets. Thus only a tiny fraction of the 400 known subglacial lakes beneath the Antarctic Ice Sheet can ever be sampled by drilling, and study of large lakes may be limited to observations at one or, at best, a few sites. Antarctic lakes are likely highly diverse in their geochemical and geothermal fluxes, the timing and duration of their glaciations, and other characteristics. They constitute a remarkable collection of natural laboratories for learning biogeochemistries and adaptations of subglacial life on Earth. Moreover, they are arguably Earth-analogs to ice-covered seas on Europa and Enceladus, closer not only in relative terms than other analogs, but also usefully close in absolute terms for learning solar-system-wide features of ice-covered seas. It is therefore essential to sample Antarctic lakes with enough range and density, in space and time, to gain better understanding of their workings than drilling alone can provide. The logistics of thermal melt probes makes them attractive, provided that key limitations can be overcome. In particular, melt probes from the 1960s through the 1990s were unreliable, all halted in their descents by electrical failures at high voltages (which are necessary for efficient power use). Moreover, the hole above a classical melt probe refreezes, so neither samples nor the probe itself can be recovered. Here we report progress in overcoming both of these limitations with modern materials and components for reliable high-voltage operation. We have demonstrated in Greenland a 6.5 cm-diameter melt probe operating at 1050V/2.15 kW (electrical) that descended at 2.4 m/hr to 80 m depth in 2013, and after restarting in 2014, to 400 m depth, where we turned it off. We also operated a probe at 2000V/4.5 kW in 2014, which descended at 6.6 m/hr (according to a validated engineering model). These results are the

  12. Acceptance and need for approval as moderators of self-esteem and satisfaction with a romantic relationship or closest friendship.

    Science.gov (United States)

    Cramer, Duncan

    2003-09-01

    According to predictions of self-esteem theorists, the association between self-esteem and satisfaction with a relationship will be negative under perceptions of high acceptance and positive under perceptions of low acceptance; consistency theorists make the opposite prediction. The author primarily sought to test those predictions. By completing 4 measures, 88 female and 62 male students described their main current romantic relationship (defined as being in love and physically intimate), and 54 female and 32 male students described their relationship with their closest friend. Results supported only the self-esteem predictions for the romantic relationship. Contrary to this perspective, need for approval did not mediate this effect. In addition, self-esteem was significantly and positively correlated with satisfaction with the romantic relationship under high but not low need for approval.

  13. Using vis-NIR to predict soil organic carbon and clay at national scale: validation of geographically closest resampling strategy

    DEFF Research Database (Denmark)

    Peng, Yi; Knadel, Maria; Greve, Mette Balslev

    2016-01-01

    with the uncertainties of traditional laboratory wet chemistry analysis. However, for organic soils (48 samples SOC >7%) originating from wetland or forested areas the SOC predictions were generally under-estimated and not satisfactory. For prediction of clay content, only 12 out of 442 predictions were unsatisfactory......The Danish soil visible-near infrared (vis-NIR) spectral library has proved capable of predicting soil properties in Denmark such as soil organic carbon (SOC) at field scale using the geographically closest resampling strategy. However, this strategy has only been tested on one Danish local field....../farm and for future application it is necessary to extend this approach to all types of Danish soils and evaluate the predictive capabilities of the library at national scale. In the present study, partial least squares regression was used to develop models and predict topsoil SOC (490 samples) and clay contents (442...

  14. Measuring the masses of the habitable planets around the 50 closest solar-type stars with Theia

    Science.gov (United States)

    Malbet, Fabien; Leger, Alain; Anglada-Escude, Guillem; Sozzetti, Alessandro; Crouzier, Antooine; Theia Consortium

    2015-07-01

    A major goal of exoplanetary science is the search for possible biosignatures on planets where life similar to ours would have emerged and modified the atmosphere. These planets can be detected by remote sensing using spectroscopic observation of O2, O3, H2O, CO2, and CH4 gases, but in the present context of funding, only missions in the range B$1-2 are seen as feasible for the next decades. This cost cap imposes serious constraints on the number of accessible targets limiting the exploration to the 20 nearest systems with space coronagraphy in the visible wavelength range and 40 systems with space interferometers working in thermal IR. It is thus imperative that promising target be identified ahead of time, to minimize several classes of risks intrinsic to the 'blind search' approach. Furthermore, the masses and the three-dimensional orbits of such habitable planets are key elements for deriving exobiological statements in the future, even the most basic ones. The mission called Theia has been submitted to the ESA call for M4 mission in 2015. Theia is a space observatory able to carry out high precision differential astrometry at the sub-microarcsecond level that allows mass determination of Earth-mass habitable planets around the 50 closest Solar-type stars using 15 - 20 % of the time of a three years mission. Theia is a single telescope designed to perform high accuracy astrometry using interferometric calibration and operating in L2. We will present the mission and its capability to measure the mass and orbit characteristics of the 50 closest planetary systems down to the Earth mass in the habitable zone of solar-type stars.

  15. Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance.

    Science.gov (United States)

    Castro-Severyn, Juan; Remonsellez, Francisco; Valenzuela, Sandro L; Salinas, Cesar; Fortt, Jonathan; Aguilar, Pablo; Pardo-Esté, Coral; Dorador, Cristina; Quatrini, Raquel; Molina, Franck; Aguayo, Daniel; Castro-Nallar, Eduardo; Saavedra, Claudia P

    2017-01-01

    The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.

  16. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

    Directory of Open Access Journals (Sweden)

    Siragusa Gregory R

    2011-06-01

    Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

  17. Extroversion-related differences in speed of premotor and motor processing as revealed by lateralized readiness potentials.

    Science.gov (United States)

    Stahl, Jutta; Rammsayer, Thomas

    2008-03-01

    To further elucidate extroversion-related differences in speed of sensorimotor processing, the authors obtained behavioral and psychophysiological measures as participants (16 introverts and 16 extroverts) performed a visual go/no-go task. Although no extroversion-related differences in reaction time emerged, introverts showed faster premotor processing but slower central and peripheral motor processing--as indicated by latencies of the lateralized readiness potential (LRP) and electromyographic (EMG) data, respectively--than extroverts did. Additional regression analyses revealed that stimulus-locked LRP latency, response-locked LRP latency, and Nl EMG amplitude accounted for 40% of overall variability in individual extroversion scores. On the basis of the present results, the authors introduce a compensation hypothesis that accounts for the common failure of researchers to demonstrate extroversion-related differences in reaction time. The present results challenge J. Brebner and C. Cooper's (1985) model of extroversion in which stimulus analysis is not slower in introverts than in extroverts. However, the present findings support the assumption of faster motor processing in extroverts.

  18. An Essential Role for Coagulase in Staphylococcus aureus Biofilm Development Reveals New Therapeutic Possibilities for Device-Related Infections.

    Science.gov (United States)

    Zapotoczna, Marta; McCarthy, Hannah; Rudkin, Justine K; O'Gara, James P; O'Neill, Eoghan

    2015-12-15

    High-level resistance to antimicrobial drugs is a major factor in the pathogenesis of chronic Staphylococcus aureus biofilm-associated, medical device-related infections. Antimicrobial susceptibility analysis revealed that biofilms grown for ≤ 24 hours on biomaterials conditioned with human plasma under venous shear in iron-free cell culture medium were significantly more susceptible to antistaphylococcal antibiotics. Biofilms formed under these physiologically relevant conditions were regulated by SaeRS and dependent on coagulase-catalyzed conversion of fibrinogen into fibrin. In contrast, SarA-regulated biofilms formed on uncoated polystyrene in nutrient-rich bacteriological medium were mediated by the previously characterized biofilm factors poly-N-acetyl glucosamine, fibronectin-binding proteins, or autolytic activity and were antibiotic resistant. Coagulase-mediated biofilms exhibited increased antimicrobial resistance over time (>48 hours) but were always susceptible to dispersal by the fibrinolytic enzymes plasmin or nattokinase. Biofilms recovered from infected central venous catheters in a rat model of device-related infection were dispersed by nattokinase, supporting the important role of the biofilm phenotype and identifying a potentially new therapeutic approach with antimicrobials and fibrinolytic drugs, particularly during the early stages of device-related infection. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. [Severe alveolar haemorrhage related to a silicone embolism syndrome revealed by a chronic penis ulcer: A case report].

    Science.gov (United States)

    Réveillon, M; Carré, D; Plaquevent, M; Alsubaiei, F; Midhat, M; Alcaix, D; Plantier, F; Dupin, N; Terrier, B; Guillevin, L; Bravard, P

    2016-07-01

    Silicone injections, in particular illegal injections, carried out in an aesthetic purpose, can cause serious complications, like silicone embolism syndrome. We present a 39-year-old man who presented with a severe acute respiratory distress syndrome related to an alveolar hemorrhage associated with a persistent penis ulcer and a genital lymphedema. It was the complications of silicone injections which revealed a severe personality disorder. Diagnosis of silicone embolism syndrome was made, a few years later, thanks to the histopathology study of a persistent penis ulcer with genital lymphedema. The outcome was favorable. A serious alveolar hemorrhage in a young patient should raise suspicion of silicone embolism syndrome, especially if there are cutaneous lesions compatible with injections. Copyright © 2015 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

  20. LiDAR-IMU Time Delay Calibration Based on Iterative Closest Point and Iterated Sigma Point Kalman Filter.

    Science.gov (United States)

    Liu, Wanli

    2017-03-08

    The time delay calibration between Light Detection and Ranging (LiDAR) and Inertial Measurement Units (IMUs) is an essential prerequisite for its applications. However, the correspondences between LiDAR and IMU measurements are usually unknown, and thus cannot be computed directly for the time delay calibration. In order to solve the problem of LiDAR-IMU time delay calibration, this paper presents a fusion method based on iterative closest point (ICP) and iterated sigma point Kalman filter (ISPKF), which combines the advantages of ICP and ISPKF. The ICP algorithm can precisely determine the unknown transformation between LiDAR-IMU; and the ISPKF algorithm can optimally estimate the time delay calibration parameters. First of all, the coordinate transformation from the LiDAR frame to the IMU frame is realized. Second, the measurement model and time delay error model of LiDAR and IMU are established. Third, the methodology of the ICP and ISPKF procedure is presented for LiDAR-IMU time delay calibration. Experimental results are presented that validate the proposed method and demonstrate the time delay error can be accurately calibrated.

  1. Space base laser torque applied on LEO satellites of various geometries at satellite’s closest approach

    Directory of Open Access Journals (Sweden)

    N.S. Khalifa

    2013-12-01

    Full Text Available In light of using laser power in space applications, the motivation of this paper is to use a space based solar pumped laser to produce a torque on LEO satellites of various shapes. It is assumed that there is a space station that fires laser beam toward the satellite so the beam spreading due to diffraction is considered to be the dominant effect on the laser beam propagation. The laser torque is calculated at the point of closest approach between the space station and some sun synchronous low Earth orbit cubesats. The numerical application shows that space based laser torque has a significant contribution on the LEO cubesats. It has a maximum value in the order of 10−8 Nm which is comparable with the residual magnetic moment. However, it has a minimum value in the order 10−11 Nm which is comparable with the aerodynamic and gravity gradient torque. Consequently, space based laser torque can be used as an active attitude control system.

  2. A Heuristic Algorithm for Constrained Multi-Source Location Problem with Closest Distance under Gauge: The Variational Inequality Approach

    Directory of Open Access Journals (Sweden)

    Jian-Lin Jiang

    2013-01-01

    Full Text Available This paper considers the locations of multiple facilities in the space , with the aim of minimizing the sum of weighted distances between facilities and regional customers, where the proximity between a facility and a regional customer is evaluated by the closest distance. Due to the fact that facilities are usually allowed to be sited in certain restricted areas, some locational constraints are imposed to the facilities of our problem. In addition, since the symmetry of distances is sometimes violated in practical situations, the gauge is employed in this paper instead of the frequently used norms for measuring both the symmetric and asymmetric distances. In the spirit of the Cooper algorithm (Cooper, 1964, a new location-allocation heuristic algorithm is proposed to solve this problem. In the location phase, the single-source subproblem with regional demands is reformulated into an equivalent linear variational inequality (LVI, and then, a projection-contraction (PC method is adopted to find the optimal locations of facilities, whereas in the allocation phase, the regional customers are allocated to facilities according to the nearest center reclassification (NCR. The convergence of the proposed algorithm is proved under mild assumptions. Some preliminary numerical results are reported to show the effectiveness of the new algorithm.

  3. Proteomic Analysis Reveals the Deregulation of Inflammation-Related Proteins in Acupuncture-Treated Rats with Asthma Onset

    Directory of Open Access Journals (Sweden)

    Yu-Dong Xu

    2012-01-01

    Full Text Available Although the beneficial effects of acupuncture in asthma treatment have been well documented, little is known regarding the biological basis of this treatment. Changes in the lung proteome of acupuncture-treated rats with asthma onset were comparatively analyzed using a two-dimensional gel electrophoresis (2DE and mass-spectrometry- (MS- based proteomic approach. Acupuncture on specific acupuncture points appeared to improve respiratory function and reduce the total number of leukocytes and eosinophils in bronchoalveolar lavage fluid in OVA-induced asthma onset. Image analysis of 2DE gels revealed 32 differentially expressed acupuncture-specific protein spots in asthma onset; 30 of which were successfully identified as 28 unique proteins using LC-MS/MS. Bioinformatic analyses indicated that these altered proteins are most likely involved in inflammation-related biological functions, and the functional associations of these proteins result in an inflammation signaling pathway. Acupuncture regulates the pathway at different levels by regulating several key nodal proteins, including downregulating of proinflammatory proteins (e.g., S100A8, RAGE, and S100A11 and upregulating of anti-inflammatory proteins (e.g., CC10, ANXA5, and sRAGE. These deregulated inflammation-related proteins may mediate, at least in part, the antiasthmatic effect of acupuncture. Further functional investigation of these acupuncture-specific effector proteins could identify new drug candidates for the prophylaxis and treatment of asthma.

  4. Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure.

    Science.gov (United States)

    Fleming, Damarius S; Weigend, Steffen; Simianer, Henner; Weigend, Annett; Rothschild, Max; Schmidt, Carl; Ashwell, Chris; Persia, Mike; Reecy, James; Lamont, Susan J

    2017-05-05

    Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions. Copyright © 2017 Fleming et al.

  5. Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

    Directory of Open Access Journals (Sweden)

    Damarius S. Fleming

    2017-05-01

    Full Text Available Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST, integrated haplotype score (iHS, and runs of homozygosity (ROH procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27 and Northern European (chromosome 2 birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population’s indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.

  6. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Jinxiong Shen

    2017-04-01

    Full Text Available Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L. salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS to identify salt tolerance-related quantitative trait loci (QTL. A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21–9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.

  7. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.).

    Science.gov (United States)

    Wan, Heping; Chen, Lunlin; Guo, Jianbin; Li, Qun; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

    2017-01-01

    Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.

  8. The Epoch of the First Star Formation in the Closest Metal-Poor Blue Compact Dwarf Galaxy UGC 4483

    Science.gov (United States)

    Aloisi, Alessandra

    2017-08-01

    Metal-poor Blue Compact Dwarf (BCD) galaxies have been interpreted as nearby galaxies in formation. This view has been challenged by HST detection of Red Giant Branch (RGB) stars in all metal-poor BCDs where an RGB tip (TRGB, brightest RGB phase) has been searched for, impling the presence of stars at least 1 Gyr old. Due to the age-metallicity degeneracy, the RGB color provides little insight into the exact star formation history (SFH) beyond 1 Gyr. So, the first SF epoch may have occurred anywhere between 13 and 1 Gyr ago. To resolve this, it is necessary to reach features in the color-magnitude diagram (CMD) that are much fainter than the TRGB. Here we propose new WFC3/UVIS observations (with ACS/WFC in parallel) of the closest metal-poor BCD, UGC 4483. These data will yield an I vs. V-I CMD that goes 4 mag deeper than the TRGB allowing to detect red clump (RC) and horizontal branch (HB) stars. Variable stars of RR Lyrae type will also be detected. With their mere presence, these variables will indisputably prove the existence of a population at least 10 Gyr old. Apparent mag and width of RC, HB and RGB will independently constrain age and metallicity of the old/evolved stars, the presence of multiple SF episodes, their duration and metallicity spread. This deep crowded-field photometric project is only possible with HST. Due to UGC 4483 location in CVZ, it can be done in half the number of orbits that it would otherwise take. Since UGC 4483 is so close, it may be the only BCD for which these questions can be answered in the near future. It provides our best chance for learning about the true cosmological age and evolutionary state of these enigmatic galaxies.

  9. Novel fusion for hybrid optical/microcomputed tomography imaging based on natural light surface reconstruction and iterated closest point

    Science.gov (United States)

    Ning, Nannan; Tian, Jie; Liu, Xia; Deng, Kexin; Wu, Ping; Wang, Bo; Wang, Kun; Ma, Xibo

    2014-02-01

    In mathematics, optical molecular imaging including bioluminescence tomography (BLT), fluorescence tomography (FMT) and Cerenkov luminescence tomography (CLT) are concerned with a similar inverse source problem. They all involve the reconstruction of the 3D location of a single/multiple internal luminescent/fluorescent sources based on 3D surface flux distribution. To achieve that, an accurate fusion between 2D luminescent/fluorescent images and 3D structural images that may be acquired form micro-CT, MRI or beam scanning is extremely critical. However, the absence of a universal method that can effectively convert 2D optical information into 3D makes the accurate fusion challengeable. In this study, to improve the fusion accuracy, a new fusion method for dual-modality tomography (luminescence/fluorescence and micro-CT) based on natural light surface reconstruction (NLSR) and iterated closest point (ICP) was presented. It consisted of Octree structure, exact visual hull from marching cubes and ICP. Different from conventional limited projection methods, it is 360° free-space registration, and utilizes more luminescence/fluorescence distribution information from unlimited multi-orientation 2D optical images. A mouse mimicking phantom (one XPM-2 Phantom Light Source, XENOGEN Corporation) and an in-vivo BALB/C mouse with implanted one luminescent light source were used to evaluate the performance of the new fusion method. Compared with conventional fusion methods, the average error of preset markers was improved by 0.3 and 0.2 pixels from the new method, respectively. After running the same 3D internal light source reconstruction algorithm of the BALB/C mouse, the distance error between the actual and reconstructed internal source was decreased by 0.19 mm.

  10. Diminished social reward anticipation in the broad autism phenotype as revealed by event-related brain potentials.

    Science.gov (United States)

    Cox, Anthony; Kohls, Gregor; Naples, Adam J; Mukerji, Cora E; Coffman, Marika C; Rutherford, Helena J V; Mayes, Linda C; McPartland, James C

    2015-10-01

    Diminished responsivity to reward incentives is a key contributor to the social-communication problems seen in autism spectrum disorders (ASDs). Social motivation theories suggest that individuals with ASD do not experience social interactions as rewarding, leading to negative consequences for the development of brain circuitry subserving social information. In this study, we examined neural responses to social and non-social reward anticipation in 35 typically developing young adults, examining modulation of reward sensitivity by level of autistic traits. Using an Event-related potential incentive-delay task incorporating novel, more ecologically valid forms of reward, higher expression of autistic traits was associated with an attenuated P3 response to the anticipation of social (simulated real-time video feedback from an observer), but not non-social (candy), rewards. Exploratory analyses revealed that this was unrelated to mentalizing ability. The P3 component reflects motivated attention to reward signals, suggesting attenuated motivation allocation specific to social incentives. The study extends prior findings of atypical reward anticipation in ASD, demonstrating that attenuated social reward responsiveness extends to autistic traits in the range of typical functioning. Results support the development of innovative paradigms for investigating social and non-social reward responsiveness. Insight into vulnerabilities in reward processing is critical for understanding social function in ASD. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  11. RAP-PCR fingerprinting reveals time-dependent expression of development-related genes following differentiation process of Bacillus thuringiensis.

    Science.gov (United States)

    Huang, Tianpei; Yu, Xiaomin; Gelbič, Ivan; Guan, Xiong

    2015-09-01

    Gene expression profiles are important data to reveal the functions of genes putatively involved in crucial biological processes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and specifically primed reverse transcription polymerase chain reaction (RT-PCR) were combined to screen differentially expressed genes following development of a commercial Bacillus thuringiensis subsp. kurstaki strain 8010 (serotype 3a3b). Six differentially expressed transcripts (RAP1 to RAP6) were obtained. RAP1 encoded a putative triple helix repeat-containing collagen or an exosporium protein H related to spore pathogenicity. RAP2 was homologous to a ClpX protease and an ATP-dependent protease La (LonB), which likely acted as virulence factors. RAP3 was homologous to a beta subunit of propionyl-CoA carboxylase required for the development of Myxococcus xanthus. RAP4 had homology to a quinone oxidoreductase involved in electron transport and ATP formation. RAP5 showed significant homology to a uridine kinase that mediates phosphorylation of uridine and azauridine. RAP6 shared high sequence identity with 3-methyl-2-oxobutanoate-hydroxymethyltransferase (also known as ketopantoate hydroxymethyltransferase or PanB) involved in the operation of the tricarboxylic acid cycle. The findings described here would help to elucidate the molecular mechanisms underlying the differentiation process of B. thuringiensis and unravel novel pathogenic genes.

  12. Metabolic and transcriptomic analysis of Huntington’s disease model reveal changes in intracellular glucose levels and related genes

    Directory of Open Access Journals (Sweden)

    Gepoliano Chaves

    2017-08-01

    Full Text Available Huntington’s Disease (HD is a neurodegenerative disorder caused by an expansion in a CAG-tri-nucleotide repeat that introduces a poly-glutamine stretch into the huntingtin protein (mHTT. Mutant huntingtin (mHTT has been associated with several phenotypes including mood disorders and depression. Additionally, HD patients are known to be more susceptible to type II diabetes mellitus (T2DM, and HD mice model develops diabetes. However, the mechanism and pathways that link Huntington’s disease and diabetes have not been well established. Understanding the underlying mechanisms can reveal potential targets for drug development in HD. In this study, we investigated the transcriptome of mHTT cell populations alongside intracellular glucose measurements using a functionalized nanopipette. Several genes related to glucose uptake and glucose homeostasis are affected. We observed changes in intracellular glucose concentrations and identified altered transcript levels of certain genes including Sorcs1, Hh-II and Vldlr. Our data suggest that these can be used as markers for HD progression. Sorcs1 may not only have a role in glucose metabolism and trafficking but also in glutamatergic pathways affecting trafficking of synaptic components.

  13. Metabolic and transcriptomic analysis of Huntington's disease model reveal changes in intracellular glucose levels and related genes.

    Science.gov (United States)

    Chaves, Gepoliano; Özel, Rıfat Emrah; Rao, Namrata V; Hadiprodjo, Hana; Costa, Yvonne Da; Tokuno, Zachary; Pourmand, Nader

    2017-08-01

    Huntington's Disease (HD) is a neurodegenerative disorder caused by an expansion in a CAG-tri-nucleotide repeat that introduces a poly-glutamine stretch into the huntingtin protein (mHTT). Mutant huntingtin (mHTT) has been associated with several phenotypes including mood disorders and depression. Additionally, HD patients are known to be more susceptible to type II diabetes mellitus (T2DM), and HD mice model develops diabetes. However, the mechanism and pathways that link Huntington's disease and diabetes have not been well established. Understanding the underlying mechanisms can reveal potential targets for drug development in HD. In this study, we investigated the transcriptome of mHTT cell populations alongside intracellular glucose measurements using a functionalized nanopipette. Several genes related to glucose uptake and glucose homeostasis are affected. We observed changes in intracellular glucose concentrations and identified altered transcript levels of certain genes including Sorcs1, Hh-II and Vldlr. Our data suggest that these can be used as markers for HD progression. Sorcs1 may not only have a role in glucose metabolism and trafficking but also in glutamatergic pathways affecting trafficking of synaptic components.

  14. Expression profiling of CD34+ hematopoietic stem/ progenitor cells reveals distinct subtypes of therapy-related acute myeloid leukemia.

    Science.gov (United States)

    Qian, Zhijian; Fernald, Anthony A; Godley, Lucy A; Larson, Richard A; Le Beau, Michelle M

    2002-11-12

    One of the most serious consequences of cytotoxic cancer therapy is the development of therapy-related acute myeloid leukemia (t-AML), a neoplastic disorder arising from a multipotential hematopoietic stem cell. To gain insights into the molecular basis of this disease, we performed gene expression profiling of CD34(+) hematopoietic progenitor cells from t-AML patients. Our analysis revealed that there are distinct subtypes of t-AML that have a characteristic gene expression pattern. Common to each of the subgroups are gene expression patterns typical of arrested differentiation in early progenitor cells. Leukemias with a -5/del(5q) have a higher expression of genes involved in cell cycle control (CCNA2, CCNE2, CDC2), checkpoints (BUB1), or growth (MYC), and loss of expression of the gene encoding IFN consensus sequence-binding protein (ICSBP). A second subgroup of t-AML is characterized by down-regulation of transcription factors involved in early hematopoiesis (TAL1, GATA1, and EKLF) and overexpression of proteins involved in signaling pathways in myeloid cells (FLT3) and cell survival (BCL2). Establishing the molecular pathways involved in t-AML may facilitate the identification of selectively expressed genes that can be exploited for the development of urgently needed targeted therapies.

  15. Close pairs of relative equilibria for identical point vortices

    DEFF Research Database (Denmark)

    Dirksen, Tobias; Aref, Hassan

    2011-01-01

    Numerical solution of the classical problem of relative equilibria for identical point vortices on the unbounded plane reveals configurations that are very close to the analytically known, centered, symmetrically arranged, nested equilateral triangles. New numerical solutions of this kind are found...... also has this property, and new relative equilibria close to the nested, symmetrically arranged, regular heptagons have been found. The centered regular nonagon is also marginally stable. Again, a new family of close relative equilibria has been found. The closest relative equilibrium pairs occur...

  16. Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae as revealed by RAPD fingerprinting

    Directory of Open Access Journals (Sweden)

    El-Bous, M.

    2011-12-01

    Full Text Available Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae as revealed by RAPD fingerprinting.- This investigation was carried out to assess the taxonomic relationships among eight taxa of the Egyptian members of Capparaceae based on random amplified polymorphic DNA markers, and to compare the results with those obtained from morphological studies. A total of 46 bands were scored for three RAPD primers corresponding to an average of 15.3 bands per primer. The three primers (A03, A07 and A09 revealed eight polymorphic RAPD markers among the studied taxa ranging in size from 200 bp to 1000 bp. Jaccard’s coefficient of similarity varied from 0.28 to 0.84, indicative of high level of genetic variation among the genotypes studied. UPGMA cluster analysis indicated three distinct clusters, one comprised Cleome amblyocarpa and Gynandropsis gynandra, while another included two clusters at 0.74 phenon line; one for Capparis decidua, and the other for Capparis sinaica and all varieties of Capparis spinosa. The four varieties of Capparis spinosa were segregated at 0.84 phenon line. However, one of these varieties was more closely related to Capparis sinaica than to the other three varieties of C. spinosa. The RAPD analysis reported here confirms previous studies based on morphological markers.Consideraciones taxonómicas sobre algunos taxones egipcios de Capparis y géneros relacionados (Capparaceae a partir de RAPDs.- El objetivo de este trabajo es investigar las relaciones taxonómicas entre ocho taxones pertenecientes a las Capparaceae en base a marcadores de tipo RAPD, y comparar los resultados con los obtenidos previamente en estudios morfológicos. Se han contabilizado un total de 46 bandas para tres pares de cebadores, con una media de 15,3 bandas por cebador. Los tres pares de cebadores (A03, A07 y A09 revelan ocho marcadores polimórficos entre los taxones estudiados, de entre 200 y 1000 pares de

  17. Study of Associated Genetic Variants in Indian Subjects Reveals the Basis of Ethnicity Related Differences in Susceptibility to Venous Thromboembolism

    Directory of Open Access Journals (Sweden)

    Babita Kumari

    2014-01-01

    Full Text Available The genetic variants linked with the susceptibility of individuals to VTE are well known; however, the studies explaining the ethnicity based difference in susceptibility to VTE are limited. Present study assesses mutations in six candidate genes contributing to the etiology of VTE in Indian subjects. The study comprised 93 VTE patients and 102 healthy controls. A PCR-RFLP based analysis was performed for nine mutations in the following genes associated with VTE: favtor V Leiden (FVL, prothrombin, tissue factor pathway inhibitor (TFPI, fibrinogen-beta, plasminogen activator inhibitor 1 (PAI-1, and methylene tetrahydrofolatereductase (MTHFR. All the subjects were found to be monomorphic for FVL 1691G/A, prothrombin 20210G/A and TFPI −536C/T mutations. The mutation in the MTHFR gene (677C/T was observed only in patients. Contrarily, higher frequency of mutation in the PAI-1 −844G/A and the fibrinogen-β −455G/A was observed in controls in comparison to the patients. This study suggests that the PAI-1 −844G/A and fibrinogen-β −455G/A could be protective variants against VTE in Indians. While MTHFR 677C/T mutation was found to be associated, in contrast to other populations, the established genetic variants FVL 1691G/A, prothrombin 20210G/A, and TFPI −536C/T may not be associated with VTE in Indians thus revealing the basis of ethnicity related differences in susceptibility of Indians to VTE.

  18. Sports-related testing protocols are required to reveal trunk stability adaptations in high-level athletes.

    Science.gov (United States)

    Barbado, David; Barbado, Luis C; Elvira, Jose L L; Dieën, Jaap H van; Vera-Garcia, Francisco J

    2016-09-01

    Trunk/core stability is considered a key component of training programs, because it could contribute to prevention of low-back and lower-limb injuries and to sports performance. Based on the specificity principle, sports-related trunk stability tests would be required in elite sports performance. However, there may be some generic qualities underlying trunk stability that can be assessed with nonspecific protocols, which are broadly used in sport and rehabilitation. To assess whether specific tests are needed in a high-performance context, we analyzed the influence of specialization in sports with large but qualitatively different balance control demands (judo and kayaking) on trunk stability and compared high-performance athletes with recreational athletes without a specific training history. Twenty-five judokas, sixteen kayakers and thirty-seven recreational athletes performed two trunk stability protocols: sudden loading, to assess trunk responses to external and unexpected perturbations; stable and unstable sitting, to assess the participant's ability to control trunk while sitting. Within-session test-retest reliability analyses were performed to support the between-groups comparison. Judokas showed lower angular displacement (0.199rad) against posterior loading than kayakers (0.221rad) probably because they are frequently challenged by higher sudden loads while they are pushed or pulled. Kayakers showed lower error (7.33mm), probably because they train and compete seated on unstable surfaces. Importantly, judokas and kayakers obtained better results than recreational athletes only in those tests designed according to the specific demands of each sport (psport training induces specific trunk stability adaptations, which are not revealed through nonspecific tests. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Event-related potentials reveal preserved attention allocation but impaired emotion regulation in patients with epilepsy and comorbid negative affect.

    Science.gov (United States)

    De Taeye, Leen; Pourtois, Gilles; Meurs, Alfred; Boon, Paul; Vonck, Kristl; Carrette, Evelien; Raedt, Robrecht

    2015-01-01

    Patients with epilepsy have a high prevalence of comorbid mood disorders. This study aims to evaluate whether negative affect in epilepsy is associated with dysfunction of emotion regulation. Event-related potentials (ERPs) are used in order to unravel the exact electrophysiological time course and investigate whether a possible dysfunction arises during early (attention) and/or late (regulation) stages of emotion control. Fifty epileptic patients with (n = 25) versus without (n = 25) comorbid negative affect plus twenty-five matched controls were recruited. ERPs were recorded while subjects performed a face- or house-matching task in which fearful, sad or neutral faces were presented either at attended or unattended spatial locations. Two ERP components were analyzed: the early vertex positive potential (VPP) which is normally enhanced for faces, and the late positive potential (LPP) that is typically larger for emotional stimuli. All participants had larger amplitude of the early face-sensitive VPP for attended faces compared to houses, regardless of their emotional content. By contrast, in patients with negative affect only, the amplitude of the LPP was significantly increased for unattended negative emotional expressions. These VPP results indicate that epilepsy with or without negative affect does not interfere with the early structural encoding and attention selection of faces. However, the LPP results suggest abnormal regulation processes during the processing of unattended emotional faces in patients with epilepsy and comorbid negative affect. In conclusion, this ERP study reveals that early object-based attention processes are not compromised by epilepsy, but instead, when combined with negative affect, this neurological disease is associated with dysfunction during the later stages of emotion regulation. As such, these new neurophysiological findings shed light on the complex interplay of epilepsy with negative affect during the processing of emotional

  20. Systems Approach Reveals Nuclear Factor Erythroid 2-Related Factor 2/Protein Kinase R Crosstalk in Human Cutaneous Leishmaniasis.

    Science.gov (United States)

    Vivarini, Áislan de Carvalho; Calegari-Silva, Teresa Cristina; Saliba, Alessandra Mattos; Boaventura, Viviane Sampaio; França-Costa, Jaqueline; Khouri, Ricardo; Dierckx, Tim; Dias-Teixeira, Karina Luiza; Fasel, Nicolas; Barral, Aldina Maria Prado; Borges, Valéria Matos; Van Weyenbergh, Johan; Lopes, Ulisses Gazos

    2017-01-01

    Leishmania parasites infect macrophages, causing a wide spectrum of human diseases, from cutaneous to visceral forms. In search of novel therapeutic targets, we performed comprehensive in vitro and ex vivo mapping of the signaling pathways upstream and downstream of antioxidant transcription factor [nuclear factor erythroid 2-related factor 2 (Nrf2)] in cutaneous leishmaniasis (CL), by combining functional assays in human and murine macrophages with a systems biology analysis of in situ (skin biopsies) CL patient samples. First, we show the PKR pathway controls the expression and activation of Nrf2 in Leishmania amazonensis infection in vitro. Nrf2 activation also required PI3K/Akt signaling and autophagy mechanisms. Nrf2- or PKR/Akt-deficient macrophages exhibited increased levels of ROS/RNS and reduced expression of Sod1 Nrf2-dependent gene and reduced parasite load. L. amazonensis counteracted the Nrf2 inhibitor Keap1 through the upregulation of p62 via PKR. This Nrf2/Keap1 observation was confirmed in situ in skin biopsies from Leishmania-infected patients. Next, we explored the ex vivo transcriptome in CL patients, as compared to healthy controls. We found the antioxidant response element/Nrf2 signaling pathway was significantly upregulated in CL, including downstream target p62. In silico enrichment analysis confirmed upstream signaling by interferon and PI3K/Akt, and validated our in vitro findings. Our integrated in vitro, ex vivo, and in silico approach establish Nrf2 as a central player in human cutaneous leishmaniasis and reveal Nrf2/PKR crosstalk and PI3K/Akt pathways as potential therapeutic targets.

  1. Twelve Years of Spectroscopic Monitoring in the Galactic Center: The Closest Look at S-stars near the Black Hole

    Science.gov (United States)

    Habibi, M.; Gillessen, S.; Martins, F.; Eisenhauer, F.; Plewa, P. M.; Pfuhl, O.; George, E.; Dexter, J.; Waisberg, I.; Ott, T.; von Fellenberg, S.; Bauböck, M.; Jimenez-Rosales, A.; Genzel, R.

    2017-10-01

    We study the young S-stars within a distance of 0.04 pc from the supermassive black hole in the center of our Galaxy. Given how inhospitable the region is for star formation, their presence is more puzzling the younger we estimate their ages. In this study, we analyze the result of 12 years of high-resolution spectroscopy within the central arcsecond of the Galactic Center (GC). By co-adding between 55 and 105 hr of spectra we have obtained high signal-to-noise H- and K-band spectra of eight stars orbiting the central supermassive black hole. Using deep H-band spectra, we show that these stars must be high surface gravity (dwarf) stars. We compare these deep spectra to detailed model atmospheres and stellar evolution models to infer the stellar parameters. Our analysis reveals an effective temperature of 21,000-28,500 K, a rotational velocity of 60-170 km s-1, and a surface gravity of 4.1-4.2. These parameters imply a spectral type of B0-B3V for these stars. The inferred masses lie within 8-14 {M}⊙ . We derive an age of {6.6}-4.7+3.4 Myr for the star S2, which is compatible with the age of the clockwise-rotating young stellar disk in the GC. We estimate the ages of all other studied S-stars to be less than 15 Myr, which is compatible with the age of S2 within the uncertainties. The relatively low ages for these S-stars favor a scenario in which the stars formed in a local disk rather than a field binary-disruption scenario that occurred over a longer period of time.

  2. Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation.

    Science.gov (United States)

    Ruan, Yunfeng; Shen, Lu; Zou, Yan; Qi, Zhengnan; Yin, Jun; Jiang, Jie; Guo, Liang; He, Lin; Chen, Zijiang; Tang, Zisheng; Qin, Shengying

    2015-02-25

    Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella. The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades. Prevotella intermedia ZT

  3. Analysis of a slow-growing line reveals wide genetic variability of carcass and meat quality-related traits.

    Science.gov (United States)

    Chabault, Marie; Baéza, Elisabeth; Gigaud, Vérane; Chartrin, Pascal; Chapuis, Hervé; Boulay, Maryse; Arnould, Cécile; D'Abbadie, François; Berri, Cécile; Le Bihan-Duval, Elisabeth

    2012-10-23

    Slow-growing lines are widely used in France for the production of high quality free-range chickens. While such production is mainly dedicated to the whole carcass market, new prospects are opening up for the development of cuts and processed products. Whether the body composition and meat quality of slow-growing birds can be improved by selection has thus become an important issue. The genetic parameters of growth, body composition and breast meat quality traits were evaluated in relation to behaviour at slaughter in a large pedigree population including 1022 male and female slow-growing birds. The heritability coefficients (h²) of body weight and body composition traits varied from 0.3 to 0.5. Abdominal fat percentage was genetically positively correlated with body weight but negatively correlated with breast muscle yield. The characteristics of the breast meat (i.e., post-mortem fall in pH, colour, drip loss, shear-force and lipid content) were all heritable, with h² estimates ranging from 0.18 to 0.48. The rate and extent of the fall in pH were under different genetic control. Strong negative genetic correlations were found between the ultimate pH and the lightness, yellowness and drip loss of the meat. Wing flapping on the shackle line was significantly heritable and exhibited marked genetic correlations with the pH at 15 min post-slaughter and the redness of the meat. The genetic relationships between meat quality traits, body weight and body composition appeared slightly different between males and females. This study suggested that there are a number of important criteria for selection on carcass and breast meat quality in slow-growing birds. Selection for reduced abdominal fatness and increased breast muscle yield should be effective as both traits were found to be highly heritable and favourably correlated. Substantial improvement in meat quality could be achieved by selection on ultimate pH which was highly heritable and strongly correlated with the

  4. The predicted secretomes of Monosiga brevicollis and Capsaspora owczarzaki, close unicellular relatives of metazoans, reveal new insights into the evolution of the metazoan extracellular matrix.

    Science.gov (United States)

    Williams, Frederike; Tew, Hannah A; Paul, Catherine E; Adams, Josephine C

    2014-07-01

    The extracellular matrix (ECM) is a major mediator of multi-cellularity in the metazoa. Multiple ECM proteins are conserved from sponges to human, raising questions about the evolutionary origin of ECM. Choanoflagellates are the closest unicellular relatives of the metazoa and proteins with domains characteristic of metazoan ECM proteins have been identified from the genome-predicted proteome of the choanoflagellate Monosiga brevicollis. However, a systematic analysis of M. brevicollis secretory signal peptide-containing proteins with ECM domains has been lacking. We analysed all predicted secretory signal-peptide-containing proteins of M. brevicollis for ECM domains. Nine domains that are widespread in metazoan ECM proteins are represented, with EGF, fibronectin III, laminin G, and von Willebrand Factor_A domains being the most numerous. Three proteins contain more than one category of ECM domain, however, no proteins correspond to the domain architecture of metazoan ECM proteins. The fibronectin III domains are all present within glycoside hydrolases and none contain an integrin-binding motif. Glycosaminoglycan-binding motifs identified in animal thrombospondin type 1 domains are conserved in some M. brevicollis representatives of this domain, whereas there is little evidence of conservation of glycosaminoglycan-binding motifs in the laminin G domains. The identified proteins were compared with the predicted secretory ECM domain-containing proteins of the integrin-expressing filasterean, Capsaspora owczarzaki. C. owczarzaki encodes a smaller number of secretory, ECM domain-containing proteins and only EGF, fibronectin type III and laminin G domains are represented. The M. brevicollis and C. owczarzaki proteins have distinct domain architectures and all proteins differ in their domain architecture to metazoan ECM proteins. These identifications provide a basis for future experiments to validate the extracellular location of these proteins and uncover their

  5. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable rates of evolution within a core genome

    Science.gov (United States)

    Background: Biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context. We sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricu...

  6. Functional MRI Representational Similarity Analysis Reveals a Dissociation between Discriminative and Relative Location Information in the Human Visual System.

    Science.gov (United States)

    Roth, Zvi N

    2016-01-01

    Neural responses in visual cortex are governed by a topographic mapping from retinal locations to cortical responses. Moreover, at the voxel population level early visual cortex (EVC) activity enables accurate decoding of stimuli locations. However, in many cases information enabling one to discriminate between locations (i.e., discriminative information) may be less relevant than information regarding the relative location of two objects (i.e., relative information). For example, when planning to grab a cup, determining whether the cup is located at the same retinal location as the hand is hardly relevant, whereas the location of the cup relative to the hand is crucial for performing the action. We have previously used multivariate pattern analysis techniques to measure discriminative location information, and found the highest levels in EVC, in line with other studies. Here we show, using representational similarity analysis, that availability of discriminative information in fMRI activation patterns does not entail availability of relative information. Specifically, we find that relative location information can be reliably extracted from activity patterns in posterior intraparietal sulcus (pIPS), but not from EVC, where we find the spatial representation to be warped. We further show that this variability in relative information levels between regions can be explained by a computational model based on an array of receptive fields. Moreover, when the model's receptive fields are extended to include inhibitory surround regions, the model can account for the spatial warping in EVC. These results demonstrate how size and shape properties of receptive fields in human visual cortex contribute to the transformation of discriminative spatial representations into relative spatial representations along the visual stream.

  7. Functional MRI Representational Similarity Analysis Reveals a Dissociation between Discriminative and Relative Location Information in the Human Visual System

    Directory of Open Access Journals (Sweden)

    Zvi N Roth

    2016-03-01

    Full Text Available Neural responses in visual cortex are governed by a topographic mapping from retinal locations to cortical responses. Moreover, at the voxel population level early visual cortex (EVC activity enables accurate decoding of stimuli locations. However, in many cases information enabling one to discriminate between locations (i.e. discriminative information may be less relevant than information regarding the relative location of two objects (i.e. relative information. For example, when planning to grab a cup, determining whether the cup is located at the same retinal location as the hand is hardly relevant, whereas the location of the cup relative to the hand is crucial for performing the action.We have previously used multivariate pattern analysis techniques to measure discriminative location information, and found the highest levels in early visual cortex, in line with other studies. Here we show, using representational similarity analysis, that availability of discriminative information in fMRI activation patterns does not entail availability of relative information. Specifically, we find that relative location information can be reliably extracted from activity patterns in posterior intraparietal sulcus (pIPS, but not from EVC, where we find the spatial representation to be warped.We further show that this variability in relative information levels between regions can be explained by a computational model based on an array of receptive fields. Moreover, when the model’s receptive fields are extended to include inhibitory surround regions, the model can account for the spatial warping in EVC.These results demonstrate how size and shape properties of receptive fields in human visual cortex contribute to the transformation of discriminative spatial representation into relative spatial representation along the visual stream.

  8. Comparative Proteome Analysis of the Tuberous Roots of Six Cassava (Manihot esculenta) Varieties Reveals Proteins Related to Phenotypic Traits.

    Science.gov (United States)

    Schmitz, Gabriela Justamante Händel; de Magalhães Andrade, Jonathan; Valle, Teresa Losada; Labate, Carlos Alberto; do Nascimento, João Roberto Oliveira

    2016-04-27

    Cassava (Manihot esculenta Crantz) is a staple food and an important source of starch, and the attributes of its tuberous root largely depend on the variety. The proteome of cassava has been investigated; however, to date, no study has focused on varieties that reveal the molecular basis of phenotypical characteristics. Therefore, we aimed to compare the proteome of the tuberous roots of six cassava varieties that differed in carbohydrates, carotenoids, and resistance to diseases, among other attributes. Two-dimensional gels showed 146 differential spots between the varieties, and the functional roles of some differential proteins were correlated to phenotypic characteristics of the varieties, such as the amount of carbohydrates or carotenoids and the resistance to biotic or abiotic stresses. The results obtained here highlight elements that might help to direct the improvement of new cultivars of cassava, which is an economically and socially relevant crop worldwide.

  9. NMR-spectroscopic screening of spider venom reveals sulfated nucleosides as major components for the brown recluse and related species.

    Science.gov (United States)

    Schroeder, Frank C; Taggi, Andrew E; Gronquist, Matthew; Malik, Rabia U; Grant, Jacqualine B; Eisner, Thomas; Meinwald, Jerrold

    2008-09-23

    Extensive chemical analyses of spider venoms from many species have revealed complex mixtures of biologically active compounds, of which several have provided important leads for drug development. We have recently shown that NMR spectroscopy can be used advantageously for a direct structural characterization of the small-molecule content of such complex mixtures. Here, we report the application of this strategy to a larger-scale analysis of a collection of spider venoms representing >70 species, which, in combination with mass spectrometric analyses, allowed the identification of a wide range of known, and several previously undescribed, small molecules. These include polyamines, common neurotransmitters, and amino acid derivatives as well as two additional members of a recently discovered family of natural products, the sulfated nucleosides. In the case of the well studied brown recluse spider, Loxosceles reclusa, sulfated guanosine derivatives were found to comprise the major small-molecule components of the venom.

  10. Transcriptome analysis of distinct Lindera glauca tissues revealed the differences in the unigenes related to terpenoid biosynthesis.

    Science.gov (United States)

    Niu, Jun; Hou, Xinyu; Fang, Chengliang; An, Jiyong; Ha, Denglong; Qiu, Lin; Ju, Yuxi; Zhao, Haiyan; Du, WenZhi; Qi, Ji; Zhang, Zhixiang; Liu, Genan; Lin, Shanzhi

    2015-03-15

    The Lindera glauca, an economically and ecologically important tree species, has emerged as a novel potential plant for the intensive studies of essential oil owing to its characteristic aroma and medicinal property in distinct tissues. However, the transcriptome information and molecular research on this species is still unknown to date. To reveal the formation and accumulation mechanism of essential oil in distinct L. glauca tissues, it is crucial to analyze transcriptome and to identify the full repertoire of potential unigenes involved in terpenoid biosynthesis. In this paper, the transcriptomes of the roots, sarcocarps, stems, leaves and kernels of L. glauca were analyzed for the first time by using short-read sequencing technology (Illumina). A total of 27.2GB valid reads (the average length=92.7bp) was obtained from distinct L. glauca tissues, and then assembled de novo into 264,831 unigenes by Trinity strategy (mean size=560.2bp). The resulting 98,141 unigenes (38%) of all the assembled unigenes were annotated in multiple public databases, of which 114 potential unigenes were identified to be involved in the terpenoid biosynthetic accumulation in L. glauca. Additionally, the differential expression profiles revealed 675, 697, 432, 1702 and 844 high tissue-specificity expressions of unigenes in the roots, sarcocarps, stems, leaves and kernels of L. glauca, respectively. Overall, these obtained comprehensive unigene resources will contribute to advance the research regarding the specific plant and more specifically discovery of genes participating in the terpenoid pathway and its regulation in specific tissues of the L. glauca, but also could help the understanding of the differential accumulation of secondary metabolites in distinct plant tissues. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Relational and procedural memory systems in the goldfish brain revealed by trace and delay eyeblink-like conditioning.

    Science.gov (United States)

    Gómez, A; Rodríguez-Expósito, B; Durán, E; Martín-Monzón, I; Broglio, C; Salas, C; Rodríguez, F

    2016-12-01

    The presence of multiple memory systems supported by different neural substrata has been demonstrated in animal and human studies. In mammals, two variants of eyeblink classical conditioning, differing only in the temporal relationships between the conditioned stimulus (CS) and the unconditioned stimulus (US), have been widely used to study the neural substrata of these different memory systems. Delay conditioning, in which both stimuli coincide in time, depends on a non-relational memory system supported by the cerebellum and associated brainstem circuits. In contrast, trace conditioning, in which a stimulus-free time gap separates the CS and the US, requires a declarative or relational memory system, thus depending on forebrain structures in addition to the cerebellum. The distinction between the explicit or relational and the implicit or procedural memory systems that support trace and delay classical conditioning has been extensively studied in mammals, but studies in other vertebrate groups are relatively scarce. In the present experiment we analyzed the differential involvement of the cerebellum and the telencephalon in delay and trace eyeblink-like classical conditioning in goldfish. The results show that whereas the cerebellum lesion prevented the eyeblink-like conditioning in both procedures, the telencephalon ablation impaired exclusively the acquisition of the trace conditioning. These data showing that comparable neural systems support delay and trace eyeblink conditioning in teleost fish and mammals suggest that these separate memory systems and their neural bases could be a shared ancestral brain feature of the vertebrate lineage. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Modulation of spontaneous locomotor and respiratory drives to hindlimb motoneurons temporally related to sympathetic drives as revealed by Mayer waves

    DEFF Research Database (Denmark)

    Wienecke, Jacob; Denton, Manuel Enríquez; Stecina, Katinka

    2015-01-01

    In this study we investigated how the networks mediating respiratory and locomotor drives to lumbar motoneurons interact and how this interaction is modulated in relation to periodic variations in blood pressure (Mayer waves). Seven decerebrate cats, under neuromuscular blockade, were used to stu...

  13. The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

    Science.gov (United States)

    Porcel, Betina M.; Denoeud, France; Opperdoes, Fred; Noel, Benjamin; Madoui, Mohammed-Amine; Hammarton, Tansy C.; Field, Mark C.; Da Silva, Corinne; Couloux, Arnaud; Poulain, Julie; Katinka, Michael; Jabbari, Kamel; Aury, Jean-Marc; Campbell, David A.; Cintron, Roxana; Dickens, Nicholas J.; Docampo, Roberto; Sturm, Nancy R.; Koumandou, V. Lila; Fabre, Sandrine; Flegontov, Pavel; Lukeš, Julius; Michaeli, Shulamit; Mottram, Jeremy C.; Szöőr, Balázs; Zilberstein, Dan; Bringaud, Frédéric; Wincker, Patrick; Dollet, Michel

    2014-01-01

    Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease. PMID:24516393

  14. Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy.

    Science.gov (United States)

    Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

    2017-10-12

    Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (PMolecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (Pmolecular spectral intensities were lower (Pmolecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (Pmolecular structure changes had an interactive relationship with rumen degradation kinetics. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Hepatitis C virus in Mexican Americans: a population-based study reveals relatively high prevalence and negative association with diabetes.

    Science.gov (United States)

    Watt, G P; Vatcheva, K P; Beretta, L; Pan, J J; Fallon, M B; McCormick, J B; Fisher-Hoch, S P

    2016-01-01

    This study aimed to estimate the prevalence and risk factors for hepatitis C virus (HCV) infection in Mexican Americans living in South Texas. We tested plasma for the presence of HCV antibody from the Cameron County Hispanic Cohort (CCHC), a randomized, population-based cohort in an economically disadvantaged Mexican American community on the United States/Mexico border with high rates of chronic disease. A weighted prevalence of HCV antibody of 2·3% [n = 1131, 95% confidence interval (CI) 1·2-3·4] was found. Participants with diabetes had low rates of HCV antibody (0·4%, 95% CI 0·0-0·9) and logistic regression revealed a statistically significant negative association between HCV and diabetes (OR 0·20, 95% CI 0·05-0·77) after adjusting for sociodemographic and clinical factors. This conflicts with reported positive associations of diabetes and HCV infection. No classic risk factors were identified, but important differences between genders emerged in analysis. This population-based study of HCV in Mexican Americans suggests that national studies do not adequately describe the epidemiology of HCV in this border community and that unique risk factors may be involved.

  16. Dengue Virus and Its Relation to Human Glycoprotein IIb/IIIa Revealed by Fluorescence Microscopy and Flow Cytometry.

    Science.gov (United States)

    Attatippaholkun, Nattapol; U-Pratya, Yaowalak; Supraditaporn, Panthipa; Lorthongpanich, Chanchao; Pattanapanyasat, Kovit; Issaragrisil, Surapol

    2017-11-01

    Understanding dengue virus (DENV)-induced hemorrhage remains a challenging jigsaw puzzle with many pieces missing to understand the complex interactions between DENV and blood coagulation system. To use flow cytometry studying the interactions between DENV and human platelet aggregation receptor, glycoprotein IIb/IIIa (gpIIb/IIIa), directly conjugated fluorochrome monoclonal antibody (mAb) is essential to facilitate multifluorochrome immunostaining. However, the obstacle was that no directly conjugated fluorochrome-anti-DENV mAb had been commercially available. To overcome, we directly conjugated fluorochrome to a primary anti-DENV mAb using a LYNX rapid conjugation kit. Flow cytometry analysis showed that this conjugated antibody and anti-gpIIb/IIIa mAb were able to detect DENV and CD41a simultaneously. Fluorescence microscopy analysis further demonstrated CD41a superficially and DENV intracellularly. Potentially, this strategy can facilitate virologists for directly conjugating any virus-specific primary antibodies, which are not commercially available with fluorochrome, to study the infectivity in any surface marker-specific hosts through flow cytometry. Together, DENV can interact with both human gpIIb/IIIa(-) and gpIIb/IIIa(+) cells revealed by flow cytometry and fluorescence microscopy for the first time.

  17. Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa.

    Science.gov (United States)

    Li, Jimeng; Liu, Bo; Cheng, Feng; Wang, Xiaowu; Aarts, Mark G M; Wu, Jian

    2014-07-01

    Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  18. Revealing the burden of maternal mortality: a probabilistic model for determining pregnancy-related causes of death from verbal autopsies

    Directory of Open Access Journals (Sweden)

    Desta Teklay

    2007-02-01

    Full Text Available Abstract Background Substantial reductions in maternal mortality are called for in Millennium Development Goal 5 (MDG-5, thus assuming that maternal mortality is measurable. A key difficulty is attributing causes of death for the many women who die unaided in developing countries. Verbal autopsy (VA can elicit circumstances of death, but data need to be interpreted reliably and consistently to serve as global indicators. Recent developments in probabilistic modelling of VA interpretation are adapted and assessed here for the specific circumstances of pregnancy-related death. Methods A preliminary version of the InterVA-M probabilistic VA interpretation model was developed and refined with adult female VA data from several sources, and then assessed against 258 additional VA interviews from Burkina Faso. Likely causes of death produced by the model were compared with causes previously determined by local physicians. Distinction was made between free-text and closed-question data in the VA interviews, to assess the added value of free-text material on the model's output. Results Following rationalisation between the model and physician interpretations, cause-specific mortality fractions were broadly similar. Case-by-case agreement between the model and any of the reviewing physicians reached approximately 60%, rising to approximately 80% when cases with a discrepancy were reviewed by an additional physician. Cardiovascular disease and malaria showed the largest differences between the methods, and the attribution of infections related to pregnancy also varied. The model estimated 30% of deaths to be pregnancy-related, of which half were due to direct causes. Data derived from free-text made no appreciable difference. Conclusion InterVA-M represents a potentially valuable new tool for measuring maternal mortality in an efficient, consistent and standardised way. Further development, refinement and validation are planned. It could become a routine

  19. Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

    OpenAIRE

    Burki, Fabien; Inagaki, Yuji; Br?te, Jon; Archibald, John M.; Keeling, Patrick J.; Cavalier-Smith, Thomas; Sakaguchi, Miako; Hashimoto, Tetsuo; Horak, Ales; Kumar,Surendra; Klaveness, Dag; Jakobsen, Kjetill S.; Pawlowski, Jan; Shalchian-Tabrizi, Kamran

    2009-01-01

    Understanding the early evolution and diversification of eukaryotes relies on a fully resolved phylogenetic tree. In recent years, most eukaryotic diversity has been assigned to six putative supergroups, but the evolutionary origin of a few major ?orphan? lineages remains elusive. Two ecologically important orphan groups are the heterotrophic Telonemia and Centroheliozoa. Telonemids have been proposed to be related to the photosynthetic cryptomonads or stramenopiles and centrohelids to haptop...

  20. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.)

    OpenAIRE

    Wan, Heping; Chen, Lunlin; Guo, Jianbin; Li, Qun; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

    2017-01-01

    Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cult...

  1. RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation

    OpenAIRE

    Crane, Yan Ma; Gelvin, Stanton B.

    2007-01-01

    We investigated the effect of RNAi-mediated gene silencing of 109 Arabidopsis thaliana chromatin-related genes (termed “chromatin genes” hereafter) on Agrobacterium-mediated root transformation. Each of the RNAi lines contains a single- or low-copy-number insertion of a hairpin construction that silences the endogenous copy of the target gene. We used three standard transient and stable transformation assays to screen 340 independent RNAi lines, representing 109 target genes, for the rat (res...

  2. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  3. Event-related potential (ERP) measures reveal the timing of memory selection processes and proactive interference resolution in working memory.

    Science.gov (United States)

    Yi, Yuji; Friedman, David

    2011-09-09

    Behavioral studies show that no-longer-relevant information, although presumably removed from working memory (WM), still engenders proactive interference (PI). However, the timing of selecting items within WM and resolving PI is relatively unknown. To assess this, we recorded ERPs during WM from 20 young adults. In all conditions, a 4-digit display was followed by a cue indicating which digits to remember. In the selection condition, 2 digits were cued. The reaction time difference between the intrusion probe, a match of a to-be-rejected digit, and the non-intrusion probe, which did not match any of the 4 digits, was reliable, indicating a robust effect of PI. In the neutral-2 (remember 2 digits) and -4 (remember all 4) conditions, participants maintained the digits following the cue. Relative to neutral-4, selection elicited larger positivity at parietal sites (approximately 260ms) and negativity at frontal sites (approximately 420ms). Relative to the non-intrusion probe ERP, that to the intrusion probe was more negative over frontal scalp (approximately 500ms). We conclude that initial selection occurs over parietal cortex and reflects top-down attention to task relevant items, whereas the subsequent negativity may reflect inhibition of no-longer-relevant items over frontal cortex. The probe-locked ERPs suggest that the frontal negativity (approximately 500ms) reflects the final resolution of PI. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing.

    Directory of Open Access Journals (Sweden)

    Hua Yang

    Full Text Available Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.

  5. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

    Science.gov (United States)

    Liu, Hong-Wei; Wu, Jun-Lan; Li, Zheng-Guo; Zhang, Liang; Jian, Jian-Bo; Li, Ye-Yun; Tai, Yu-Ling; Zhang, Jing; Zhang, Zheng-Zhu; Jiang, Chang-Jun; Xia, Tao; Wan, Xiao-Chun

    2016-01-01

    Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants. PMID:26962860

  6. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing.

    Science.gov (United States)

    Yang, Hua; Wei, Chao-Ling; Liu, Hong-Wei; Wu, Jun-Lan; Li, Zheng-Guo; Zhang, Liang; Jian, Jian-Bo; Li, Ye-Yun; Tai, Yu-Ling; Zhang, Jing; Zhang, Zheng-Zhu; Jiang, Chang-Jun; Xia, Tao; Wan, Xiao-Chun

    2016-01-01

    Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.

  7. Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance.

    Science.gov (United States)

    Serrano, Soraya; Huarte, Nerea; Rujas, Edurne; Andreu, David; Nieva, José L; Jiménez, María Angeles

    2017-10-17

    Despite extensive characterization of the human immunodeficiency virus type 1 (HIV-1) hydrophobic fusion peptide (FP), the structure-function relationships underlying its extraordinary degree of conservation remain poorly understood. Specifically, the fact that the tandem repeat of the FLGFLG tripeptide is absolutely conserved suggests that high hydrophobicity may not suffice to unleash FP function. Here, we have compared the nuclear magnetic resonance (NMR) structures adopted in nonpolar media by two FP surrogates, wtFP-tag and scrFP-tag, which had equal hydrophobicity but contained wild-type and scrambled core sequences LFLGFLG and FGLLGFL, respectively. In addition, these peptides were tagged at their C-termini with an epitope sequence that folded independently, thereby allowing Western blot detection without interfering with FP structure. We observed similar α-helical FP conformations for both specimens dissolved in the low-polarity medium 25% (v/v) 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), but important differences in contact with micelles of the membrane mimetic dodecylphosphocholine (DPC). Thus, whereas wtFP-tag preserved a helix displaying a Gly-rich ridge, the scrambled sequence lost in great part the helical structure upon being solubilized in DPC. Western blot analyses further revealed the capacity of wtFP-tag to assemble trimers in membranes, whereas membrane oligomers were not observed in the case of the scrFP-tag sequence. We conclude that, beyond hydrophobicity, preserving sequence order is an important feature for defining the secondary structures and oligomeric states adopted by the HIV FP in membranes.

  8. Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

    Science.gov (United States)

    Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

    2018-02-01

    Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

  9. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions.

    Science.gov (United States)

    Badur, Ahmet H; Plutz, Matthew J; Yalamanchili, Geethika; Jagtap, Sujit Sadashiv; Schweder, Thomas; Unfried, Frank; Markert, Stephanie; Polz, Martin F; Hehemann, Jan-Hendrik; Rao, Christopher V

    2017-08-04

    Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyase genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Event-related potentials associated with masked priming of test cues reveal multiple potential contributions to recognition memory.

    Science.gov (United States)

    Woollams, Anna M; Taylor, Jason R; Karayanidis, Frini; Henson, Richard N

    2008-06-01

    The relationship between recognition memory and repetition priming remains unclear. Priming is believed to reflect increased processing fluency for previously studied items relative to new items. Manipulations that affect fluency can also affect the likelihood that participants will judge items as studied in recognition tasks. This attribution of fluency to memory has been related to the familiarity process, as distinct from the recollection process, that is assumed by dual-process models of recognition memory. To investigate the time courses and neural sources of fluency, familiarity, and recollection, we conducted an event-related potential (ERP) study of recognition memory using masked priming of test cues and a remember/know paradigm. During the recognition test, studied and unstudied words were preceded by a brief, masked word that was either the same or different. Participants decided quickly whether each item had been studied ("old" or "new"), and for items called old, indicated whether they "remembered" (R) the encoding event, or simply "knew" (K) the item had been studied. Masked priming increased the proportion of K, but not R, judgments. Priming also decreased response times for hits but not correct rejections (CRs). Four distinct ERP effects were found. A medial-frontal FN400 (300-500 msec) was associated with familiarity (R, K Hits > CRs) and a centro-parietal late positivity (500-800 msec) with recollection (R Hits > K Hits, CRs). A long-term repetition effect was found for studied items judged "new" (Misses > CRs) in the same time window as the FN400, but with a posterior distribution. Finally, a centrally distributed masked priming effect was visible between 150 and 250 msec and continued into the 300-500 msec time window, where it was topographically dissociable from the FN400. These results suggest that multiple neural signals are associated with repetition and potentially contribute to recognition memory.

  11. Genome-Wide Detection of SNP and SV Variations to Reveal Early Ripening-Related Genes in Grape.

    Directory of Open Access Journals (Sweden)

    Yanshuai Xu

    Full Text Available Early ripening in grape (Vitis vinifera L. is a crucial agronomic trait. The fruits of the grape line 'Summer Black' (SBBM, which contains a bud mutation, can be harvested approximately one week earlier than the 'Summer Black' (SBCcontrol. To investigate the molecular mechanism of the bud mutation related to early ripening, we detected genome-wide genetic variations based on re-sequencing. In total, 3,692,777 single nucleotide polymorphisms (SNPs and 81,223 structure variations (SVs in the SBC genome and 3,823,464 SNPs and 85,801 SVs in the SBBM genome were detected compared with the reference grape sequence. Of these, 635 SBC-specific genes and 665 SBBM-specific genes were screened. Ripening and colour-associated unigenes with non-synonymous mutations (NS, SVs or frame-shift mutations (F were analysed. The results showed that 90 unigenes in SBC, 76 unigenes in SBBM and 13 genes that mapped to large fragment indels were filtered. The expression patterns of eight genes were confirmed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR.The re-sequencing data showed that 635 SBC-specific genes and 665 SBBM-specific genes associated with early ripening were screened. Among these, NCED6 expression appears to be related to NCED1 and is involved in ABA biosynthesis in grape, which might play a role in the onset of anthocyanin accumulation. The SEP and ERF genes probably play roles in ethylene response.

  12. A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen

    Directory of Open Access Journals (Sweden)

    Lebedeva Galina

    2012-11-01

    Full Text Available Abstract Background Estrogen receptors alpha (ER are implicated in many types of female cancers, and are the common target for anti-cancer therapy using selective estrogen receptor modulators (SERMs, such as tamoxifen. However, cell-type specific and patient-to-patient variability in response to SERMs (from suppression to stimulation of cancer growth, as well as frequent emergence of drug resistance, represents a serious problem. The molecular processes behind mixed effects of SERMs remain poorly understood, and this strongly motivates application of systems approaches. In this work, we aimed to establish a mathematical model of ER-dependent gene expression to explore potential mechanisms underlying the variable actions of SERMs. Results We developed an equilibrium model of ER binding with 17β-estradiol, tamoxifen and DNA, and linked it to a simple ODE model of ER-induced gene expression. The model was parameterised on the broad range of literature available experimental data, and provided a plausible mechanistic explanation for the dual agonism/antagonism action of tamoxifen in the reference cell line used for model calibration. To extend our conclusions to other cell types we ran global sensitivity analysis and explored model behaviour in the wide range of biologically plausible parameter values, including those found in cancer cells. Our findings suggest that transcriptional response to tamoxifen is controlled in a complex non-linear way by several key parameters, including ER expression level, hormone concentration, amount of ER-responsive genes and the capacity of ER-tamoxifen complexes to stimulate transcription (e.g. by recruiting co-regulators of transcription. The model revealed non-monotonic dependence of ER-induced transcriptional response on the expression level of ER, that was confirmed experimentally in four variants of the MCF-7 breast cancer cell line. Conclusions We established a minimal mechanistic model of ER-dependent gene

  13. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

    Science.gov (United States)

    2012-01-01

    Background Age-related macular degeneration (AMD) is a leading cause of blindness that affects the central region of the retinal pigmented epithelium (RPE), choroid, and neural retina. Initially characterized by an accumulation of sub-RPE deposits, AMD leads to progressive retinal degeneration, and in advanced cases, irreversible vision loss. Although genetic analysis, animal models, and cell culture systems have yielded important insights into AMD, the molecular pathways underlying AMD's onset and progression remain poorly delineated. We sought to better understand the molecular underpinnings of this devastating disease by performing the first comparative transcriptome analysis of AMD and normal human donor eyes. Methods RPE-choroid and retina tissue samples were obtained from a common cohort of 31 normal, 26 AMD, and 11 potential pre-AMD human donor eyes. Transcriptome profiles were generated for macular and extramacular regions, and statistical and bioinformatic methods were employed to identify disease-associated gene signatures and functionally enriched protein association networks. Selected genes of high significance were validated using an independent donor cohort. Results We identified over 50 annotated genes enriched in cell-mediated immune responses that are globally over-expressed in RPE-choroid AMD phenotypes. Using a machine learning model and a second donor cohort, we show that the top 20 global genes are predictive of AMD clinical diagnosis. We also discovered functionally enriched gene sets in the RPE-choroid that delineate the advanced AMD phenotypes, neovascular AMD and geographic atrophy. Moreover, we identified a graded increase of transcript levels in the retina related to wound response, complement cascade, and neurogenesis that strongly correlates with decreased levels of phototransduction transcripts and increased AMD severity. Based on our findings, we assembled protein-protein interactomes that highlight functional networks likely to be

  14. In vivo imaging reveals rapid astrocyte depletion and axon damage in a model of neuromyelitis optica-related pathology

    DEFF Research Database (Denmark)

    Herwerth, Marina; Kalluri, Sudhakar Reddy; Srivastava, Rajneesh

    2016-01-01

    of astrocyte injury in NMO and the mechanisms by which toxicity spreads to axons are not understood. METHODS: Here, we establish in vivo imaging of the spinal cord, one of the main sites of NMO pathology, as a powerful tool to study the formation of experimental NMO-related lesions caused by human AQP4...... antibodies in mice. RESULTS: We found that human AQP4 antibodies caused acute astrocyte depletion with initial oligodendrocyte survival. Within two hours of antibody application, we observed secondary axon injury in the form of progressive swellings. Astrocyte toxicity and axon damage were dependent on AQP4...... of NMO pathology beyond astrocytes, as well as in evaluating potential neuroprotective interventions. This article is protected by copyright. All rights reserved....

  15. Studies of Physcomitrella patens reveal that ethylene-mediated submergence responses arose relatively early in land-plant evolution

    KAUST Repository

    Yasumura, Yuki

    2012-10-18

    Colonization of the land by multicellular green plants was a fundamental step in the evolution of life on earth. Land plants evolved from fresh-water aquatic algae, and the transition to a terrestrial environment required the acquisition of developmental plasticity appropriate to the conditions of water availability, ranging from drought to flood. Here we show that extant bryophytes exhibit submergence-induced developmental plasticity, suggesting that submergence responses evolved relatively early in the evolution of land plants. We also show that a major component of the bryophyte submergence response is controlled by the phytohormone ethylene, using a perception mechanism that has subsequently been conserved throughout the evolution of land plants. Thus a plant environmental response mechanism with major ecological and agricultural importance probably had its origins in the very earliest stages of the colonization of the land. © 2012 Blackwell Publishing Ltd.

  16. Xenotropic murine leukemia virus-related virus-associated chronic fatigue syndrome reveals a distinct inflammatory signature.

    Science.gov (United States)

    Lombardi, Vincent C; Hagen, Kathryn S; Hunter, Kenneth W; Diamond, John W; Smith-Gagen, Julie; Yang, Wei; Mikovits, Judy A

    2011-01-01

    The recent identification of xenotropic murine leukemia virus-related virus (XMRV) in the blood of patients with chronic fatigue syndrome (CFS) establishes that a retrovirus may play a role in the pathology in this disease. Knowledge of the immune response might lead to a better understanding of the role XMRV plays in this syndrome. Our objective was to investigate the cytokine and chemokine response in XMRV-associated CFS. Using Luminex multi-analyte profiling technology, we measured cytokine and chemokine values in the plasma of XMRV-infected CFS patients and compared these data to those of healthy controls. Analysis was performed using the Gene Expression Pattern Analysis Suite and the Random Forest tree classification algorithm. This study identifies a signature of 10 cytokines and chemokines which correctly identifies XMRV/CFS patients with 93% specificity and 96% sensitivity. These data show, for the first time, an immunological pattern associated with XMRV/CFS.

  17. Modulation of spontaneous locomotor and respiratory drives to hindlimb motoneurons temporally related to sympathetic drives as revealed by Mayer waves

    Directory of Open Access Journals (Sweden)

    Katinka eStecina

    2015-02-01

    Full Text Available In this study we investigated how the networks mediating respiratory and locomotor drives to lumbar motoneurons interact and how this interaction is modulated in relation to periodic variations in blood pressure (Mayer waves. Seven decerebrate cats, under neuromuscular blockade, were used to study central respiratory drive potentials (CRDPs, usually enhanced by added CO2 and spontaneously occurring locomotor drive potentials (LDPs in hindlimb motoneurons, together with hindlimb and phrenic nerve discharges. In four of the cats both drives and their voltage-dependent amplification were absent or modest, but in the other three, one or other of these drives was common and the voltage-dependent amplification was frequently strong. Moreover, in these three cats the blood pressure showed marked periodic variation (Mayer waves, with a slow rate (periods 9 - 104 s, mean 39 ± 17 SD. Profound modulation, synchronized with the Mayer waves was seen in the occurrence and/or in the amplification of the CRDPs or LDPs. In one animal, where CRDPs were present in most cells and the amplification was strong, the CRDP consistently triggered sustained plateaux at one phase of the Mayer wave cycle. In the other two animals, LDPs were common, and the occurrence of the locomotor drive was gated by the Mayer wave cycle, sometimes in alternation with the respiratory drive. Other interactions between the two drives involved respiration providing leading events, including co-activation of flexors and extensors during post-inspiration or a locomotor drive gated or sometimes entrained by respiration. We conclude that the respiratory drive in hindlimb motoneurons is transmitted via elements of the locomotor central pattern generator. The rapid modulation related to Mayer waves suggests the existence of a more direct and specific descending modulatory control than has previously been demonstrated.

  18. Analysis of Relations between Spatiotemporal Movement Regulation and Performance of Discrete Actions Reveals Functionality in Skilled Climbing.

    Science.gov (United States)

    Orth, Dominic; Kerr, Graham; Davids, Keith; Seifert, Ludovic

    2017-01-01

    In this review of research on climbing expertise, we focus on different measures of climbing performance, including spatiotemporal measures related to fluency and activity states (i.e., discrete actions), adopted by climbers for achieving overall performance goals of getting to the end of a route efficiently and safely. Currently, a broad range of variables have been reported, however, many of these fail to capture how climbers adapt to a route whilst climbing. We argue that spatiotemporal measures should be considered concurrently with evaluation of activity states (such as reaching or exploring) in order gain a more comprehensive picture of how climbers successfully adapt to a route. Spatial and temporal movement measures taken at the hip are a traditional means of assessing efficiency of climbing behaviors. More recently, performatory and exploratory actions of the limbs have been used in combination with spatiotemporal indicators, highlighting the influence of limb states on climbing efficiency and skill transfer. However, only a few studies have attempted to combine spatiotemporal and activity state measures taken during route climbing. This review brings together existing approaches for observing climbing skill at performance outcome (i.e., spatiotemporal assessments) and process (i.e., limb activity states) levels of analysis. Skill level is associated with a spatially efficient route progression and lower levels of immobility. However, more difficult hold architecture designs require significantly greater mobility and more complex movement patterning to maintain performance. Different forms of functional, or goal-supportive, movement variability, including active recovery and hold exploration, have been implicated as important adaptations to physiological and environmental dynamics that emerge during the act of climbing. Indeed, recently it has also been shown that, when climbing on new routes, efficient exploration can improve the transfer of skill. This

  19. Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon.

    Science.gov (United States)

    Gao, Lei; Zhao, Shengjie; Lu, Xuqiang; He, Nan; Zhu, Hongju; Dou, Junling; Liu, Wenge

    2018-01-01

    Soluble sugars and organic acids are important components of fruit flavor and have a strong impact on the overall organoleptic quality of watermelon (Citrullus lanatus) fruit. Several studies have analyzed the expression levels of the genes related to soluble sugar accumulation and the dynamic changes in their content during watermelon fruit development and ripening. Nevertheless, to date, there have been no reports on the organic acid content in watermelon or the genes regulating their synthesis. In this study, the soluble sugars and organic acids in watermelon were measured and a comparative transcriptome analysis was performed to identify the key genes involved in the accumulation of these substances during fruit development and ripening. The watermelon cultivar '203Z' and its near-isogenic line (NIL) 'SW' (in the '203Z' background) were used as experimental materials. The results suggested that soluble sugar consist of fructose, glucose and sucrose while malic-, citric-, and oxalic acids are the primary organic acids in watermelon fruit. Several differentially expressed genes (DEGs) related to soluble sugar- and organic acid accumulation and metabolism were identified. These include the DEGs encoding raffinose synthase, sucrose synthase (SuSy), sucrose-phosphate synthase (SPSs), insoluble acid invertases (IAI), NAD-dependent malate dehydrogenase (NAD-cyt MDH), aluminum-activated malate transporter (ALMT), and citrate synthase (CS). This is the first report addressing comparative transcriptome analysis via NILs materials in watermelon fruit. These findings provide an important basis for understanding the molecular mechanism that leads to soluble sugar and organic acid accumulation and metabolism during watermelon fruit development and ripening.

  20. Analysis of Relations between Spatiotemporal Movement Regulation and Performance of Discrete Actions Reveals Functionality in Skilled Climbing

    Directory of Open Access Journals (Sweden)

    Dominic Orth

    2017-10-01

    Full Text Available In this review of research on climbing expertise, we focus on different measures of climbing performance, including spatiotemporal measures related to fluency and activity states (i.e., discrete actions, adopted by climbers for achieving overall performance goals of getting to the end of a route efficiently and safely. Currently, a broad range of variables have been reported, however, many of these fail to capture how climbers adapt to a route whilst climbing. We argue that spatiotemporal measures should be considered concurrently with evaluation of activity states (such as reaching or exploring in order gain a more comprehensive picture of how climbers successfully adapt to a route. Spatial and temporal movement measures taken at the hip are a traditional means of assessing efficiency of climbing behaviors. More recently, performatory and exploratory actions of the limbs have been used in combination with spatiotemporal indicators, highlighting the influence of limb states on climbing efficiency and skill transfer. However, only a few studies have attempted to combine spatiotemporal and activity state measures taken during route climbing. This review brings together existing approaches for observing climbing skill at performance outcome (i.e., spatiotemporal assessments and process (i.e., limb activity states levels of analysis. Skill level is associated with a spatially efficient route progression and lower levels of immobility. However, more difficult hold architecture designs require significantly greater mobility and more complex movement patterning to maintain performance. Different forms of functional, or goal-supportive, movement variability, including active recovery and hold exploration, have been implicated as important adaptations to physiological and environmental dynamics that emerge during the act of climbing. Indeed, recently it has also been shown that, when climbing on new routes, efficient exploration can improve the transfer

  1. Behavioral characterization of A53T mice reveals early and late stage deficits related to Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Katrina L Paumier

    Full Text Available Parkinson's disease (PD pathology is characterized by the formation of intra-neuronal inclusions called Lewy bodies, which are comprised of alpha-synuclein (α-syn. Duplication, triplication or genetic mutations in α-syn (A53T, A30P and E46K are linked to autosomal dominant PD; thus implicating its role in the pathogenesis of PD. In both PD patients and mouse models, there is increasing evidence that neuronal dysfunction occurs before the accumulation of protein aggregates (i.e., α-syn and neurodegeneration. Characterization of the timing and nature of symptomatic dysfunction is important for understanding the impact of α-syn on disease progression. Furthermore, this knowledge is essential for identifying pathways and molecular targets for therapeutic intervention. To this end, we examined various functional and morphological endpoints in the transgenic mouse model expressing the human A53T α-syn variant directed by the mouse prion promoter at specific ages relating to disease progression (2, 6 and 12 months of age. Our findings indicate A53T mice develop fine, sensorimotor, and synaptic deficits before the onset of age-related gross motor and cognitive dysfunction. Results from open field and rotarod tests show A53T mice develop age-dependent changes in locomotor activity and reduced anxiety-like behavior. Additionally, digigait analysis shows these mice develop an abnormal gait by 12 months of age. A53T mice also exhibit spatial memory deficits at 6 and 12 months, as demonstrated by Y-maze performance. In contrast to gross motor and cognitive changes, A53T mice display significant impairments in fine- and sensorimotor tasks such as grooming, nest building and acoustic startle as early as 1-2 months of age. These mice also show significant abnormalities in basal synaptic transmission, paired-pulse facilitation and long-term depression (LTD. Combined, these data indicate the A53T model exhibits early- and late-onset behavioral and synaptic

  2. Behavioral characterization of A53T mice reveals early and late stage deficits related to Parkinson's disease.

    Science.gov (United States)

    Paumier, Katrina L; Sukoff Rizzo, Stacey J; Berger, Zdenek; Chen, Yi; Gonzales, Cathleen; Kaftan, Edward; Li, Li; Lotarski, Susan; Monaghan, Michael; Shen, Wei; Stolyar, Polina; Vasilyev, Dmytro; Zaleska, Margaret; D Hirst, Warren; Dunlop, John

    2013-01-01

    Parkinson's disease (PD) pathology is characterized by the formation of intra-neuronal inclusions called Lewy bodies, which are comprised of alpha-synuclein (α-syn). Duplication, triplication or genetic mutations in α-syn (A53T, A30P and E46K) are linked to autosomal dominant PD; thus implicating its role in the pathogenesis of PD. In both PD patients and mouse models, there is increasing evidence that neuronal dysfunction occurs before the accumulation of protein aggregates (i.e., α-syn) and neurodegeneration. Characterization of the timing and nature of symptomatic dysfunction is important for understanding the impact of α-syn on disease progression. Furthermore, this knowledge is essential for identifying pathways and molecular targets for therapeutic intervention. To this end, we examined various functional and morphological endpoints in the transgenic mouse model expressing the human A53T α-syn variant directed by the mouse prion promoter at specific ages relating to disease progression (2, 6 and 12 months of age). Our findings indicate A53T mice develop fine, sensorimotor, and synaptic deficits before the onset of age-related gross motor and cognitive dysfunction. Results from open field and rotarod tests show A53T mice develop age-dependent changes in locomotor activity and reduced anxiety-like behavior. Additionally, digigait analysis shows these mice develop an abnormal gait by 12 months of age. A53T mice also exhibit spatial memory deficits at 6 and 12 months, as demonstrated by Y-maze performance. In contrast to gross motor and cognitive changes, A53T mice display significant impairments in fine- and sensorimotor tasks such as grooming, nest building and acoustic startle as early as 1-2 months of age. These mice also show significant abnormalities in basal synaptic transmission, paired-pulse facilitation and long-term depression (LTD). Combined, these data indicate the A53T model exhibits early- and late-onset behavioral and synaptic impairments

  3. Behavioral Characterization of A53T Mice Reveals Early and Late Stage Deficits Related to Parkinson’s Disease

    Science.gov (United States)

    Paumier, Katrina L.; Sukoff Rizzo, Stacey J.; Berger, Zdenek; Chen, Yi; Gonzales, Cathleen; Kaftan, Edward; Li, Li; Lotarski, Susan; Monaghan, Michael; Shen, Wei; Stolyar, Polina; Vasilyev, Dmytro; Zaleska, Margaret; D. Hirst, Warren; Dunlop, John

    2013-01-01

    Parkinson's disease (PD) pathology is characterized by the formation of intra-neuronal inclusions called Lewy bodies, which are comprised of alpha-synuclein (α-syn). Duplication, triplication or genetic mutations in α-syn (A53T, A30P and E46K) are linked to autosomal dominant PD; thus implicating its role in the pathogenesis of PD. In both PD patients and mouse models, there is increasing evidence that neuronal dysfunction occurs before the accumulation of protein aggregates (i.e., α-syn) and neurodegeneration. Characterization of the timing and nature of symptomatic dysfunction is important for understanding the impact of α-syn on disease progression. Furthermore, this knowledge is essential for identifying pathways and molecular targets for therapeutic intervention. To this end, we examined various functional and morphological endpoints in the transgenic mouse model expressing the human A53T α-syn variant directed by the mouse prion promoter at specific ages relating to disease progression (2, 6 and 12 months of age). Our findings indicate A53T mice develop fine, sensorimotor, and synaptic deficits before the onset of age-related gross motor and cognitive dysfunction. Results from open field and rotarod tests show A53T mice develop age-dependent changes in locomotor activity and reduced anxiety-like behavior. Additionally, digigait analysis shows these mice develop an abnormal gait by 12 months of age. A53T mice also exhibit spatial memory deficits at 6 and 12 months, as demonstrated by Y-maze performance. In contrast to gross motor and cognitive changes, A53T mice display significant impairments in fine- and sensorimotor tasks such as grooming, nest building and acoustic startle as early as 1–2 months of age. These mice also show significant abnormalities in basal synaptic transmission, paired-pulse facilitation and long-term depression (LTD). Combined, these data indicate the A53T model exhibits early- and late-onset behavioral and synaptic impairments

  4. QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome.

    Directory of Open Access Journals (Sweden)

    Ezio Portis

    Full Text Available In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L. genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross '305E40' x '67/3' was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL per trait were identified and the percentage of the phenotypic variance (PV explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥ 10% was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.

  5. Artificial selection on relative brain size reveals a positive genetic correlation between brain size and proactive personality in the guppy.

    Science.gov (United States)

    Kotrschal, Alexander; Lievens, Eva J P; Dahlbom, Josefin; Bundsen, Andreas; Semenova, Svetlana; Sundvik, Maria; Maklakov, Alexei A; Winberg, Svante; Panula, Pertti; Kolm, Niclas

    2014-04-01

    Animal personalities range from individuals that are shy, cautious, and easily stressed (a "reactive" personality type) to individuals that are bold, innovative, and quick to learn novel tasks, but also prone to routine formation (a "proactive" personality type). Although personality differences should have important consequences for fitness, their underlying mechanisms remain poorly understood. Here, we investigated how genetic variation in brain size affects personality. We put selection lines of large- and small-brained guppies (Poecilia reticulata), with known differences in cognitive ability, through three standard personality assays. First, we found that large-brained animals were faster to habituate to, and more exploratory in, open field tests. Large-brained females were also bolder. Second, large-brained animals excreted less cortisol in a stressful situation (confinement). Third, large-brained animals were slower to feed from a novel food source, which we interpret as being caused by reduced behavioral flexibility rather than lack of innovation in the large-brained lines. Overall, the results point toward a more proactive personality type in large-brained animals. Thus, this study provides the first experimental evidence linking brain size and personality, an interaction that may affect important fitness-related aspects of ecology such as dispersal and niche exploration. © 2013 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  6. Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes.

    Science.gov (United States)

    Vilardell, Mireia; Rasche, Axel; Thormann, Anja; Maschke-Dutz, Elisabeth; Pérez-Jurado, Luis A; Lehrach, Hans; Herwig, Ralf

    2011-05-11

    Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies.

  7. Event-related potentials reveal linguistic suppression effect but not enhancement effect on categorical perception of color.

    Science.gov (United States)

    Lu, Aitao; Yang, Ling; Yu, Yanping; Zhang, Meichao; Shao, Yulan; Zhang, Honghong

    2014-08-01

    The present study used the event-related potential technique to investigate the nature of linguistic effect on color perception. Four types of stimuli based on hue differences between a target color and a preceding color were used: zero hue step within-category color (0-WC); one hue step within-category color (1-WC); one hue step between-category color (1-BC); and two hue step between-category color (2-BC). The ERP results showed no significant effect of stimulus type in the 100-200 ms time window. However, in the 200-350 ms time window, ERP responses to 1-WC target color overlapped with that to 0-WC target color for right visual field (RVF) but not left visual field (LVF) presentation. For the 1-BC condition, ERP amplitudes were comparable in the two visual fields, both being significantly different from the 0-WC condition. The 2-BC condition showed the same pattern as the 1-BC condition. These results suggest that the categorical perception of color in RVF is due to linguistic suppression on within-category color discrimination but not between-category color enhancement, and that the effect is independent of early perceptual processes. © 2014 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  8. De Novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Science.gov (United States)

    Annadurai, Ramasamy S; Neethiraj, Ramprasad; Jayakumar, Vasanthan; Damodaran, Anand C; Rao, Sudha Narayana; Katta, Mohan A V S K; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

  9. De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids

    Science.gov (United States)

    Jayakumar, Vasanthan; Damodaran, Anand C.; Rao, Sudha Narayana; Katta, Mohan A. V. S. K.; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C.

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa. PMID:23468859

  10. Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

    Science.gov (United States)

    Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

    2014-01-01

    Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

  11. Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes

    Directory of Open Access Journals (Sweden)

    Pérez-Jurado Luis A

    2011-05-01

    Full Text Available Abstract Background Down syndrome (DS; trisomy 21 is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. Results We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62. Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Conclusions Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies.

  12. ARTIFICIAL SELECTION ON RELATIVE BRAIN SIZE REVEALS A POSITIVE GENETIC CORRELATION BETWEEN BRAIN SIZE AND PROACTIVE PERSONALITY IN THE GUPPY

    Science.gov (United States)

    Kotrschal, Alexander; Lievens, Eva JP; Dahlbom, Josefin; Bundsen, Andreas; Semenova, Svetlana; Sundvik, Maria; Maklakov, Alexei A; Winberg, Svante; Panula, Pertti; Kolm, Niclas; Morrow, E

    2014-01-01

    Animal personalities range from individuals that are shy, cautious, and easily stressed (a “reactive” personality type) to individuals that are bold, innovative, and quick to learn novel tasks, but also prone to routine formation (a “proactive” personality type). Although personality differences should have important consequences for fitness, their underlying mechanisms remain poorly understood. Here, we investigated how genetic variation in brain size affects personality. We put selection lines of large- and small-brained guppies (Poecilia reticulata), with known differences in cognitive ability, through three standard personality assays. First, we found that large-brained animals were faster to habituate to, and more exploratory in, open field tests. Large-brained females were also bolder. Second, large-brained animals excreted less cortisol in a stressful situation (confinement). Third, large-brained animals were slower to feed from a novel food source, which we interpret as being caused by reduced behavioral flexibility rather than lack of innovation in the large-brained lines. Overall, the results point toward a more proactive personality type in large-brained animals. Thus, this study provides the first experimental evidence linking brain size and personality, an interaction that may affect important fitness-related aspects of ecology such as dispersal and niche exploration. PMID:24359469

  13. Event-related brain potentials reveal the time-course of language change detection in early bilinguals.

    Science.gov (United States)

    Kuipers, Jan-Rouke; Thierry, Guillaume

    2010-05-01

    Using event-related brain potentials, we investigated the temporal course of language change detection in proficient bilinguals as compared to matched controls. Welsh-English bilingual participants and English controls were presented with a variant of the oddball paradigm involving picture-word pairs. The language of the spoken word was manipulated such that English was the frequent stimulus (75%) and Welsh the infrequent stimulus (25%). We also manipulated semantic relatedness between pictures and words, such that only half of the pictures were followed by a word that corresponded with the identity of the picture. The P2 wave was significantly modulated by language in the bilingual group only, suggesting that this group detected a language change as early as 200 ms after word onset. Monolinguals also reliably detected the language change, but at a later stage of semantic integration (N400 range), since Welsh words were perceived as meaningless. The early detection of a language change in bilinguals triggered stimulus re-evaluation mechanisms reflected by a significant P600 modulation by Welsh words. Furthermore, compared to English unrelated words, English words matching the picture identity elicited significantly greater P2 amplitudes in the bilingual group only, suggesting that proficient bilinguals validate an incoming word against their expectation based on the context. Overall, highly proficient bilinguals appear to detect language changes very early on during speech perception and to consciously monitor language changes when they occur. 2010 Elsevier Inc. All rights reserved.

  14. Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers.

    Science.gov (United States)

    Ibanez, Sébastien; Manneville, Olivier; Miquel, Christian; Taberlet, Pierre; Valentini, Alice; Aubert, Serge; Coissac, Eric; Colace, Marie-Pascale; Duparc, Quentin; Lavorel, Sandra; Moretti, Marco

    2013-12-01

    Food preferences and food availability are two major determinants of the diet of generalist herbivores and of their spatial distribution. How do these factors interact and eventually lead to diet differentiation in co-occurring herbivores? We quantified the diet of four grasshopper species co-occurring in subalpine grasslands using DNA barcoding of the plants contained in the faeces of individuals sampled in the field. The food preferences of each grasshopper species were assessed by a choice (cafeteria) experiment from among 24 plant species common in five grassland plots, in which the four grasshoppers were collected, while the habitat was described by the relative abundance of plant species in the grassland plots. Plant species were characterised by their leaf economics spectrum (LES), quantifying their nutrient vs. structural tissue content. The grasshoppers' diet, described by the mean LES of the plants eaten, could be explained by their plant preferences but not by the available plants in their habitat. The diet differed significantly across four grasshopper species pairs out of six, which validates food preferences assessed in standardised conditions as indicators for diet partitioning in nature. In contrast, variation of the functional diversity (FD) for LES in the diet was mostly correlated to the FD of the available plants in the habitat, suggesting that diet mixing depends on the environment and is not an intrinsic property of the grasshopper species. This study sheds light on the mechanisms determining the feeding niche of herbivores, showing that food preferences influence niche position whereas habitat diversity affects niche breadth.

  15. De Novo transcriptome assembly (NGS of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Directory of Open Access Journals (Sweden)

    Ramasamy S Annadurai

    Full Text Available Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

  16. Calibrated imaging reveals altered grey matter metabolism related to white matter microstructure and symptom severity in multiple sclerosis.

    Science.gov (United States)

    Hubbard, Nicholas A; Turner, Monroe P; Ouyang, Minhui; Himes, Lyndahl; Thomas, Binu P; Hutchison, Joanna L; Faghihahmadabadi, Shawheen; Davis, Scott L; Strain, Jeremy F; Spence, Jeffrey; Krawczyk, Daniel C; Huang, Hao; Lu, Hanzhang; Hart, John; Frohman, Teresa C; Frohman, Elliot M; Okuda, Darin T; Rypma, Bart

    2017-11-01

    Multiple sclerosis (MS) involves damage to white matter microstructures. This damage has been related to grey matter function as measured by standard, physiologically-nonspecific neuroimaging indices (i.e., blood-oxygen-level dependent signal [BOLD]). Here, we used calibrated functional magnetic resonance imaging and diffusion tensor imaging to examine the extent to which specific, evoked grey matter physiological processes were associated with white matter diffusion in MS. Evoked changes in BOLD, cerebral blood flow (CBF), and oxygen metabolism (CMRO2 ) were measured in visual cortex. Individual differences in the diffusion tensor measure, radial diffusivity, within occipital tracts were strongly associated with MS patients' BOLD and CMRO2 . However, these relationships were in opposite directions, complicating the interpretation of the relationship between BOLD and white matter microstructural damage in MS. CMRO2 was strongly associated with individual differences in patients' fatigue and neurological disability, suggesting that alterations to evoked oxygen metabolic processes may be taken as a marker for primary symptoms of MS. This work demonstrates the first application of calibrated and diffusion imaging together and details the first application of calibrated functional MRI in a neurological population. Results lend support for neuroenergetic hypotheses of MS pathophysiology and provide an initial demonstration of the utility of evoked oxygen metabolism signals for neurology research. Hum Brain Mapp 38:5375-5390, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms.

    Directory of Open Access Journals (Sweden)

    Jonna Jalanka-Tuovinen

    Full Text Available BACKGROUND: While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point. PRINCIPAL FINDINGS: A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected. CONCLUSIONS/SIGNIFICANCE: A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the

  18. Proteomic profiles reveal age-related changes in coelomic fluid of sea urchin species with different life spans.

    Science.gov (United States)

    Bodnar, Andrea

    2013-05-01

    Sea urchins have a different life history from humans and traditional model organisms used to study the process of aging. Sea urchins grow indeterminately, reproduce throughout their life span and some species have been shown to exhibit negligible senescence with no increase in mortality rate at advanced ages. Despite these properties, different species of sea urchins are reported to have very different natural life spans providing a unique model to investigate cellular mechanisms underlying life span determination and negligible senescence. To gain insight into the biological changes that accompany aging in these animals, proteomic profiles were examined in coelomic fluid from young and old sea urchins of three species with different life spans: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate life span. The proteomic profiles of cell-free coelomic fluid were complex with many proteins exhibiting different forms and extensive post-translational modifications. Approximately 20% of the protein spots on 2-D gels showed more than two-fold change with age in each of the species. Changes that are consistent with age in all three species may prove to be useful biomarkers for age-determination for these commercially fished marine invertebrates and also may provide clues to mechanisms of negligible senescence. Among the proteins that change with age, the ectodomain of low-density lipoprotein receptor-related protein 4 (LRP4) was significantly increased in the coelomic fluid of all three sea urchin species suggesting that the Wnt signaling pathway should be further investigated for its role in negligible senescence. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease

    Science.gov (United States)

    Plaza-Izurieta, Leticia; Fernandez-Jimenez, Nora; Irastorza, Iñaki; Jauregi-Miguel, Amaia; Romero-Garmendia, Irati; Vitoria, Juan Carlos; Bilbao, Jose Ramon

    2015-01-01

    Celiac disease is a chronic immune-mediated disorder with an important genetic component. To date, there are 57 independent association signals from 39 non-HLA loci, and a total of 66 candidate genes have been proposed. We aimed to scrutinize the functional implication of 45 of those genes by analyzing their expression in the disease tissue of celiac patients (at diagnosis/treatment) compared with non-celiac controls. Moreover, we investigated the SNP genotype effect in gene expression and performed coexpression analyses. Several genes showed differential expression among disease groups, most of them related to immune response. Multiple trans-eQTLs but only four cis-eQTLs were found, and surprisingly the genotype effect seems to be stimulus dependent as it differs among groups. Coexpression levels vary from higher to lower levels in active patients at diagnosis, treated patients and non-celiac controls respectively. A subset of 18 genes tightly correlated in both groups of patients but not in controls was identified. Interestingly, this subset of genes was influenced by the genotype of three SNPs. One of the SNPs, rs1018326 on chromosome two is on top of a known lincRNA whose function is not yet described, and whose expression seems to be upregulated in active disease when comparing biopsy pairs from the same individuals. Our results strongly suggest that the effects of disease-associated SNPs go far beyond the oversimplistic idea of transcriptional control at a nearby locus. Further investigations are needed to determine how each variant disrupts fine-tuning mechanisms in the genome that eventually lead to disease. PMID:25388004

  20. Different frontal involvement in ALS and PLS revealed by Stroop event-related potentials and reaction times

    Directory of Open Access Journals (Sweden)

    Ninfa eAmato

    2013-12-01

    Full Text Available BACKGROUND: A growing body of evidence suggests a link between cognitive and pathological changes in amyotrophic lateral sclerosis (ALS and in frontotemporal lobar dementia (FTLD. Cognitive deficits have been investigated much less extensively in primary lateral sclerosis (PLS than in ALS. OBJECTIVE: to investigate bioelectrical activity to Stroop test, assessing frontal function, in ALS, PLS and control groups. METHODS: 32 non-demented ALS patients, 10 non-demented PLS patients and 27 healthy subjects were included. Twenty-nine electroencephalography (EEG channels with binaural reference were recorded during covert Stroop task performance, involving mental discrimination of the stimuli and not vocal or motor response. Group effects on event related potentials (ERPs latency were analyzed using statistical multivariate analysis. Topographic analysis was performed using low resolution brain electromagnetic tomography (LORETA. RESULTS: ALS patients committed more errors in the execution of the task but they were not slower, whereas PLS patients did not show reduced accuracy, despite a slowing of reaction times (RTs. The main ERP components were delayed in ALS, but not in PLS, compared with controls. Moreover, RTs speed but not ERP latency correlated with clinical scores. ALS had decreased frontotemporal activity in the P2, P3 and N4 time windows compared to controls. CONCLUSION: These findings suggest a different pattern of psychophysiological involvement in ALS compared with PLS. The former is increasingly recognized to be a multisystems disorder, with a spectrum of executive and behavioural impairments reflecting frontotemporal dysfunction. The latter seems to mainly involve the motor system, with largely spared cognitive functions. Moreover, our results suggest that the covert version of the Stroop task used in the present study, may be useful to assess cognitive state in the very advanced stage of the disease, when other cognitive tasks are not

  1. Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

    Directory of Open Access Journals (Sweden)

    Stella A G D Salvo

    Full Text Available Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.

  2. Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains.

    Science.gov (United States)

    Barberis, Claudia; Budia, Mabel; Palombarani, Susana; Rodriguez, Carlos Hernán; Ramírez, María Soledad; Arias, Barbara; Bonofiglio, Laura; Famiglietti, Angela; Mollerach, Marta; Almuzara, Marisa; Vay, Carlos

    2017-03-01

    Patterns of antimicrobial susceptibility in Actinomyces and related genera are very limited in the literature. Data of predominant susceptibility profiles could contribute to the establishment of an accurate empirical treatment. A total of 113 isolates from clinical samples were included in this study. Each isolate was identified using phenotypic methods and MALDI-TOF/MS. When discrepancies were observed, 16S rRNA gene sequencing was performed. The minimum inhibitory concentrations (MICs) of nine antimicrobial agents (penicillin, ceftriaxone, linezolid, tetracycline, clindamycin, erythromycin, ciprofloxacin, levofloxacin and vancomycin) were tested against the species Actinotignum schaalii (n=23), Actinomyces turicensis (n=18), Actinomyces europaeus (n=13), Actinomyces naeslundii/Actinomyces viscosus group (n=12), Actinomyces urogenitalis (n=11), Actinomyces radingae (n=11), Actinomyces neuii (n=9), Actinomyces odontolyticus (n=8), Bifidobacterium scardovii (n=3), Actinomyces graevenitzii (n=2), Alloscardovia omnicolens (n=2) and Varibaculum cambriense (n=1). All of the isolates were susceptible to penicillin, ceftriaxone, vancomycin and linezolid. Almost all of the A. urogenitalis isolates (8/11) were resistant to clindamycin and showed susceptibility to erythromycin, suggesting an L-phenotype, however no determinants of clindamycin resistance (lnu and lsa genes) were detected by PCR. High MIC values to quinolones were observed in 54/113 isolates (47.8%). All of the A. urogenitalis isolates were highly resistant to ciprofloxacin and levofloxacin. These data highlight the importance of ongoing surveillance to provide relevant information for empirical management of infections caused by these organisms. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  3. Non-linear Bio-geophysical and Remote Sensing Relations Revealed in Neural Network Training for Fractional Snow Cover Estimation

    Science.gov (United States)

    Czyzowska-Wisniewski, E. H.; Van Leeuwen, W. J. D.; Marsh, S. E.; Hirschboeck, K. K.; Wisniewski, W. T.

    2014-12-01

    Accurate estimation of Fractional Snow Cover (FSC) in complex alpine-forested terrain is now possible with appropriate remote sensing data and analysis techniques. This research examines what minimum combination of input variables are required to obtain state-of-the-art FSC estimates for heterogeneous alpine-forested terrains. Currently, one of the most accurate FSC estimators for alpine regions is based on training an Artificial Neural Network (ANN) that can deconvolve the relationships between numerous compounded and possibly non-linear bio-geophysical relations encountered in rugged terrain. Under the assumption that the ANN optimally extracts available information from its input data, we can exploit the ANN as a tool to assess the contributions toward FSC estimation of each of the data sources, and combinations thereof. By assessing the quality of the modeled FSC estimates versus ground equivalent data, suitable combinations of input variables can be identified. High spatial resolution imagery from IKONOS are used to estimate snow cover for ANN training and validation, and also for error assessment of the ANN FSC results. Input variables are initially chosen representing information already incorporated into leading snow cover estimators. Additional variables such as topographic slope, aspect, and shadow distribution are evaluated to observe the ANN as it accounts for illumination incidence and directional reflectance of surfaces affecting the viewed radiance in complex terrain. Snow usually covers vegetation and underlying geology partially, therefore the ANN also has to resolve spectral mixtures of unobscured surfaces surrounded by snow. Multispectral imagery if therefore acquired in the fall prior to the first snow of the season and are included in the ANN analyses for assessing the baseline reflectance values of the environment that later become modified by the snow. The best ANN FSC model performance was achieved when all 15 pre-selected inputs were used

  4. Comparative transcriptome analysis of ovary and testis reveals potential sex-related genes and pathways in spotted knifejaw Oplegnathus punctatus.

    Science.gov (United States)

    Du, Xinxin; Wang, Bo; Liu, Xiumei; Liu, Xiaobing; He, Yan; Zhang, Quanqi; Wang, Xubo

    2017-12-30

    The spotted knifejaw (Oplegnathus punctatus) is a newly emerging fishery species inhabiting the Pacific Ocean around Hawaii, China, Japan and Korean Peninsula. Little information on the mechanism of gonadal development and gametogenesis in this species could be used for research and breeding work. In this study, RNA-seq technology was applied to generate a deep-coverage sequencing data of spotted knifejaw testis and ovary. A total of 262,392,754 reads (ovary 133,403,270, testis 128,989,484) were generated from the cDNA library. After filtering and assembling, a total of 113,794 unigenes were obtained with the N50 of 1658bp. Unigenes were annotated with multiple public databases, including non-redundant protein databases (NR) (42,460, 37.31%), Swiss-Prot (33,632, 29.56%), eukaryotic Orthologus Groups (KOG) (26,195, 23.02%), Kyoto Encyclopedia of Genes and Genomes (KEGG) (10,978, 9.65%), and Gene Ontology (GO) (30,514, 26.82%). By comparing ovary and testis, 4496 differentially expressed unigenes (1986 in female, 2510 in male) were identified, in which 469 were specially expressed in females and 859 in males. The expression levels of 12 unigenes were confirmed by qRT-PCR. In addition, 35,054 simple sequence repeats were identified. By GO and KEGG analyses, a set of unigenes related to gonadal development and gametogenesis were filtered. foxl2 was deduced to be a key regulator for gonadal development and gametogenesis in females and dmrt1 in males. bmp15, nanos3, sox9 and amh were likely to function in the regulation of gonad physiology and germ line cells maintenance in ovary and testis. Interestingly, p53, apoptosis, Jak-STAT and neuroactive ligand-receptor interaction pathways were found to be pivotal in regulating gonadal development and gametogenesis of spotted knifejaw in various aspects. This study provides a fundamental support for further research in reproduction biology, population genetics and functional genomics in spotted knifejaw. Copyright © 2017

  5. Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.).

    Science.gov (United States)

    Naz, Ali Ahmad; Arifuzzaman, Md; Muzammil, Shumaila; Pillen, Klaus; Léon, Jens

    2014-10-07

    Root is the prime organ that sucks water and nutrients from deep layer of soil. Wild barley diversity exhibits remarkable variation in root system architecture that seems crucial in its adaptation to abiotic stresses like drought. In the present study, we performed quantitative trait locus (QTL) mapping of root and related shoot traits under control and drought conditions using a population of wild barley introgression lines (ILs). This population (S42IL) comprising of genome-wide introgressions of wild barley accession ISR42-8 in the cultivar Scarlett background. Here, we aimed to detect novel QTL alleles for improved root and related shoot features and to introduce them in modern cultivars. The cultivar Scarlett and wild barley accession ISR42-8 revealed significant variation of root and related shoot traits. ISR42-8 showed a higher performance in root system attributes like root dry weight (RDW), root volume (RV), root length (RL) and tiller number per plant (TIL) than Scarlett. Whereas, Scarlett exhibited erect type growth habit (GH) as compared to spreading growth habit in ISR42-8. The S42IL population revealed significant and wide range of variation for the investigated traits. Strong positive correlations were found among the root related traits whereas GH revealed negative correlation with root and shoot traits. The trait-wise comparison of phenotypic data with the ILs genetic map revealed six, eight, five, five and four QTL for RL, RDW, RV, TIL and GH, respectively. These QTL were linked to one or several traits simultaneously and localized to 15 regions across all chromosomes. Among these, beneficial QTL alleles of wild origin for RL, RDW, RV, TIL and GH, have been fixed in the cultivar Scarlett background. The present study revealed 15 chromosomal regions where the exotic QTL alleles showed improvement for root and related shoot traits. These data suggest that wild barley accession ISR42-8 bears alleles different from those of Scarlett. Hence, the

  6. Correct names for some of the closest relatives of Carica papaya: A review of the Mexican/Guatemalan genera Jarilla and Horovitzia.

    Science.gov (United States)

    Carvalho, Fernanda Antunes; Renner, Susanne S

    2013-01-01

    Using molecular data, we recently showed that Carica papaya L. is sister to a Mexican/Guatemalan clade of two genera, Jarilla Rusby with three species and Horovitzia V.M. Badillo with one. These species are herbs or thin-stemmed trees and may be of interest for future genomics-enabled papaya breeding. Here we clarify the correct names of Jarilla heterophylla (Cerv. ex La Llave) Rusby and Jarilla caudata (Brandegee) Standl., which were confused in a recent systematic treatment of Jarilla (McVaugh 2001). We designate epitypes for both, provide weblinks to type specimens, a key to the species of Jarilla and Horovitzia, and notes on their habitats and distribution.

  7. Correct names for some of the closest relatives of Carica papaya: A review of the Mexican/Guatemalan genera Jarilla and Horovitzia

    Directory of Open Access Journals (Sweden)

    Fernanda Carvalho

    2013-11-01

    Full Text Available Using molecular data, we recently showed that Carica papaya L. is sister to a Mexican/Guatemalan clade of two genera, Jarilla Rusby with three species and Horovitzia V.M. Badillo with one. These species are herbs or thin-stemmed trees and may be of interest for future genomics-enabled papaya breeding. Here we clarify the correct names of J. heterophylla (Cerv. ex La Llave Rusby and J. caudata (Brandegee Standl., which were confused in a recent systematic treatment of Jarilla (McVaugh 2001. We designate epitypes for both, provide weblinks to type specimens, a key to the species of Jarilla and Horovitzia, and notes on their habitats and distribution.

  8. Slip in Great Megathrust Earthquakes and its Relation to Crustal Structure as Revealed by Satellite Free-air Gravity

    Science.gov (United States)

    Wells, R. E.; Blakely, R. J.; Scholl, D.

    2007-12-01

    In 2003, Song and Simons and Wells et al. showed that approximately 70% of the moment released during past large, shallow subduction zone thrust earthquakes occurred beneath trench-parallel, free-air gravity lows outlining the deep-sea slope terrace and its basins. The authors suggested that the basin-centered, fore-arc gravity lows might be good predictors of high seismic slip in future earthquakes. Since 2001, ten megathrust earthquakes have occurred with magnitudes greater than Mw 7.7, including the giant, Mw 9.17 Sumatra earthquake of 2004. These earthquakes provide a robust test of the idea that seismic slip is focused beneath basin-centered gravity lows, and also the related ideas that the landward maximum gravity gradient marks the effective down-dip limit of large coseismic slip, and that intrabasin, transverse gravity highs are areas of lower slip. A compilation of seismic and geodetic slip inversions for the post-2001 earthquakes and new analyses of slip for the great Antofagasta, Jalisco, and Peru events in 1995 and 1996 indicate that more than 80% of the high-slip areas occur beneath deep-sea terrace gravity lows (DSTL), and that half of the earthquake asperities lie beneath fore-arc basins or local gravity lows. The maximum gravity gradient along the landward margin of the deep-sea terrace may mark the point where thicker overlying crust and higher temperatures on the megathrust limit the down dip extent of stick-slip behavior. Onland analogues are the mountain front of the Himalaya, which approximately marks the down-dip limit of large coseismic slip along the Main Frontal Thrust, and the front of the Taiwan Central Ranges, which coincides with the limit of slip during the 1999 Chi-Chi earthquake (Mw 7.6). In the up dip direction, coseismic slip may be partitioned onto splay faults in the wedge, as occurred in the 1964 Alaska earthquake. The observed pattern of greater slip at depth beneath fore arc basins is consistent with partitioning of slip up

  9. Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin.

    Science.gov (United States)

    Zamora, David O; Riviere, Michael; Choi, Dongseok; Pan, Yuzhen; Planck, Stephen R; Rosenbaum, James T; David, Larry L; Smith, Justine R

    2007-10-30

    The ocular vascular endothelium plays a key role in the development of several leading retinal causes of blindness in Western nations. Choroidal endothelial cells are integral to the subretinal neovascular lesions that characterize the exudative form of late age-related macular degeneration (AMD), and retinal endothelial cells participate in the initiation of diabetic retinopathy and posterior uveitis. Vascular endothelial cells at different sites exhibit considerable molecular diversity. This diversity has implications for understanding the pathogenesis of tissue-specific diseases and for the development of targeted therapies to treat these conditions. Previous work from our group has identified significant differences in the gene transcript profiles of human retinal and choroidal endothelial cells. Because the proteome ultimately determines the behavior of any given cell, however, it is critical to determine whether molecular differences exist at the level of protein expression. Retinal and choroidal endothelial cells were separately isolated from five sets of human eyes by enzymatic digestion with type II collagenase followed by anti-CD31 antibody-conjugated magnetic bead separation. Cells were washed to remove serum peptides in the culture medium, and lysed by sonication in buffer containing 2% sodium dodecyl sulfate. Protein was then precipitated with acetone. Retinal and choroidal endothelial samples from each donor were labeled with Cy3 and Cy5, respectively, mixed with a Cy2-labeled pooled protein sample to facilitate spot matching across gels, and separated by two-dimensional difference gel electrophoresis (2D-DIGE). Following a global normalization, differentially abundant protein spots that were visible in at least four of five donor gels were detected by the significance analysis of microarrays method, with false discovery rate set at 5%. Corresponding spots were excised from additional DIGE-labeled or Coomassie-stained 2D electrophoretic gels. Protein

  10. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus; Perrea, Toula; Zhou, Yanfeng

    2011-01-01

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the food related...... lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument...... values, attitudes and purchase behaviour, using frequency of consumption of pork products as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern replicates partly those identified in Western cultures. Moreover, all three segments showed consistent...

  11. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Perrea, Toula; Zhou, Yanfeng

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the Food Related...... Lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument......, which was tested for statistical robustness and used as a basis for the derivation of consumer segments. Construct validity of the instrument was then investigated by profiling the segments in terms of consumer values, attitudes and purchase behaviour, using frequency of consumption of pork products...

  12. Suppression of Amplitude dependent closest tune approach and first tests of the ADT as an AC-dipole (MD 1412)

    CERN Document Server

    Persson, Tobias Hakan Bjorn; Maclean, Ewen Hamish; Olexa, Jakub; Tomas Garcia, Rogelio; Valuch, Daniel; Wierichs, David Alexander; Carlier, Felix Simon; CERN. Geneva. ATS Department

    2016-01-01

    The amplitude detuning has been observed to decrease significantly as the horizontal and vertical tunes are approaching each other. The measured tune split (Qₓ −Qᵧ) versus amplitude was several times bigger than what can be explained with linear coupling during the non-linear MD in 2012 [1]. This effect is potentially harmful since it might cause a loss of Landau damping, hence giving rise to instabilities. In this MD we validated the findings in the MD from 2012 and demonstrated the possibility to mitigate this effect through having opposite polarity of the focusing and defocusing octupoles (MOD and MOF). The amplitude dependent dependent closest tune approach was also measured with the AC-dipole and gave unexpected results. A first test of using the ADT as an AC-dipole was also performed.

  13. The conserved mitochondrial gene distribution in relatives of Turritopsis nutricula, an immortal jellyfish.

    Science.gov (United States)

    Devarapalli, Pratap; Kumavath, Ranjith N; Barh, Debmalya; Azevedo, Vasco

    2014-01-01

    Turritopsis nutricula (T. nutricula) is the one of the known reported organisms that can revert its life cycle to the polyp stage even after becoming sexually mature, defining itself as the only immortal organism in the animal kingdom. Therefore, the animal is having prime importance in basic biological, aging, and biomedical researches. However, till date, the genome of this organism has not been sequenced and even there is no molecular phylogenetic study to reveal its close relatives. Here, using phylogenetic analysis based on available 16s rRNA gene and protein sequences of Cytochrome oxidase subunit-I (COI or COX1) of T. nutricula, we have predicted the closest relatives of the organism. While we found Nemopsis bachei could be closest organism based on COX1 gene sequence; T. dohrnii may be designated as the closest taxon to T. nutricula based on rRNA. Moreover, we have figured out four species that showed similar root distance based on COX1 protein sequence.

  14. Violence-related content in video game may lead to functional connectivity changes in brain networks as revealed by fMRI-ICA in young men.

    Science.gov (United States)

    Zvyagintsev, M; Klasen, M; Weber, R; Sarkheil, P; Esposito, F; Mathiak, K A; Schwenzer, M; Mathiak, K

    2016-04-21

    In violent video games, players engage in virtual aggressive behaviors. Exposure to virtual aggressive behavior induces short-term changes in players' behavior. In a previous study, a violence-related version of the racing game "Carmageddon TDR2000" increased aggressive affects, cognitions, and behaviors compared to its non-violence-related version. This study investigates the differences in neural network activity during the playing of both versions of the video game. Functional magnetic resonance imaging (fMRI) recorded ongoing brain activity of 18 young men playing the violence-related and the non-violence-related version of the video game Carmageddon. Image time series were decomposed into functional connectivity (FC) patterns using independent component analysis (ICA) and template-matching yielded a mapping to established functional brain networks. The FC patterns revealed a decrease in connectivity within 6 brain networks during the violence-related compared to the non-violence-related condition: three sensory-motor networks, the reward network, the default mode network (DMN), and the right-lateralized frontoparietal network. Playing violent racing games may change functional brain connectivity, in particular and even after controlling for event frequency, in the reward network and the DMN. These changes may underlie the short-term increase of aggressive affects, cognitions, and behaviors as observed after playing violent video games. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  15. Quantitative phosphoproteomic study of pressure-overloaded mouse heart reveals dynamin-related protein 1 as a modulator of cardiac hypertrophy.

    Science.gov (United States)

    Chang, Yu-Wang; Chang, Ya-Ting; Wang, Qinchuan; Lin, Jim Jung-Ching; Chen, Yu-Ju; Chen, Chien-Chang

    2013-11-01

    Pressure-overload stress to the heart causes pathological cardiac hypertrophy, which increases the risk of cardiac morbidity and mortality. However, the detailed signaling pathways induced by pressure overload remain unclear. Here we used phosphoproteomics to delineate signaling pathways in the myocardium responding to acute pressure overload and chronic hypertrophy in mice. Myocardial samples at 4 time points (10, 30, 60 min and 2 weeks) after transverse aortic banding (TAB) in mice underwent quantitative phosphoproteomics assay. Temporal phosphoproteomics profiles showed 360 phosphorylation sites with significant regulation after TAB. Multiple mechanical stress sensors were activated after acute pressure overload. Gene ontology analysis revealed differential phosphorylation between hearts with acute pressure overload and chronic hypertrophy. Most interestingly, analysis of the cardiac hypertrophy pathway revealed phosphorylation of the mitochondrial fission protein dynamin-related protein 1 (DRP1) by prohypertrophic kinases. Phosphorylation of DRP1 S622 was confirmed in TAB-treated mouse hearts and phenylephrine (PE)-treated rat neonatal cardiomyocytes. TAB-treated mouse hearts showed phosphorylation-mediated mitochondrial translocation of DRP1. Inhibition of DRP1 with the small-molecule inhibitor mdivi-1 reduced the TAB-induced hypertrophic responses. Mdivi-1 also prevented PE-induced hypertrophic growth and oxygen consumption in rat neonatal cardiomyocytes. We reveal the signaling responses of the heart to pressure stress in vivo and in vitro. DRP1 may be important in the development of cardiac hypertrophy.

  16. Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages.

    Science.gov (United States)

    Liu, Huiquan; Fu, Yanping; Xie, Jiatao; Cheng, Jiasen; Ghabrial, Said A; Li, Guoqing; Peng, Youliang; Yi, Xianhong; Jiang, Daohong

    2012-06-20

    Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses. In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families. Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses.

  17. Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages

    Directory of Open Access Journals (Sweden)

    Liu Huiquan

    2012-06-01

    Full Text Available Abstract Background Double-stranded (ds RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT among dsRNA viruses. Results In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families. Conclusions Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses.

  18. OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY REVEALS BLOOD FLOW IN CHOROIDAL NEOVASCULAR MEMBRANE IN REMISSION PHASE OF NEOVASCULAR AGE-RELATED MACULAR DEGENERATION.

    Science.gov (United States)

    Ichiyama, Yusuke; Sawada, Tomoko; Ito, Yuka; Kakinoki, Masashi; Ohji, Masahito

    2017-04-01

    The aim of the study was to investigate blood flow in choroidal neovascular membrane in remission phase of neovascular age-related macular degeneration using optical coherence tomography (OCT) angiography. OCT angiography was obtained in eyes with remission phase of neovascular age-related macular degeneration after treatments, defined as no exudative change (such as macular edema, subretinal fluid, and subretinal hemorrhage) observed in eyes without any treatment for neovascular age-related macular degeneration within the previous 6 months. Irregular blood flows shown in the segmentation of outer retina detected by OCT angiography were considered as blood flows in choroidal neovascular membrane. The vascular area and vessel density were obtained from OCT angiography images. Twenty eyes of 20 patients were included in this analysis. The blood flows in choroidal neovascular membrane were observed in all eyes (100%) using OCT angiography. The mean vascular area was 3.81 ± 3.41 mm and the mean vessel density of lesion was 28.9 ± 8.2%. The vessel density was significantly correlated with best-corrected visual acuity and duration of remission (best-corrected visual acuity: P = 0.008, r = -0.576; duration of remission: P = 0.017, r = -0.525, respectively). Optical coherence tomography angiography revealed that blood flows in choroidal neovascular membrane remained in eyes with clinically inactive neovascular age-related macular degeneration.

  19. Molecular basis of structural make-up of feeds in relation to nutrient absorption in ruminants, revealed with advanced molecular spectroscopy: A review on techniques and models

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Md. Mostafizar [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    2017-01-31

    Progress in ruminant feed research is no more feasible only based on wet chemical analysis, which is merely able to provide information on chemical composition of feeds regardless of their digestive features and nutritive value in ruminants. Studying internal structural make-up of functional groups/feed nutrients is often vital for understanding the digestive behaviors and nutritive values of feeds in ruminant because the intrinsic structure of feed nutrients is more related to its overall absorption. In this article, the detail information on the recent developments in molecular spectroscopic techniques to reveal microstructural information of feed nutrients and the use of nutrition models in regards to ruminant feed research was reviewed. The emphasis of this review was on (1) the technological progress in the use of molecular spectroscopic techniques in ruminant feed research; (2) revealing spectral analysis of functional groups of biomolecules/feed nutrients; (3) the use of advanced nutrition models for better prediction of nutrient availability in ruminant systems; and (4) the application of these molecular techniques and combination of nutrient models in cereals, co-products and pulse crop research. The information described in this article will promote better insight in the progress of research on molecular structural make-up of feed nutrients in ruminants.

  20. Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.).

    Science.gov (United States)

    Nie, Shanshan; Xu, Liang; Wang, Yan; Huang, Danqiong; Muleke, Everlyne M; Sun, Xiaochuan; Wang, Ronghua; Xie, Yang; Gong, Yiqin; Liu, Liwang

    2015-09-15

    MicroRNAs (miRNAs) play vital regulatory roles in plant growth and development. The phase transition from vegetative growth to flowering is crucial in the life cycle of plants. To date, miRNA-mediated flowering regulatory networks remain largely unexplored in radish. In this study, two small RNA libraries from radish leaves at vegetative and reproductive stages were constructed and sequenced by Solexa sequencing. A total of 94 known miRNAs representing 21 conserved and 13 non-conserved miRNA families, and 44 potential novel miRNAs, were identified from the two libraries. In addition, 42 known and 17 novel miRNAs were significantly differentially expressed and identified as bolting-related miRNAs. RT-qPCR analysis revealed that some miRNAs exhibited tissue- or developmental stage-specific expression patterns. Moreover, 154 target transcripts were identified for 50 bolting-related miRNAs, which were predominately involved in plant development, signal transduction and transcriptional regulation. Based on the characterization of bolting-related miRNAs and their target genes, a putative schematic model of miRNA-mediated bolting and flowering regulatory network was proposed. These results could provide insights into bolting and flowering regulatory networks in radish, and facilitate dissecting the molecular mechanisms underlying bolting and flowering time regulation in vegetable crops.

  1. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China.

    Science.gov (United States)

    Grunert, Klaus G; Perrea, Toula; Zhou, Yanfeng; Huang, Guang; Sørensen, Bjarne T; Krystallis, Athanasios

    2011-04-01

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the food related lifestyle (FRL) instrument to reveal food consumption patterns in a Chinese context. Data were collected from 479 respondents in 6 major Chinese cities using a Chinese version of the FRL instrument. Analysis of reliability and dimensionality of the scales resulted in a revised version of the instrument, in which a number of dimensions of the original instrument had to be omitted. This revised instrument was tested for statistical robustness and used as a basis for the derivation of consumer segments. Construct validity of the instrument was then investigated by profiling the segments in terms of consumer values, attitudes and purchase behaviour, using frequency of consumption of pork products as an example. Three consumer segments were identified: concerned, uninvolved and traditional. This pattern replicates partly those identified in Western cultures. Moreover, all three segments showed consistent value-attitude-behaviour profiles. The results also suggest which dimensions may be missing in the instrument in a more comprehensive instrument adapted to Chinese conditions, most notably a broader treatment of eating out activities. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. Age-Related Changes in Locomotor Performance Reveal a Similar Pattern for Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens.

    Science.gov (United States)

    Marck, Adrien; Berthelot, Geoffroy; Foulonneau, Vincent; Marc, Andy; Antero-Jacquemin, Juliana; Noirez, Philippe; Bronikowski, Anne M; Morgan, Theodore J; Garland, Theodore; Carter, Patrick A; Hersen, Pascal; Di Meglio, Jean-Marc; Toussaint, Jean-François

    2017-04-01

    Locomotion is one of the major physiological functions for most animals. Previous studies have described aging mechanisms linked to locomotor performance among different species. However, the precise dynamics of these age-related changes, and their interactions with development and senescence, are largely unknown. Here, we use the same conceptual framework to describe locomotor performances in Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens. We show that locomotion is a consistent biomarker of age-related changes, with an asymmetrical pattern throughout life, regardless of the type of effort or its duration. However, there is variation (i) among species for the same mode of locomotion, (ii) within species for different modes of locomotion, and (iii) among individuals of the same species for the same mode of locomotion. Age-related patterns are modulated by genetic (such as selective breeding) as well as environmental conditions (such as temperature). However, in all cases, the intersection of the rising developmental phase and the declining senescent phase reveals neither a sharp transition nor a plateau, but a smooth transition, emphasizing a crucial moment: the age at peak performance. This transition may define a specific target for future investigations on the dynamics of such biological interactions. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Clustering patterns of LOD scores for asthma-related phenotypes revealed by a genome-wide screen in 295 French EGEA families.

    Science.gov (United States)

    Bouzigon, Emmanuelle; Dizier, Marie-Hélène; Krähenbühl, Christine; Lemainque, Arnaud; Annesi-Maesano, Isabella; Betard, Christine; Bousquet, Jean; Charpin, Denis; Gormand, Frédéric; Guilloud-Bataille, Michel; Just, Jocelyne; Le Moual, Nicole; Maccario, Jean; Matran, Régis; Neukirch, Françoise; Oryszczyn, Marie-Pierre; Paty, Evelyne; Pin, Isabelle; Rosenberg-Bourgin, Myriam; Vervloet, Daniel; Kauffmann, Francine; Lathrop, Mark; Demenais, Florence

    2004-12-15

    A genome-wide scan for asthma phenotypes was conducted in the whole sample of 295 EGEA families selected through at least one asthmatic subject. In addition to asthma, seven phenotypes involved in the main asthma physiopathological pathways were considered: SPT (positive skin prick test response to at least one of 11 allergens), SPTQ score being the number of positive skin test responses to 11 allergens, Phadiatop (positive specific IgE response to a mixture of allergens), total IgE levels, eosinophils, bronchial responsiveness (BR) to methacholine challenge and %predicted FEV(1). Four regions showed evidence for linkage (PLOD scores. This analysis revealed clustering of LODs for asthma, SPT and Phadiatop on one axis and clustering of LODs for %FEV(1), BR and SPTQ on the other, while LODs for IgE and eosinophils appeared to be independent from all other LODs. These results provide new insights into the potential sharing of genetic determinants by asthma-related phenotypes.

  4. Elastic-Plastic Numerical Analysis of Tunnel Stability Based on the Closest Point Projection Method Considering the Effect of Water Pressure

    Directory of Open Access Journals (Sweden)

    Zhan-ping Song

    2016-01-01

    Full Text Available To study the tunnel stability at various static water pressures and determine the mechanical properties and deformation behavior of surrounding rock, a modified effective stress formula was introduced into a numerical integration algorithm of elastic-plastic constitutive equation, that is, closest point projection method (CPPM. Taking the effects of water pressure and seepage into account, a CPPM-based formula was derived and a CPPM algorithm based on Drucker-Prager yield criterion considering the effect of pore water pressure was provided. On this basis, a CPPM-based elastic-plastic numerical analysis program considering pore water pressure was developed, which can be applied in the engineering of tunnels and other underground structures. The algorithm can accurately take the effects of groundwater on stability of surrounding rock mass into account and it can show the more pronounced effect of pore water pressure on stress, deformation, and the plastic zone in a tunnel. The stability of water flooding in Fusong tunnel was systematically analyzed using the developed program. The analysis results showed that the existence of groundwater seepage under tunnel construction will give rise to stress redistribution in the surrounding rock mass. Pore water pressure has a significant effect on the surrounding rock mass.

  5. Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Radke, Brittany; Findley, Seth; Abernathy, Brian; Vallejos, C Eduardo; Jackson, Scott A

    2016-04-07

    Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2-4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species. Copyright © 2016 Iwata-Otsubo et al.

  6. Fluorescence In Situ Hybridization (FISH-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris and Relatives

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    Aiko Iwata-Otsubo

    2016-04-01

    Full Text Available Fluorescence in situ hybridization (FISH-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.

  7. Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome.

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    Badri, Dayakar V; Chaparro, Jacqueline M; Zhang, Ruifu; Shen, Qirong; Vivanco, Jorge M

    2013-02-15

    The roots of plants have the ability to influence its surrounding microbiology, the so-called rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals. Here we report how these phytochemicals could modulate the microbial composition of a soil in the absence of the plant. For this purpose, root exudates of Arabidopsis were collected and fractionated to obtain natural blends of phytochemicals at various relative concentrations that were characterized by GC-MS and applied repeatedly to a soil. Soil bacterial changes were monitored by amplifying and pyrosequencing the 16 S ribosomal small subunit region. Our analyses reveal that one phytochemical can culture different operational taxonomic units (OTUs), mixtures of phytochemicals synergistically culture groups of OTUs, and the same phytochemical can act as a stimulator or deterrent to different groups of OTUs. Furthermore, phenolic-related compounds showed positive correlation with a higher number of unique OTUs compared with other groups of compounds (i.e. sugars, sugar alcohols, and amino acids). For instance, salicylic acid showed positive correlations with species of Corynebacterineae, Pseudonocardineae and Streptomycineae, and GABA correlated with species of Sphingomonas, Methylobacterium, Frankineae, Variovorax, Micromonosporineae, and Skermanella. These results imply that phenolic compounds act as specific substrates or signaling molecules for a large group of microbial species in the soil.

  8. Differences in the relative timing of developmental events during oogenesis in lower dipterans (Nematocera) reveal the autonomy of follicular cells' differentiation program.

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    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.

  9. Dissecting the social brain: Introducing the EmpaToM to reveal distinct neural networks and brain-behavior relations for empathy and Theory of Mind.

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    Kanske, Philipp; Böckler, Anne; Trautwein, Fynn-Mathis; Singer, Tania

    2015-11-15

    Successful social interactions require both affect sharing (empathy) and understanding others' mental states (Theory of Mind, ToM). As these two functions have mostly been investigated in isolation, the specificity of the underlying neural networks and the relation of these networks to the respective behavioral indices could not be tested. Here, we present a novel fMRI paradigm (EmpaToM) that independently manipulates both empathy and ToM. Experiments 1a/b (N=90) validated the task with established empathy and ToM paradigms on a behavioral and neural level. Experiment 2 (N=178) employed the EmpaToM and revealed clearly separable neural networks including anterior insula for empathy and ventral temporoparietal junction for ToM. These distinct networks could be replicated in task-free resting state functional connectivity. Importantly, brain activity in these two networks specifically predicted the respective behavioral indices, that is, inter-individual differences in ToM related brain activity predicted inter-individual differences in ToM performance, but not empathic responding, and vice versa. Taken together, the validated EmpaToM allows separation of affective and cognitive routes to understanding others. It may thus benefit future clinical, developmental, and intervention studies on identifying selective impairments and improvement in specific components of social cognition. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Touchscreen-based cognitive tasks reveal age-related impairment in a primate aging model, the grey mouse lemur (Microcebus murinus).

    Science.gov (United States)

    Joly, Marine; Ammersdörfer, Sandra; Schmidtke, Daniel; Zimmermann, Elke

    2014-01-01

    Mouse lemurs are suggested to represent promising novel non-human primate models for aging research. However, standardized and cross-taxa cognitive testing methods are still lacking. Touchscreen-based testing procedures have proven high stimulus control and reliability in humans and rodents. The aim of this study was to adapt these procedures to mouse lemurs, thereby exploring the effect of age. We measured appetitive learning and cognitive flexibility of two age groups by applying pairwise visual discrimination (PD) and reversal learning (PDR) tasks. On average, mouse lemurs needed 24 days of training before starting with the PD task. Individual performances in PD and PDR tasks correlate significantly, suggesting that individual learning performance is unrelated to the respective task. Compared to the young, aged mouse lemurs showed impairments in both PD and PDR tasks. They needed significantly more trials to reach the task criteria. A much higher inter-individual variation in old than in young adults was revealed. Furthermore, in the PDR task, we found a significantly higher perseverance in aged compared to young adults, indicating an age-related deficit in cognitive flexibility. This study presents the first touchscreen-based data on the cognitive skills and age-related dysfunction in mouse lemurs and provides a unique basis to study mechanisms of inter-individual variation. It furthermore opens exciting perspectives for comparative approaches in aging, personality, and evolutionary research.

  11. Touchscreen-based cognitive tasks reveal age-related impairment in a primate aging model, the grey mouse lemur (Microcebus murinus.

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    Marine Joly

    Full Text Available Mouse lemurs are suggested to represent promising novel non-human primate models for aging research. However, standardized and cross-taxa cognitive testing methods are still lacking. Touchscreen-based testing procedures have proven high stimulus control and reliability in humans and rodents. The aim of this study was to adapt these procedures to mouse lemurs, thereby exploring the effect of age. We measured appetitive learning and cognitive flexibility of two age groups by applying pairwise visual discrimination (PD and reversal learning (PDR tasks. On average, mouse lemurs needed 24 days of training before starting with the PD task. Individual performances in PD and PDR tasks correlate significantly, suggesting that individual learning performance is unrelated to the respective task. Compared to the young, aged mouse lemurs showed impairments in both PD and PDR tasks. They needed significantly more trials to reach the task criteria. A much higher inter-individual variation in old than in young adults was revealed. Furthermore, in the PDR task, we found a significantly higher perseverance in aged compared to young adults, indicating an age-related deficit in cognitive flexibility. This study presents the first touchscreen-based data on the cognitive skills and age-related dysfunction in mouse lemurs and provides a unique basis to study mechanisms of inter-individual variation. It furthermore opens exciting perspectives for comparative approaches in aging, personality, and evolutionary research.

  12. An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism

    Science.gov (United States)

    Mélade, Julien; Wieseke, Nicolas; Ramasindrazana, Beza; Flores, Olivier; Lagadec, Erwan; Gomard, Yann; Goodman, Steven M.; Dellagi, Koussay; Pascalis, Hervé

    2016-01-01

    An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats. PMID:27068130

  13. Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.).

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    Hu, Jihong; Chen, Guanglong; Zhang, Hongyuan; Qian, Qian; Ding, Yi

    2016-08-05

    Cytoplasmic male sterility (CMS) is an ideal model for investigating the mitochondrial-nuclear interaction and down-regulated genes in CMS lines which might be the candidate genes for pollen development in rice. In this study, a set of rice alloplasmic sporophytic CMS lines was obtained by successive backcrossing of Meixiang B, with three different cytoplasmic types: D62A (D type), ZS97A (WA type) and XQZ-A (DA type). Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expressed genes (DEGs) in each of the three CMS lines compared with the maintainer line Meixiang B. GO and MapMan analysis indicated that these DEGs were mainly involved in lipid metabolism and cell wall organization. Compared with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were identified and 56 of them were down-regulated in all the CMS lines of rice. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. Weighted gene co-expression network analysis (WGCNA) revealed that two modules were significantly associated with male sterility and many hub genes that were differentially expressed in the CMS lines. A large set of putative genes involved in anther development was identified in the present study. The results will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide a rich resource for further functional research on the pollen development in rice.

  14. Task-Related Edge Density (TED-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.

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    Gabriele Lohmann

    Full Text Available The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED. TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function.

  15. Task-Related Edge Density (TED)-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.

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    Lohmann, Gabriele; Stelzer, Johannes; Zuber, Verena; Buschmann, Tilo; Margulies, Daniel; Bartels, Andreas; Scheffler, Klaus

    2016-01-01

    The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED). TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function.

  16. 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

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    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.

  17. Functional MRI examination of empathy for pain in people with schizophrenia reveals abnormal activation related to cognitive perspective-taking but typical activation linked to affective sharing

    Science.gov (United States)

    Vistoli, Damien; Lavoie, Marie-Audrey; Sutliff, Stephanie; Jackson, Philip L.; Achim, Amélie M.

    2017-01-01

    Background Schizophrenia is associated with important disturbances in empathy that are related to everyday functioning. Empathy is classically defined as including affective (sharing others’ emotions) and cognitive (taking others’ cognitive perspectives) processes. In healthy individuals, studies on empathy for pain revealed specific brain systems associated with these sets of processes, notably the anterior middle cingulate (aMCC) and anterior insula (AI) for affective sharing and the bilateral temporoparietal junction (TPJ) for the cognitive processes, but the integrity of these systems in patients with schizophrenia remains uncertain. Methods Patients with schizophrenia and healthy controls performed a pain empathy task while undergoing fMRI scanning. Participants observed pictures of hands in either painful or nonpainful situations and rated the level of pain while imagining either themselves (self) or an unknown person (other) in these situations. Results We included 27 patients with schizophrenia and 21 healthy controls in our analyses. For the pain versus no pain contrast, patients showed overall typical activation patterns in the aMCC and AI, with only a small part of the aMCC showing reduced activation compared with controls. For the other versus self contrast, patients showed an abnormal modulation of activation in the TPJ bilaterally (extending to the posterior superior temporal sulcus, referred to as the TPJ/pSTS). Limitations The design included an unnecessary manipulation of the visual perspective that reduced the number of trials for analysis. The sample size may not account for the heterogeneity of schizophrenia. Conclusion People with schizophrenia showed relatively intact brain activation when observing others’ pain, but showed abnormalities when asked to take the cognitive perspectives of others. PMID:28556774

  18. Screening sourdough samples for gliadin-degrading activity revealed Lactobacillus casei strains able to individually metabolize the coeliac-disease-related 33-mer peptide.

    Science.gov (United States)

    Alvarez-Sieiro, Patricia; Redruello, Begoña; Ladero, Victor; Martín, Maria Cruz; Fernández, María; Alvarez, Miguel A

    2016-05-01

    A selective culture medium containing acid-hydrolyzed gliadins as the sole nitrogen source was used in the search for sourdough-indigenous lactic acid bacteria (LAB) with gliadin-metabolizing activity. Twenty gliadin-degrading LAB strains were isolated from 10 sourdoughs made in different ways and from different geographical regions. Fifteen of the 20 isolated strains were identified as Lactobacillus casei, a species usually reported as subdominant in sourdough populations. The other 5 gliadin-degrading strains belonged to the more commonly encountered sourdough species Leuconostoc mesenteroides and Lactobacillus plantarum. All these strains were shown to be safe in terms of their resistance to antimicrobial agents. When individually incubated with the α2-gliadin-derived immunotoxic 33-mer peptide (97.5 ppm), half of the L. casei strains metabolized at least 50% of it within 24 h. One strain metabolized 82% of the 33-mer peptide within 8 h and made it fully disappear within 12 h. These results reveal for the first time the presence in sourdough of proteolytic L. casei strains with the capacity to individually metabolize the coeliac-disease-related 33-mer peptide.

  19. The oscillatory activities and its synchronization in auditory-visual integration as revealed by event-related potentials to bimodal stimuli

    Science.gov (United States)

    Guo, Jia; Xu, Peng; Yao, Li; Shu, Hua; Zhao, Xiaojie

    2012-03-01

    Neural mechanism of auditory-visual speech integration is always a hot study of multi-modal perception. The articulation conveys speech information that helps detect and disambiguate the auditory speech. As important characteristic of EEG, oscillations and its synchronization have been applied to cognition research more and more. This study analyzed the EEG data acquired by unimodal and bimodal stimuli using time frequency and phase synchrony approach, investigated the oscillatory activities and its synchrony modes behind evoked potential during auditory-visual integration, in order to reveal the inherent neural integration mechanism under these modes. It was found that beta activity and its synchronization differences had relationship with gesture N1-P2, which happened in the earlier stage of speech coding to pronouncing action. Alpha oscillation and its synchronization related with auditory N1-P2 might be mainly responsible for auditory speech process caused by anticipation from gesture to sound feature. The visual gesture changing enhanced the interaction of auditory brain regions. These results provided explanations to the power and connectivity change of event-evoked oscillatory activities which matched ERPs during auditory-visual speech integration.

  20. The memory that’s right and the memory that’s left: Event-related potentials reveal hemispheric asymmetries in the encoding and retention of verbal information

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    Evans, Karen M.; Federmeier, Kara D.

    2009-01-01

    We examined the nature and timecourse of hemispheric asymmetries in verbal memory by recording event-related potentials (ERPs) in a continuous recognition task. Participants made overt recognition judgments to test words presented in central vision that were either novel (new words) or had been previously presented in the left or right visual field (old words). An ERP memory effect linked to explicit retrieval revealed no asymmetries for words repeated at short and medium retention intervals, but at longer repetition lags (20–50 intervening words) this ‘old/new effect’ was more pronounced for words whose study presentation had been biased to the right hemisphere (RH). Additionally, a repetition effect linked to more implicit recognition processes (P2 amplitude changes) was observed at all lags for words preferentially encoded by the RH but was not observed for left hemisphere (LH)-encoded words. These results are consistent with theories that the RH encodes verbal stimuli more veridically whereas the LH encodes in a more abstract manner. The current findings provide a critical link between prior work on memory asymmetries, which has emphasized general LH advantages for verbal material, and on language comprehension, which has pointed to an important role for the RH in language processes that require the retention and integration of verbal information over long time spans. PMID:17291547

  1. Comparative molecular epidemiology of two closely related coronaviruses, bovine coronavirus (BCoV) and human coronavirus OC43 (HCoV-OC43), reveals a different evolutionary pattern.

    Science.gov (United States)

    Kin, Nathalie; Miszczak, Fabien; Diancourt, Laure; Caro, Valérie; Moutou, François; Vabret, Astrid; Ar Gouilh, Meriadeg

    2016-06-01

    Bovine coronaviruses (BCoVs) are widespread around the world and cause enteric or respiratory infections among cattle. The current study includes 13 samples from BCoVs collected in Normandy during an 11-year period (from 2003 to 2014), 16 French HCoV-OC43s, and 113 BCoVs or BCoVs-like sequence data derived from partial or complete genome sequences available on GenBank. According to a genotyping method developed previously for HCoV-OC43, BCoVs and BCoVs-like are distributed on three main sub-clusters named C1, C2, and C3. Sub-cluster C1 includes BCoVs and BCoVs-like from America and Asia. Sub-cluster C2 includes BCoVs from Europe. Sub-cluster C3 includes prototype, vaccine, or attenuated BCoV strains. The phylogenetic analyses revealed the monophyletic status of the BCoVs from France reported here for the first time. Moreover, BCoV exhibits a relative genetic stability when compared to HCoV-OC43 we previously described from the same region. The numerous recombination detected between HCoV-OC43 were much less frequent for BCoV. The analysis points thus to the influence of different evolutive constraints in these two close groups. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Utilizing the Iterative Closest Point (ICP) algorithm for enhanced registration of high resolution surface models - more than a simple black-box application

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    Stöcker, Claudia; Eltner, Anette

    2016-04-01

    Advances in computer vision and digital photogrammetry (i.e. structure from motion) allow for fast and flexible high resolution data supply. Within geoscience applications and especially in the field of small surface topography, high resolution digital terrain models and dense 3D point clouds are valuable data sources to capture actual states as well as for multi-temporal studies. However, there are still some limitations regarding robust registration and accuracy demands (e.g. systematic positional errors) which impede the comparison and/or combination of multi-sensor data products. Therefore, post-processing of 3D point clouds can heavily enhance data quality. In this matter the Iterative Closest Point (ICP) algorithm represents an alignment tool which iteratively minimizes distances of corresponding points within two datasets. Even though tool is widely used; it is often applied as a black-box application within 3D data post-processing for surface reconstruction. Aiming for precise and accurate combination of multi-sensor data sets, this study looks closely at different variants of the ICP algorithm including sub-steps of point selection, point matching, weighting, rejection, error metric and minimization. Therefore, an agricultural utilized field was investigated simultaneously by terrestrial laser scanning (TLS) and unmanned aerial vehicle (UAV) sensors two times (once covered with sparse vegetation and once bare soil). Due to different perspectives both data sets show diverse consistency in terms of shadowed areas and thus gaps so that data merging would provide consistent surface reconstruction. Although photogrammetric processing already included sub-cm accurate ground control surveys, UAV point cloud exhibits an offset towards TLS point cloud. In order to achieve the transformation matrix for fine registration of UAV point clouds, different ICP variants were tested. Statistical analyses of the results show that final success of registration and therefore

  3. Real-time estimation of prostate tumor rotation and translation with a kV imaging system based on an iterative closest point algorithm

    Science.gov (United States)

    Nasehi Tehrani, Joubin; O'Brien, Ricky T.; Rugaard Poulsen, Per; Keall, Paul

    2013-12-01

    Previous studies have shown that during cancer radiotherapy a small translation or rotation of the tumor can lead to errors in dose delivery. Current best practice in radiotherapy accounts for tumor translations, but is unable to address rotation due to a lack of a reliable real-time estimate. We have developed a method based on the iterative closest point (ICP) algorithm that can compute rotation from kilovoltage x-ray images acquired during radiation treatment delivery. A total of 11 748 kilovoltage (kV) images acquired from ten patients (one fraction for each patient) were used to evaluate our tumor rotation algorithm. For each kV image, the three dimensional coordinates of three fiducial markers inside the prostate were calculated. The three dimensional coordinates were used as input to the ICP algorithm to calculate the real-time tumor rotation and translation around three axes. The results show that the root mean square error was improved for real-time calculation of tumor displacement from a mean of 0.97 mm with the stand alone translation to a mean of 0.16 mm by adding real-time rotation and translation displacement with the ICP algorithm. The standard deviation (SD) of rotation for the ten patients was 2.3°, 0.89° and 0.72° for rotation around the right-left (RL), anterior-posterior (AP) and superior-inferior (SI) directions respectively. The correlation between all six degrees of freedom showed that the highest correlation belonged to the AP and SI translation with a correlation of 0.67. The second highest correlation in our study was between the rotation around RL and rotation around AP, with a correlation of -0.33. Our real-time algorithm for calculation of rotation also confirms previous studies that have shown the maximum SD belongs to AP translation and rotation around RL. ICP is a reliable and fast algorithm for estimating real-time tumor rotation which could create a pathway to investigational clinical treatment studies requiring real

  4. Comparative study of two immunity-related GTPase genes in Chinese soft-shell turtle reveals their molecular characteristics and functional activity in immune defense.

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    Shi, Yan; Shen, Sixian; Hu, Sufei; Ding, Tie; Hong, Xiaoyou; Chen, Chen; Zhu, Xinping; Zhao, Zhe

    2018-04-01

    The immunity-related GTPases (IRGs) are a family of proteins that play critical roles in innate resistance to intracellular pathogens. The number and diversity of IRG genes differ greatly in different species. Although IRG proteins have been well studies in mammals, they remain poorly characterized in lower vertebrates. In this study, we cloned two IRG genes, PsIRG5 and PsIRG8, from the Chinese soft-shelled turtle and compared their characterization and functional activity with mammalian IRGs. The PsIRG5 is a gene of 1896 bp that encodes a protein of 413 amino acid and PsIRG8 is 1543 bp in length encoding another 413 aa protein. Sequence alignment between all turtle IRG-like genes and mammalian IRGs showed that both PsIRG5 and PsIRG8 were conserved with mammalian GKS IRGs, while PsIRG5 appeared a closer evolutionary relationship with mammalian GMS IRGs. The expression and subcellular characterization revealed that PsIRG5 was dramatically upregulated under Aeromonas hydrophila challenge and exhibited co-localization with lysosomes in cells; whereas PsIRG8 was downregulated and has no distinct localization. Functional activity assay demonstrated that PsIRG5 plays a role in autophagy induction and IFN-γ contributes to enhance the induction, since it has IFN-inducible elements in its promoter region. These data above unravel the molecular characterization and functional activity of IRGs in lower vertebrate for the first time and will provide insights into the comparative immunity and evolutionary relationships of IRGs between mammals and reptiles. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

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    Claude Pasquier

    2017-07-01

    Full Text Available Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson–Crick duplex. The “triplex-forming oligonucleotide” (TFO can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the “triplex-forming oligonucleotide” in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster. These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

  6. Metabolomic Profiling of Extracellular Vesicles and Alternative Normalization Methods Reveal Enriched Metabolites and Strategies to Study Prostate Cancer-Related Changes.

    Science.gov (United States)

    Puhka, Maija; Takatalo, Maarit; Nordberg, Maria-Elisa; Valkonen, Sami; Nandania, Jatin; Aatonen, Maria; Yliperttula, Marjo; Laitinen, Saara; Velagapudi, Vidya; Mirtti, Tuomas; Kallioniemi, Olli; Rannikko, Antti; Siljander, Pia R-M; Af Hällström, Taija Maria

    2017-01-01

    and relatively small amount of sample material. With the knowledge about the specific enrichment of metabolites and normalization methods, EV metabolomics could be used to gain novel biomarker data not revealed by the analysis of the original EV source materials.

  7. Changes in hemp secondary fiber production related to technical fiber variability revealed by light microscopy and attenuated total reflectance Fourier transform infrared spectroscopy.

    Science.gov (United States)

    Fernandez-Tendero, Eva; Day, Arnaud; Legros, Sandrine; Habrant, Anouck; Hawkins, Simon; Chabbert, Brigitte

    2017-01-01

    Interest in hemp (Cannabis sativa L.) is increasing due to the development of a new range of industrial applications based on bast fibers. However the variability of bast fiber yield and quality represents an important barrier to further exploitation. Primary and secondary fiber content was examined in two commercial hemp varieties (Fedora 17, Santhica 27) grown under contrasted sowing density and irrigation conditions. Both growing conditions and hemp varieties impact stem tissue architecture with a large effect on the proportion of secondary fibers but not primary fibers. Attenuated total reflectance infrared spectroscopy allowed the discrimination of manually-isolated native primary fibers and secondary fibers but did not reveal any clustering according to growing conditions and variety. Infrared data were confirmed by wet chemistry analyses that revealed slight but significant differences between primary and secondary fiber cell wall composition. Infrared spectroscopy of technical fibers obtained after mechanical defibering revealed differences with native primary, but not secondary fibers and also discriminated samples obtained from plants grown under different conditions. Altogether the results suggested that the observed variability of hemp technical fibers could be partially explained by i) differences in secondary fiber production and ii) differential behavior during mechanical defibering resulting in unequal separation of primary and secondary fibers.

  8. A Deep Phenotype Association Study Reveals Specific Phenotype Associations with Genetic Variants in Age-related Macular Degeneration: Age-Related Eye Disease Study 2 (AREDS2) Report No. 14.

    Science.gov (United States)

    van Asten, Freekje; Simmons, Michael; Singhal, Ayush; Keenan, Tiarnan D; Ratnapriya, Rinki; Agrón, Elvira; Clemons, Traci E; Swaroop, Anand; Lu, Zhiyong; Chew, Emily Y

    2017-10-30

    Age-related macular degeneration (AMD), a multifactorial disease with variable phenotypic presentation, was associated with 52 single nucleotide polymorphisms (SNPs) at 34 loci in a genome-wide association study (GWAS). These genetic variants could modulate different biological pathways involved in AMD, contributing to phenotypic variability. To better understand the effects of these SNPs, we performed a deep phenotype association study (DeePAS) in the Age-Related Eye Disease Study 2 (AREDS2), followed by replication using AREDS participants, to identify genotype associations with AMD and non-AMD ocular and systemic phenotypes. Cohort study. AREDS and AREDS2 participants. AREDS2 participants (discovery cohort) had detailed phenotyping for AMD; other eye conditions; cardiovascular, neurologic, gastrointestinal, and endocrine disease; cognitive function; serum nutrient levels; and others (total of 139 AMD and non-AMD phenotypes). Genotypes of the 52 GWAS SNPs were obtained. The DeePAS was performed by correlating the 52 SNPs to all phenotypes using logistic and linear regression models. Associations that reached Bonferroni-corrected statistical significance were replicated in AREDS. Genotype-phenotype associations. A total of 1776 AREDS2 participants had 5 years follow-up; 1435 AREDS participants had 10 years. The DeePAS revealed a significant association of the rs3750846 SNP at the ARMS2/HTRA1 locus with subretinal/sub-retinal pigment epithelial (RPE) hemorrhage related to neovascular AMD (odds ratio 1.55 [95% confidence interval 1.31-1.84], P = 2.67 × 10(-7)). This novel association remained significant after conditioning on participants with neovascular AMD (P = 2.42 × 10(-4)). Carriers of rs3750846 had poorer visual acuity during follow-up (P = 6.82 × 10(-7)) and were more likely to have a first-degree relative with AMD (P = 5.38 × 10(-6)). Two SNPs at the CFH locus, rs10922109 and rs570618, were associated with the drusen area in the Early Treatment

  9. Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system

    DEFF Research Database (Denmark)

    Fusco, Salvatore; Liguori, Rossana; Limauro, Danila

    2015-01-01

    in a double-infected strain to explore both virus-host and virus-virus interactions. Whereas SSV1 did not induce major changes of the host gene expression, SSV2 elicited a strong host response, which includes the transcriptional activation of CRISPR loci and cas genes. As a consequence, a significant decrease...... of the SSV2 copy number has been observed, which in turn led to provirus-capture into the host chromosome. Results of this study have revealed novel aspects of the host-viral interaction in the frame of the CRISPR-response....

  10. Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.

    Science.gov (United States)

    Ariani, Pietro; Regaiolo, Alice; Lovato, Arianna; Giorgetti, Alejandro; Porceddu, Andrea; Camiolo, Salvatore; Wong, Darren; Castellarin, Simone; Vandelle, Elodie; Polverari, Annalisa

    2016-12-02

    The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.

  11. Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins.

    Science.gov (United States)

    La, My-Van; Crapoulet, Nicolas; Barbry, Pascal; Raoult, Didier; Renesto, Patricia

    2007-10-02

    The aim of this study was to analyze the genomic diversity of several Tropheryma whipplei strains by microarray-based comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples recovered from different countries were compared with the T. whipplei Twist strain. For each isolate, the genes were defined as either present or absent/divergent using the GACK analysis software. Genomic changes were then further characterized by PCR and sequencing. The results revealed a limited genetic variation among the T. whipplei isolates, with at most 2.24% of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding the WiSP membrane protein family. This work also demonstrated a 19.2 kb-pair deletion within the T. whipplei DIG15 strain. This deletion occurs in the same region as the previously described large genomic rearrangement between Twist and TW08/27. Thus, this can be considered as a major hot-spot for intra-specific T. whipplei differentiation. Analysis of this deleted region confirmed the role of WND domains in generating T. whipplei diversity. This work provides the first comprehensive genomic comparison of several T. whipplei isolates. It reveals that clinical isolates originating from various geographic and biological sources exhibit a high conservation rate, indicating that T. whipplei rarely interacts with exogenous DNA. Remarkably, frequent inter-strain variations were dicovered that affected members of the WiSP family.

  12. Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2007-10-01

    Full Text Available Abstract Background The aim of this study was to analyze the genomic diversity of several Tropheryma whipplei strains by microarray-based comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples recovered from different countries were compared with the T. whipplei Twist strain. For each isolate, the genes were defined as either present or absent/divergent using the GACK analysis software. Genomic changes were then further characterized by PCR and sequencing. Results The results revealed a limited genetic variation among the T. whipplei isolates, with at most 2.24% of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding the WiSP membrane protein family. This work also demonstrated a 19.2 kb-pair deletion within the T. whipplei DIG15 strain. This deletion occurs in the same region as the previously described large genomic rearrangement between Twist and TW08/27. Thus, this can be considered as a major hot-spot for intra-specific T. whipplei differentiation. Analysis of this deleted region confirmed the role of WND domains in generating T. whipplei diversity. Conclusion This work provides the first comprehensive genomic comparison of several T. whipplei isolates. It reveals that clinical isolates originating from various geographic and biological sources exhibit a high conservation rate, indicating that T. whipplei rarely interacts with exogenous DNA. Remarkably, frequent inter-strain variations were dicovered that affected members of the WiSP family.

  13. Relativity

    CERN Document Server

    Einstein, Albert

    2013-01-01

    Time magazine's ""Man of the Century"", Albert Einstein is the founder of modern physics and his theory of relativity is the most important scientific idea of the modern era. In this short book, Einstein explains, using the minimum of mathematical terms, the basic ideas and principles of the theory that has shaped the world we live in today. Unsurpassed by any subsequent books on relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge.With a new foreword by Derek Raine.

  14. Sapromyza lopesi sp. n. from Brazil: a species related to S. duodecimvittata (Frey, 1919 (Diptera: Lauxaniidae

    Directory of Open Access Journals (Sweden)

    G. E. Shewell

    1989-01-01

    Full Text Available A new species, Sapromyza lopesi, is described from Brazil, and compared with its closest relative, S. duodecimvittata (Frey. Some remarks are made on the generic classification of South American Lauxaniidae as it affects these and other species.

  15. Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker-trait associations.

    Science.gov (United States)

    Parra-Londono, Sebastian; Kavka, Mareike; Samans, Birgit; Snowdon, Rod; Wieckhorst, Silke; Uptmoor, Ralf

    2018-02-12

    Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P system development on chromosomes SBI-02 and SBI-03. Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions of the present study.

  16. Enhanced Botrytis cinerea Resistance of Arabidopsis Plants Grown in Compost May Be Explained by Increased Expression of Defense-Related Genes, as Revealed by Microarray Analysis

    Science.gov (United States)

    Segarra, Guillem; Santpere, Gabriel; Elena, Georgina; Trillas, Isabel

    2013-01-01

    Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses. PMID:23405252

  17. Large-scale proteomic analysis of the grapevine leaf apoplastic fluid reveals mainly stress-related proteins and cell wall modifying enzymes.

    Science.gov (United States)

    Delaunois, Bertrand; Colby, Thomas; Belloy, Nicolas; Conreux, Alexandra; Harzen, Anne; Baillieul, Fabienne; Clément, Christophe; Schmidt, Jürgen; Jeandet, Philippe; Cordelier, Sylvain

    2013-02-08

    The extracellular space or apoplast forms a path through the whole plant and acts as an interface with the environment. The apoplast is composed of plant cell wall and space within which apoplastic fluid provides a means of delivering molecules and facilitates intercellular communications. However, the apoplastic fluid extraction from in planta systems remains challenging and this is particularly true for grapevine (Vitis vinifera L.), a worldwide-cultivated fruit plant. Large-scale proteomic analysis reveals the protein content of the grapevine leaf apoplastic fluid and the free interactive proteome map considerably facilitates the study of the grapevine proteome. To obtain a snapshot of the grapevine apoplastic fluid proteome, a vacuum-infiltration-centrifugation method was optimized to collect the apoplastic fluid from non-challenged grapevine leaves. Soluble apoplastic protein patterns were then compared to whole leaf soluble protein profiles by 2D-PAGE analyses. Subsequent MALDI-TOF/TOF mass spectrometry of tryptically digested protein spots was used to identify proteins. This large-scale proteomic analysis established a well-defined proteomic map of whole leaf and leaf apoplastic soluble proteins, with 223 and 177 analyzed spots, respectively. All data arising from proteomic, MS and MS/MS analyses were deposited in the public database world-2DPAGE. Prediction tools revealed a high proportion of (i) classical secreted proteins but also of non-classical secreted proteins namely Leaderless Secreted Proteins (LSPs) in the apoplastic protein content and (ii) proteins potentially involved in stress reactions and/or in cell wall metabolism. This approach provides free online interactive reference maps annotating a large number of soluble proteins of the whole leaf and the apoplastic fluid of grapevine leaf. To our knowledge, this is the first detailed proteome study of grapevine apoplastic fluid providing a comprehensive overview of the most abundant proteins

  18. Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis.

    Directory of Open Access Journals (Sweden)

    Guillem Segarra

    Full Text Available Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses.

  19. Bioinformatics Reveal Five Lineages of Oleosins and the Mechanism of Lineage Evolution Related to Structure/Function from Green Algae to Seed Plants1[OPEN

    Science.gov (United States)

    Huang, Ming-Der; Huang, Anthony H.C.

    2015-01-01

    Plant cells contain subcellular lipid droplets with a triacylglycerol matrix enclosed by a layer of phospholipids and the small structural protein oleosin. Oleosins possess a conserved central hydrophobic hairpin of approximately 72 residues penetrating into the lipid droplet matrix and amphipathic amino- and carboxyl (C)-terminal peptides lying on the phospholipid surface. Bioinformatics of 1,000 oleosins of green algae and all plants emphasizing biological implications reveal five oleosin lineages: primitive (in green algae, mosses, and ferns), universal (U; all land plants), and three in specific organs or phylogenetic groups, termed seed low-molecular-weight (SL; seed plants), seed high-molecular-weight (SH; angiosperms), and tapetum (T; Brassicaceae) oleosins. Transition from one lineage to the next is depicted from lineage intermediates at junctions of phylogeny and organ distributions. Within a species, each lineage, except the T oleosin lineage, has one to four genes per haploid genome, only approximately two of which are active. Primitive oleosins already possess all the general characteristics of oleosins. U oleosins have C-terminal sequences as highly conserved as the hairpin sequences; thus, U oleosins including their C-terminal peptide exert indispensable, unknown functions. SL and SH oleosin transcripts in seeds are in an approximately 1:1 ratio, which suggests the occurrence of SL-SH oleosin dimers/multimers. T oleosins in Brassicaceae are encoded by rapidly evolved multitandem genes for alkane storage and transfer. Overall, oleosins have evolved to retain conserved hairpin structures but diversified for unique structures and functions in specific cells and plant families. Also, our studies reveal oleosin in avocado (Persea americana) mesocarp and no acyltransferase/lipase motifs in most oleosins. PMID:26232488

  20. Bioinformatics Reveal Five Lineages of Oleosins and the Mechanism of Lineage Evolution Related to Structure/Function from Green Algae to Seed Plants.

    Science.gov (United States)

    Huang, Ming-Der; Huang, Anthony H C

    2015-09-01

    Plant cells contain subcellular lipid droplets with a triacylglycerol matrix enclosed by a layer of phospholipids and the small structural protein oleosin. Oleosins possess a conserved central hydrophobic hairpin of approximately 72 residues penetrating into the lipid droplet matrix and amphipathic amino- and carboxyl (C)-terminal peptides lying on the phospholipid surface. Bioinformatics of 1,000 oleosins of green algae and all plants emphasizing biological implications reveal five oleosin lineages: primitive (in green algae, mosses, and ferns), universal (U; all land plants), and three in specific organs or phylogenetic groups, termed seed low-molecular-weight (SL; seed plants), seed high-molecular-weight (SH; angiosperms), and tapetum (T; Brassicaceae) oleosins. Transition from one lineage to the next is depicted from lineage intermediates at junctions of phylogeny and organ distributions. Within a species, each lineage, except the T oleosin lineage, has one to four genes per haploid genome, only approximately two of which are active. Primitive oleosins already possess all the general characteristics of oleosins. U oleosins have C-terminal sequences as highly conserved as the hairpin sequences; thus, U oleosins including their C-terminal peptide exert indispensable, unknown functions. SL and SH oleosin transcripts in seeds are in an approximately 1:1 ratio, which suggests the occurrence of SL-SH oleosin dimers/multimers. T oleosins in Brassicaceae are encoded by rapidly evolved multitandem genes for alkane storage and transfer. Overall, oleosins have evolved to retain conserved hairpin structures but diversified for unique structures and functions in specific cells and plant families. Also, our studies reveal oleosin in avocado (Persea americana) mesocarp and no acyltransferase/lipase motifs in most oleosins. © 2015 American Society of Plant Biologists. All Rights Reserved.

  1. Heart – Brain Signaling in PFO Related Stroke: Differential Plasma Proteomic Expression Patterns Revealed with a Two-Pass LC-MS/MS Discovery Workflow

    Science.gov (United States)

    Lopez, Mary F; Sarracino, David A; Vogelsang, Maryann; Sutton, Jennifer N; Athanas, Michael; Krastins, Bryan; Garces, Alejandra; Prakash, Amol; Peterman, Scott; Demirjian, Zareh; Ignacio, Inglessis-Azuaje I; Feeney, Kathleen; Elia, Mikaela; McMullin, David; William Dec, G; Palacios, Igor; Lo, Eng H; Buonanno, Ferdinand; Ning, MingMing

    2013-01-01

    Patent foramen ovale (PFO) is highly prevalent and associated with more than 150,000 strokes per year. Traditionally, it is thought that PFOs facilitate strokes by allowing venous clots to travel directly to the brain. However, only a small portion of PFO stroke patients have a known tendency to form blood clots, and the best treatment for this multi-organ disease is unclear. Therefore, mapping the changes in systemic circulation of PFO-related stroke is crucial in understanding the pathophysiology in order to individualize the best clinical treatment for each patient. We initiated a study using a novel quantitative, Two-Pass discovery workflow using high-resolution LC-MS/MS coupled with label-free analysis to track protein expression in PFO patients before and after endovascular closure of the PFO. Using this approach, we were able to demonstrate quantitative differences in protein expression between both PFO-related and non PFO-related ischemic stroke groups as well as before and after PFO closure. As an initial step in understanding the molecular landscape of PFO-related physiology, our methods have yielded biologically relevant information on the synergistic and functional redundancy of various cell-signaling molecules with respect to PFO circulatory physiology. The resulting protein expression patterns were related to canonical pathways including prothrombin activation, atherosclerosis signaling, acute phase response, LXR/RXR activation and coagulation system. In particular, post PFO closure, numerous proteins demonstrated reduced expression in stroke-related canonical pathways such as acute inflammatory response and coagulation signaling. These findings demonstrate the feasibility and robustness of using a proteomic approach for biomarker discovery to help gauge therapeutic efficacy in stroke. PMID:23147404

  2. The Memory That's Right and the Memory That's Left: Event-Related Potentials Reveal Hemispheric Asymmetries in the Encoding and Retention of Verbal Information

    Science.gov (United States)

    Evans, Karen M.; Federmeier, Kara D.

    2007-01-01

    We examined the nature and timecourse of hemispheric asymmetries in verbal memory by recording event-related potentials (ERPs) in a continuous recognition task. Participants made overt recognition judgments to test words presented in central vision that were either novel (new words) or had been previously presented in the left or right visual…

  3. mixed modelassociation scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments

    NARCIS (Netherlands)

    Comadran, J.; Russell, J.R.; Booth, A.; Pswarayi, A.; Ceccarelli, S.; Grando, S.; Stanca, A.M.; Pecchioni, N.; Akar, T.; Al-Yassin, A.; Benbelkacem, A.; Ouabbou, H.; Bort, J.; Eeuwijk, van F.A.; Thomas, W.T.; Romagosa, I.

    2011-01-01

    An association panel consisting of 185 accessions representative of the barley germplasm cultivated in the Mediterranean basin was used to localise quantitative trait loci (QTL) controlling grain yield and yield related traits. The germplasm set was genotyped with 1,536 SNP markers and tested for

  4. A genome-wide scan reveals important roles of DNA methylation in human longevity by regulating age-related disease genes.

    Directory of Open Access Journals (Sweden)

    Fu-Hui Xiao

    Full Text Available It is recognized that genetic factors contribute to human longevity. Besides the hypothesis of existence of longevity genes, another suggests that a lower frequency of risk alleles decreases the incidence of age-related diseases in the long-lived people. However, the latter finds no support from recent genetic studies. Considering the crucial role of epigenetic modification in gene regulation, we then hypothesize that suppressing disease-related genes in longevity individuals is likely achieved by epigenetic modification, e.g. DNA methylation. To test this hypothesis, we investigated the genome-wide methylation profile in 4 Chinese female centenarians and 4 middle-aged controls using methyl-DNA immunoprecipitation sequencing. 626 differentially methylated regions (DMRs were observed between both groups. Interestingly, genes with these DMRs were enriched in age-related diseases, including type-2 diabetes, cardiovascular disease, stroke and Alzheimer's disease. This pattern remains rather stable after including methylomes of two white individuals. Further analyses suggest that the observed DMRs likely have functional roles in regulating disease-associated gene expressions, with some genes [e.g. caspase 3 (CASP3] being down-regulated whereas the others [i.e. interleukin 1 receptor, type 2 (IL1R2] up-regulated. Therefore, our study suggests that suppressing the disease-related genes via epigenetic modification is an important contributor to human longevity.

  5. Comparative mapping reveals similar linkage of functional genes to QTL of yield-related traits between Brassica napus and Oryza sativa.

    Science.gov (United States)

    Li, Fupeng; Ma, Chaozhi; Chen, Qingfang; Liu, Touming; Shen, Jinxiong; Tu, Jinxing; Xing, Yongzhong; Fu, Tingdong

    2012-08-01

    Oryza sativa and Brassica napus-two important crops for food and oil, respectively-share high seed yield as a common breeding goal. As a model plant, O. sativa genomics have been intensively investigated and its agronomic traits have been advanced. In the present study, we used the available information on O. sativa to conduct comparative mapping between O. sativa and B. napus, with the aim of advancing research on seed-yield and yield-related traits in B. napus. Firstly, functional markers (from 55 differentially expressed genes between a hybrid and its parents) were used to detect B. napus genes that co-localized with yield-related traits in an F(2:3) population. Referring to publicly available sequences of 55 B. napus genes, 53 homologous O. sativa genes were subsequently detected by screening, and their chromosomal locations were determined using silico mapping. Comparative location of yield-related QTL between the two species showed that a total of 37 O. sativa and B. napus homologues were located in similar yield-related QTL between species. Our results indicate that homologous genes between O. sativa and B. napus may have consistent function and control similar traits, which may be helpful for agronomic gene characterization in B. napus based on what is known in O. sativa.

  6. A molecular phylogeny of rose chafers (Coleoptera: Scarabaeidae: Cetoniinae) reveals a complex and concerted morphological evolution related to their flight mode.

    Science.gov (United States)

    Šípek, Petr; Fabrizi, Silvia; Eberle, Jonas; Ahrens, Dirk

    2016-08-01

    Rose chafers (Cetoniinae) are a large group of flower visitors within the pleurostict Scarabaeidae that are characterized by their distinctive flight mode with nearly closed forewings. Despite their popularity, this is the first study to use molecular data to infer their phylogenetic relationships. We used partial gene sequences for 28S rRNA, cytochrome oxidase I (cox1) and 16S rRNA (rrnL) for 299 species, representing most recognized subfamilies of Scarabaeidae, including 125 species of Cetoniinae. Combined analyses using maximum parsimony, maximum likelihood and Bayesian inferences recovered Cetoniinae as monophyletic in all analyses, with the sister clade composed of Rutelinae and Dynastinae. Rutelinae was always recovered as paraphyletic with respect to Dynastinae. Trichiini sensu lato (s.l.) was recovered as a polyphyletic clade, while Cetoniini s.l. was recovered as paraphyletic. The inferred topologies were also supported by site bootstrapping of the ML trees. With the exception of Cremastochelini, most tribes of Cetoniinae were poly- or paraphyletic, indicating the critical need for a careful revision of rose chafer classification. Analysis of elytral base structure (including 11 scored characters) in the context of phylogeny, revealed a complex, concerted and rapid transformation of the single trait elements linked to a modified flight mode with closed elytra. This appears to be unlinked to the lateral sinuation of the elytra, which originated independently several times at later stages in the evolution of the group. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato.

    Science.gov (United States)

    Zhang, Kai; Wu, Zhengdan; Tang, Daobin; Luo, Kai; Lu, Huixiang; Liu, Yingying; Dong, Jie; Wang, Xin; Lv, Changwen; Wang, Jichun; Lu, Kun

    2017-01-01

    The starch properties of the storage root (SR) affect the quality of sweet potato ( Ipomoea batatas (L.) Lam.). Although numerous studies have analyzed the accumulation and properties of starch in sweet potato SRs, the transcriptomic variation associated with starch properties in SR has not been quantified. In this study, we measured the starch and sugar contents and analyzed the transcriptome profiles of SRs harvested from sweet potatoes with high, medium, and extremely low starch contents, at five developmental stages [65, 80, 95, 110, and 125 days after transplanting (DAP)]. We found that differences in both water content and starch accumulation in the dry matter affect the starch content of SRs in different sweet potato genotypes. Based on transcriptome sequencing data, we assembled 112336 unigenes, and identified several differentially expressed genes (DEGs) involved in starch and sucrose metabolism, and revealed the transcriptional regulatory network controlling starch and sucrose metabolism in sweet potato SRs. Correlation analysis between expression patterns and starch and sugar contents suggested that the sugar-starch conversion steps catalyzed by sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) may be essential for starch accumulation in the dry matter of SRs, and IbβFRUCT2, a vacuolar acid invertase, might also be a key regulator of starch content in the SRs. Our results provide valuable resources for future investigations aimed at deciphering the molecular mechanisms determining the starch properties of sweet potato SRs.

  8. Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution.

    Science.gov (United States)

    Acharya, Debarun; Ghosh, Tapash C

    2016-01-22

    Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution.

  9. Human Globozoospermia-Related Gene Spata16 Is Required for Sperm Formation Revealed by CRISPR/Cas9-Mediated Mouse Models

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    Yoshitaka Fujihara

    2017-10-01

    Full Text Available A recent genetic analysis of infertile globozoospermic patients identified causative mutations in three genes: a protein interacting with C kinase 1 (PICK1, dpy 19-like 2 (DPY19L2, and spermatogenesis associated 16 (SPATA16. Although mouse models have clarified the physiological functions of Pick1 and Dpy19l2 during spermatogenesis, Spata16 remains to be determined. Globozoospermic patients carried a homozygous point mutation in SPATA16 at 848G→A/R283Q. We generated CRISPR/Cas9-mediated mutant mice with the same amino acid substitution in the fourth exon of Spata16 to analyze the mutation site at R284Q, which corresponded with R283Q of mutated human SPATA16. We found that the point mutation in Spata16 was not essential for male fertility; however, deletion of the fourth exon of Spata16 resulted in infertile male mice due to spermiogenic arrest but not globozoospermia. This study demonstrates that Spata16 is indispensable for male fertility in mice, as well as in humans, as revealed by CRISPR/Cas9-mediated mouse models.

  10. Genome-metabolite associations revealed low heritability, high genetic complexity, and causal relations for leaf metabolites in winter wheat (Triticum aestivum).

    Science.gov (United States)

    Matros, Andrea; Liu, Guozheng; Hartmann, Anja; Jiang, Yong; Zhao, Yusheng; Wang, Huange; Ebmeyer, Erhard; Korzun, Viktor; Schachschneider, Ralf; Kazman, Ebrahim; Schacht, Johannes; Longin, Friedrich; Reif, Jochen Christoph; Mock, Hans-Peter

    2017-01-01

    We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabilities of 0.5-0.6. The average heritability of 0.25 was unaffected by the heading date. Correlations among metabolites reflected their functional grouping, highlighting the strict coordination of various routes of the citric acid cycle. Genome-wide association studies identified significant associations for six metabolic traits, namely oxalic acid, ornithine, L-arginine, pentose alcohol III, L-tyrosine, and a sugar oligomer (oligo II), with between one and 17 associated SNPs. Notable associations with genes regulating transcription or translation explained between 2.8% and 32.5% of the genotypic variance (pG). Further candidate genes comprised metabolite carriers (pG 32.5-38.1%), regulatory proteins (pG 0.3-11.1%), and metabolic enzymes (pG 2.5-32.5%). The combinatorial use of genomic and metabolic data to construct partially directed networks revealed causal inferences in the correlated metabolite traits and associated SNPs. The evaluated causal relationships will provide a basis for predicting the effects of genetic interferences on groups of correlated metabolic traits, and thus on specific metabolic phenotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Model-Assisted Analysis of Sugar Metabolism throughout Tomato Fruit Development Reveals Enzyme and Carrier Properties in Relation to Vacuole Expansion[W

    Science.gov (United States)

    Beauvoit, Bertrand P.; Colombié, Sophie; Monier, Antoine; Andrieu, Marie-Hélène; Biais, Benoit; Bénard, Camille; Chéniclet, Catherine; Dieuaide-Noubhani, Martine; Nazaret, Christine; Mazat, Jean-Pierre; Gibon, Yves

    2014-01-01

    A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features. Cell division was characterized by a high sucrolytic activity of the vacuole, whereas sucrose cleavage during expansion was sustained by both sucrose synthase and neutral invertase, associated with minimal futile cycling. Most importantly, a tight correlation between flux rate and enzyme capacity was found for fructokinase and PPi-dependent phosphofructokinase during cell division and for sucrose synthase, UDP-glucopyrophosphorylase, and phosphoglucomutase during expansion, thus suggesting an adaptation of enzyme abundance to metabolic needs. In contrast, for most enzymes, flux rates varied irrespectively of enzyme capacities, and most enzymes functioned at <5% of their maximal catalytic capacity. One of the major findings with the model was the high accumulation of soluble sugars within the vacuole together with organic acids, thus enabling the osmotic-driven vacuole expansion that was found during cell division. PMID:25139005

  12. Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans

    OpenAIRE

    Yin, Fei; Qian, Dong

    2017-01-01

    Background False kelpfish (Sebastiscus marmoratus) is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection. Methods We carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues. A ...

  13. Alcohol-related amnesia and dementia: Animal models have revealed the contributions of different etiological factors on neuropathology, neurochemical dysfunction and cognitive impairment

    Science.gov (United States)

    Vetreno, Ryan P.; Hall, Joseph M.; Savage, Lisa M.

    2011-01-01

    Chronic alcoholism is associated with impaired cognitive functioning. Over 75% of autopsied chronic alcoholics have significant brain damage and over 50% of detoxified alcoholics display some degree of learning and memory impairment. However, the relative contributions of different etiological factors to the development of alcohol-related neuropathology and cognitive impairment are questioned. One reason for this quandary is that both alcohol toxicity and thiamine deficiency result in brain damage and cognitive problems. Two alcohol-related neurological disorders, alcohol-associated dementia and Wernicke-Korsakoff syndrome have been modeled in rodents. These pre-clinical models have elucidated the relative contributions of ethanol toxicity and thiamine deficiency to the development of dementia and amnesia. What is observed in these models—from repeated and chronic ethanol exposure to thiamine deficiency—is a progression of both neural and cognitive dysregulation. Repeated binge exposure to ethanol leads to changes in neural plasticity by reducing GABAergic inhibition and facilitating glutamatergic excitation, long-term chronic ethanol exposure results in hippocampal and cortical cell loss as well as reduced hippocampal neurotrophin protein content critical for neural survival, and thiamine deficiency results in gross pathological lesions in the diencephalon, reduced neurotrophic protein levels, and neurotransmitters levels in the hippocampus and cortex. Behaviorally, after recovery from repeated or chronic ethanol exposure there is impairment in working or episodic memory that can recover with prolonged abstinence. In contrast, after thiamine deficiency there is severe and persistent spatial memory impairments and increased perseverative behavior. The interaction between ethanol and thiamine deficiency does not produce more behavioral or neural pathology, with the exception of reduction of white matter, than long-term thiamine deficiency alone. PMID:21256970

  14. GPS deformation related to the Mw 7.3, 2014, Papanoa earthquake (Mexico) reveals the aseismic behavior of the Guerrero seismic gap

    Science.gov (United States)

    Gualandi, A.; Perfettini, H.; Radiguet, M.; Cotte, N.; Kostoglodov, V.

    2017-06-01

    We present the study of 21 continuous GPS (cGPS) stations in Mexico during the time interval that goes from 1 October 2013 to 31 December 2014. The area under investigation produced a slow slip event (SSE) that started in February 2014 and lasted at least until December 2014. Superimposed on this transient signal, the Mw7.3 Papanoa earthquake struck the region on 18 April 2014 and affected multiple stations. Thanks to an independent component analysis (ICA) technique we are able to separate the postseismic deformation associated with this earthquake from the deformation related to the ongoing SSE. We infer the slip distributions associated with the three tectonically related processes: the coseismic and postseismic slip and the SSE. The inferred postseismic slip distribution reduces the amount of slip related to the SSE in the updip portion of the slab. The moment released by the postseismic processes (afterslip and aftershocks) is estimated to be [8.06 ± 0.24] × 1019 Nm, equivalent to [71 ± 4]% of the moment associated with the main shock. More than 88% of the postseismic moment is released aseismically and the afterslip spatially correlates with the Guerrero seismic gap, suggesting that the region is controlled by stable sliding behavior and rate-strengthening frictional properties.

  15. Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma

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    Chenglin Liu

    2017-01-01

    Full Text Available The regulation of transcriptome expression level is a complex process involving multiple-level interactions among molecules such as protein coding RNA (mRNA, long noncoding RNA (lncRNA, and microRNA (miRNA, which are essential for the transcriptome stability and maintenance and regulation of body homeostasis. The availability of multilevel expression data enables a comprehensive view of the regulatory network. In this study, we analyzed the coding and noncoding gene expression profiles of 301 patients with uterine corpus endometrial carcinoma (UCEC. A new method was proposed to construct a genome-wide integrative network based on variance inflation factor (VIF regression method. The cross-regulation relations of mRNA, lncRNA, and miRNA were then selected based on clique-searching algorithm from the network, when any two molecules of the three were shown as interacting according to the integrative network. Such relation, which we call the mRNA-lncRNA-miRNA triplet, demonstrated the complexity in transcriptome regulation process. Finally, six UCEC-related triplets were selected in which the mRNA participates in endometrial carcinoma pathway, such as CDH1 and TP53. The multi-type RNAs are proved to be cross-regulated as to each of the six triplets according to literature. All the triplets demonstrated the association with the initiation and progression of UCEC. Our method provides a comprehensive strategy for the investigation of transcriptome regulation mechanism.

  16. Event related potentials reveal that increasing perceptual load leads to increased responses for target stimuli and decreased responses for irrelevant stimuli

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    Chris Rorden

    2008-05-01

    Full Text Available Lavie and colleagues (1995, JEP:HPP 9: 497- have suggested that perceptual processing is influenced by perceptual load. Specifically, relevant information receives additional processing in high load situations exhausting the available capacity. On the other hand, irrelevant information receives less processing with increasing load on a relevant task, as there is a reduced amount of residual processing available. Rees et al. (1997, Science 278: 1616- provided the first physiological evidence for this model, showing this pattern in a functional magnetic resonance imaging (fMRI study. Likewise, Handy et al. (2001, Psych Sci 12: 213- offered supporting evidence measuring event related potentials (ERPs. Both of these studies presented irrelevant information in peripheral vision. Here we manipulated load while using the identical stimuli and the same task (a peripheral gap judgment task with centrally presented irrelevant stimuli. Event related potentials show the pattern predicted by Lavie and colleagues, specifically for the N1 component. This work offers further evidence that visual attention modulates relatively early processing of perceptual information. Specifically, increasing load resulted in stronger N1 responses to relevant information and weaker N1 responses to irrelevant information.

  17. Memory retrieval of smoking-related images induce greater insula activation as revealed by an fMRI-based delayed matching to sample task.

    Science.gov (United States)

    Janes, Amy C; Ross, Robert S; Farmer, Stacey; Frederick, Blaise B; Nickerson, Lisa D; Lukas, Scott E; Stern, Chantal E

    2015-03-01

    Nicotine dependence is a chronic and difficult to treat disorder. While environmental stimuli associated with smoking precipitate craving and relapse, it is unknown whether smoking cues are cognitively processed differently than neutral stimuli. To evaluate working memory differences between smoking-related and neutral stimuli, we conducted a delay-match-to-sample (DMS) task concurrently with functional magnetic resonance imaging (fMRI) in nicotine-dependent participants. The DMS task evaluates brain activation during the encoding, maintenance and retrieval phases of working memory. Smoking images induced significantly more subjective craving, and greater midline cortical activation during encoding in comparison to neutral stimuli that were similar in content yet lacked a smoking component. The insula, which is involved in maintaining nicotine dependence, was active during the successful retrieval of previously viewed smoking versus neutral images. In contrast, neutral images required more prefrontal cortex-mediated active maintenance during the maintenance period. These findings indicate that distinct brain regions are involved in the different phases of working memory for smoking-related versus neutral images. Importantly, the results implicate the insula in the retrieval of smoking-related stimuli, which is relevant given the insula's emerging role in addiction. © 2013 Society for the Study of Addiction.

  18. Integrated analysis of miRNAs and transcriptomes in Aedes albopictus midgut reveals the differential expression profiles of immune-related genes during dengue virus serotype-2 infection.

    Science.gov (United States)

    Liu, Yan-Xia; Li, Fen-Xiang; Liu, Zhuan-Zhuan; Jia, Zhi-Rong; Zhou, Yan-He; Zhang, Hao; Yan, Hui; Zhou, Xian-Qiang; Chen, Xiao-Guang

    2016-06-01

    Mosquito microRNAs (miRNAs) are involved in host-virus interaction, and have been reported to be altered by dengue virus (DENV) infection in Aedes albopictus (Diptera: Culicidae). However, little is known about the molecular mechanisms of Aedes albopictus midgut-the first organ to interact with DENV-involved in its resistance to DENV. Here we used high-throughput sequencing to characterize miRNA and messenger RNA (mRNA) expression patterns in Aedes albopictus midgut in response to dengue virus serotype 2. A total of three miRNAs and 777 mRNAs were identified to be differentially expressed upon DENV infection. For the mRNAs, we identified 198 immune-related genes and 31 of them were differentially expressed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses also showed that the differentially expressed immune-related genes were involved in immune response. Then the differential expression patterns of six immune-related genes and three miRNAs were confirmed by real-time reverse transcription polymerase chain reaction. Furthermore, seven known miRNA-mRNA interaction pairs were identified by aligning our two datasets. These analyses of miRNA and mRNA transcriptomes provide valuable information for uncovering the DENV response genes and provide a basis for future study of the resistance mechanisms in Aedes albopictus midgut. © 2016 Institute of Zoology, Chinese Academy of Sciences.

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

    Science.gov (United States)

    Asad, Abu Bakar Ali; Seah, Stephanie; Baumgartner, Richard; Feng, Dai; Jensen, Andres; Manigbas, Elaine; Henry, Brian; Houghton, Andrea; Evelhoch, Jeffrey L; Derbyshire, Stuart W G; Chin, Chih-Liang

    2016-01-01

    Approximately 20% of the adult population suffer from chronic pain that is not adequately treated by current therapies, highlighting a great need for improved treatment options. To develop effective analgesics, experimental human and animal models of pain are critical. Topically/intra-dermally applied capsaicin induces hyperalgesia and allodynia to thermal and tactile stimuli that mimics chronic pain and is a useful translation from preclinical research to clinical investigation. Many behavioral and self-report studies of pain have exploited the use of the capsaicin pain model, but objective biomarker correlates of the capsaicin augmented nociceptive response in nonhuman primates remains to be explored. Here we establish an aversive capsaicin-induced fMRI model using non-noxious heat stimuli in Cynomolgus monkeys (n = 8). BOLD fMRI data were collected during thermal challenge (ON:20 s/42°C; OFF:40 s/35°C, 4-cycle) at baseline and 30 min post-capsaicin (0.1 mg, topical, forearm) application. Tail withdrawal behavioral studies were also conducted in the same animals using 42°C or 48°C water bath pre- and post- capsaicin application (0.1 mg, subcutaneous, tail). Group comparisons between pre- and post-capsaicin application revealed significant BOLD signal increases in brain regions associated with the 'pain matrix', including somatosensory, frontal, and cingulate cortices, as well as the cerebellum (paired t-test, pinduced reduction of latency at both temperatures. These findings provide insights into the specific brain regions involved with aversive, 'pain-like', responses in a nonhuman primate model. Future studies may employ both behavioral and fMRI measures as translational biomarkers to gain deeper understanding of pain processing and evaluate the preclinical efficacy of novel analgesics.

  20. A novel method for assessing bladder-related pain reveals the involvement of nerve growth factor in pain associated with cyclophosphamide-induced chronic cystitis in mice.

    Science.gov (United States)

    Fujita, M; Kasai, E; Omachi, S; Sakaguchi, G; Shinohara, S

    2016-01-01

    Pain is a prominent feature of interstitial cystitis/painful bladder syndrome (IC/PBS), but the underlying mechanisms are not fully understood. There is a lack of well-characterized research tools, such as pain evaluation methods and experimental animal models, for investigating non-ulcerative cystitis. We developed a novel method for evaluating bladder pain in mice with cyclophosphamide (CYP)-induced cystitis. Cystitis was produced by a single intraperitoneal injection of CYP (300 mg/kg) or repeated injections of CYP (150 mg/kg once daily for 4 days). Blunt stimulation with a cotton probe was applied to the abdominal region, and the thresholds for withdrawal responses were measured quantitatively using an anaesthesiometer. The single injection of CYP provoked acute cystitis with severe bladder inflammation in mice. In these mice, we could detect an increased sensitivity to blunt stimulation, which was abolished by intravesical lidocaine. The stimulation induced phosphorylation of extracellular signal-regulated kinases in bladder-projecting sensory neurons. Chronic treatment with CYP produced persistent pain responses to the blunt stimulus. Although there were few signs of bladder inflammation in these mice, the concentration of nerve growth factor (NGF) was elevated in bladder tissue, and NGF antiserum inhibited the hypersensitivity. The blunt probe method is useful for evaluating bladder pain signalling in mice, and revealed the involvement of an NGF-sensitive pain pathway in chronic cystitis pain. This assessment method may be useful for studying the pathophysiology of bladder pain and for developing therapeutic strategies for non-ulcerative IC/PBS in patients. © 2015 European Pain Federation - EFIC®

  1. Diversity of Vibrio navarrensis Revealed by Genomic Comparison: Veterinary Isolates Are Related to Strains Associated with Human Illness and Sewage Isolates While Seawater Strains Are More Distant.

    Science.gov (United States)

    Schwartz, Keike; Kukuc, Cindy; Bier, Nadja; Taureck, Karin; Hammerl, Jens A; Strauch, Eckhard

    2017-01-01

    Strains of Vibrio navarrensis are present in aquatic environments like seawater, rivers, and sewage. Recently, strains of this species were identified in human clinical specimens. In this study, V. navarrensis strains isolated from livestock in Germany were characterized that were found in aborted fetuses and/or placentas after miscarriages. The veterinary strains were analyzed using phenotypical and genotypical methods and compared to isolates from marine environments of the Baltic Sea and North Sea. The investigated phenotypical traits were similar in all German strains. Whole genome sequencing (WGS) was used to evaluate a phylogenetic relationship by performing a single nucleotide polymorphism (SNP) analysis. For the SNP analysis, WGS data of two American human pathogenic strains and two Spanish environmental isolates from sewage were included. A phylogenetic analysis of concatenated sequences of five protein-coding housekeeping genes (gyrB, pyrH, recA, atpA, and rpoB), was additionally performed. Both phylogenetic analyses reveal a greater distance of the environmental seawater strains to the other strains. The phylogenetic tree constructed from concatenated sequences of housekeeping genes places veterinary, human pathogenic and Spanish sewage strains into one cluster. Presence and absence of virulence-associated genes were investigated based on WGS data and confirmed by PCR. However, this analysis showed no clear pattern for the potentially pathogenic strains. The detection of V. navarrensis in human clinical specimens strongly suggests that this species should be regarded as a potential human pathogen. The identification of V. navarrensis strains in domestic animals implicates a zoonotic potential of this species. This could indicate a potential threat for humans, as according to the "One Health" concept, human, animal, and environmental health are linked. Future studies are necessary to search for reservoirs of these bacteria in the environment and/or in

  2. Event-related potentials reveal task-dependence and inter-individual differences in negation processing during silent listening and explicit truth-value evaluation.

    Science.gov (United States)

    Herbert, C; Kissler, J

    2014-09-26

    In sentences such as dogs cannot fly/bark, evaluation of the truth-value of the sentence is assumed to appear after the negation has been integrated into the sentence structure. Moreover negation processing and truth-value processing are considered effortful processes, whereas processing of the semantic relatedness of the words within sentences is thought to occur automatically. In the present study, modulation of event-related brain potentials (N400 and late positive potential, LPP) was investigated during an implicit task (silent listening) and active truth-value evaluation to test these theoretical assumptions and determine if truth-value evaluation will be modulated by the way participants processed the negated information implicitly prior to truth-value verification. Participants first listened to negated sentences and then evaluated these sentences for their truth-value in an active evaluation task. During passive listening, the LPP was generally more pronounced for targets in false negative (FN) than true negative (TN) sentences, indicating enhanced attention allocation to semantically-related but false targets. N400 modulation by truth-value (FN>TN) was observed in 11 out of 24 participants. However, during active evaluation, processing of semantically-unrelated but true targets (TN) elicited larger N400 and LPP amplitudes as well as a pronounced frontal negativity. This pattern was particularly prominent in those 11 individuals, whose N400 modulation during silent listening indicated that they were more sensitive to violations of the truth-value than to semantic priming effects. The results provide evidence for implicit truth-value processing during silent listening of negated sentences and for task dependence related to inter-individual differences in implicit negation processing. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Newborn brain event-related potentials revealing atypical processing of sound frequency and the subsequent association with later literacy skills in children with familial dyslexia.

    Science.gov (United States)

    Leppänen, Paavo H T; Hämäläinen, Jarmo A; Salminen, Hanne K; Eklund, Kenneth M; Guttorm, Tomi K; Lohvansuu, Kaisa; Puolakanaho, Anne; Lyytinen, Heikki

    2010-01-01

    The role played by an auditory-processing deficit in dyslexia has been debated for several decades. In a longitudinal study using brain event-related potentials (ERPs) we investigated 1) whether dyslexic children with familial risk background would show atypical pitch processing from birth and 2) how these newborn ERPs later relate to these same children's pre-reading cognitive skills and literacy outcomes. Auditory ERPs were measured at birth for tones varying in pitch and presented in an oddball paradigm (1100 Hz, 12%, and 1000 Hz, 88%). The brain responses of the typically reading control group children (TRC group, N=25) showed clear differentiation between the frequencies, while those of the group of reading disability with familial risk (RDFR, 8 children) and the group of typical readers with familial risk (TRFR, 14 children) did not differentiate between the tones. The ERPs of the latter two groups differed from those of the TRC group. However, the two risk groups also showed a differential hemispheric ERP pattern. Furthermore, newborn ERPs reflecting passive change detection were associated with phonological skills and letter knowledge prior to school age and with phoneme duration perception, reading speed (RS) and spelling accuracy in the 2nd grade of school. The early obligatory response was associated with more general pre-school language skills, as well as with RS and reading accuracy (RA). Results suggest that a proportion of dyslexic readers with familial risk background are affected by atypical auditory processing. This is already present at birth and also relates to pre-reading phonological processing and speech perception. These early differences in auditory processing could later affect phonological representations and reading development. However, atypical auditory processing is unlikely to suffice as a sole explanation for dyslexia but rather as one risk factor, dependent on the genetic profile of the child. Copyright © 2010 Elsevier Srl. All

  4. Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC: A Comprehensive Informatics Approach

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    Faryal Mehwish Awan

    2017-01-01

    Full Text Available Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC. Post-translational modifications (PTMs and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A, 1 in LC3B (S92C, 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.

  5. Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach.

    Science.gov (United States)

    Awan, Faryal Mehwish; Obaid, Ayesha; Ikram, Aqsa; Janjua, Hussnain Ahmed

    2017-01-11

    Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC). Post-translational modifications (PTMs) and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A), 1 in LC3B (S92C), 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H) and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C) coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.

  6. Genetic mapping reveals a dominant awn-inhibiting gene related to differentiation of the variety anathera in the wild diploid wheat Aegilops tauschii.

    Science.gov (United States)

    Nishijima, Ryo; Ikeda, Tatsuya M; Takumi, Shigeo

    2018-02-01

    Aegilops tauschii, a wild wheat relative, is the D-genome donor of common wheat. Subspecies and varieties of Ae. tauschii are traditionally classified based on differences in their inflorescence architecture. However, the genetic information for their diversification has been quite limited in the wild wheat relatives. The variety anathera has no awn on the lemma, but the genetic basis for this diagnostic character is unknown. Wide variations in awn length traits at the top and middle spikes were found in the Ae. tauschii core collection, and the awn length at the middle spike was significantly smaller in the eastward-dispersed sublineage than in those in other sublineages. To clarify loci controlling the awnless phenotype of var. anathera, we measured awn length of an intervariety F2 mapping population, and found that the F2 individuals could be divided into two groups mainly based on the awn length at the middle of spike, namely short and long awn groups, significantly fitting a 3:1 segregation ratio, which indicated that a single locus controls the awnless phenotype. The awnless locus, Anathera (Antr), was assigned to the distal region of the short arm of chromosome 5D. Quantitative trait locus analysis using the awn length data of each F2 individual showed that only one major locus was at the same chromosomal position as Antr. These results suggest that a single dominant allele determines the awnless diagnostic character in the variety anathera. The Antr dominant allele is a novel gene inhibiting awn elongation in wheat and its relatives.

  7. Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans

    Directory of Open Access Journals (Sweden)

    Fei Yin

    2017-11-01

    Full Text Available Abstract Background False kelpfish (Sebastiscus marmoratus is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection. Methods We carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues. A paired-end library was constructed from the cDNA synthesized using a Genomic Sample Prep Kit. Five normalized cDNA libraries were constructed using RNA from the control group and the four groups of C. irritans-infected fish. The libraries were sequenced on an Illumina Mi-Seq platform, and functional annotation of the transcriptome was performed using bioinformatics software. Results The data produced a total of 149,983,397 clean reads from five cDNA libraries constructed from S. marmoratus immune-related tissues. A total of 33,291 unigenes were assembled with an average length of 1768 bp. In eggNOG (Evolutionary Genealogy of Genes: non-supervised orthologous groups categories, 333 unigenes (0.94% were assigned to defense mechanisms. In the immune system process sub-categories of gene ontology (GO enrichment analysis, with the passage of time post-infection, the number of differentially expressed genes (DEGs was reduced from 24 h to 48 h but then increased from 72 h to 96 h. Specifically, the immune-related differentially expressed genes (IRDEGs, which belong to the KEGG (Kyoto encyclopedia of genes and genomes pathways, such as the complement and coagulation cascades, chemokine signalling pathways and toll-like receptor signalling pathways were mainly observed at 24 h post-infection. Conclusions Infection with C. irritans resulted in a large number of DEGs in the immune-related tissues of S. marmoratus. The rapid and significant response of the

  8. Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans.

    Science.gov (United States)

    Yin, Fei; Qian, Dong

    2017-11-21

    False kelpfish (Sebastiscus marmoratus) is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection. We carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues. A paired-end library was constructed from the cDNA synthesized using a Genomic Sample Prep Kit. Five normalized cDNA libraries were constructed using RNA from the control group and the four groups of C. irritans-infected fish. The libraries were sequenced on an Illumina Mi-Seq platform, and functional annotation of the transcriptome was performed using bioinformatics software. The data produced a total of 149,983,397 clean reads from five cDNA libraries constructed from S. marmoratus immune-related tissues. A total of 33,291 unigenes were assembled with an average length of 1768 bp. In eggNOG (Evolutionary Genealogy of Genes: non-supervised orthologous groups) categories, 333 unigenes (0.94%) were assigned to defense mechanisms. In the immune system process sub-categories of gene ontology (GO) enrichment analysis, with the passage of time post-infection, the number of differentially expressed genes (DEGs) was reduced from 24 h to 48 h but then increased from 72 h to 96 h. Specifically, the immune-related differentially expressed genes (IRDEGs), which belong to the KEGG (Kyoto encyclopedia of genes and genomes) pathways, such as the complement and coagulation cascades, chemokine signalling pathways and toll-like receptor signalling pathways were mainly observed at 24 h post-infection. Infection with C. irritans resulted in a large number of DEGs in the immune-related tissues of S. marmoratus. The rapid and significant response of the S. marmoratus immune signalling pathways following C

  9. A Descriptive Examination of the Types of Relationships Formed between Children with Developmental Disability and Their Closest Peers in Inclusive School Settings

    Science.gov (United States)

    Webster, Amanda A.; Carter, Mark

    2013-01-01

    Background: One of the most commonly cited rationales for inclusive education is to enable the development of quality relationships with typically developing peers. Relatively few researchers have examined the features of the range of relationships that children with developmental disability form in inclusive school settings. Method: Interviews…

  10. RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response.

    Science.gov (United States)

    Rodrigues, Carolina M; de Souza, Alessandra A; Takita, Marco A; Kishi, Luciano T; Machado, Marcos A

    2013-10-03

    Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is one the most important citrus diseases, and affects all varieties of sweet orange (Citrus sinensis L. Osb). On the other hand, among the Citrus genus there are different sources of resistance against X. fastidiosa. For these species identifying these defense genes could be an important step towards obtaining sweet orange resistant varieties through breeding or genetic engineering. To assess these genes we made use of mandarin (C. reticulata Blanco) that is known to be resistant to CVC and shares agronomical characteristics with sweet orange. Thus, we investigated the gene expression in Ponkan mandarin at one day after infection with X. fastidiosa, using RNA-seq. A set of genes considered key elements in the resistance was used to confirm its regulation in mandarin compared with the susceptible sweet orange. Gene expression analysis of mock inoculated and infected tissues of Ponkan mandarin identified 667 transcripts repressed and 724 significantly induced in the later. Among the induced transcripts, we identified genes encoding proteins similar to Pattern Recognition Receptors. Furthermore, many genes involved in secondary metabolism, biosynthesis and cell wall modification were upregulated as well as in synthesis of abscisic acid, jasmonic acid and auxin. This work demonstrated that the defense response to the perception of bacteria involves cell wall modification and activation of hormone pathways, which probably lead to the induction of other defense-related genes. We also hypothesized the induction of auxin-related genes indicates that resistant plants initially recognize X. fastidiosa as a necrotrophic pathogen.

  11. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).

    Science.gov (United States)

    Huang, Daisie I; Hefer, Charles A; Kolosova, Natalia; Douglas, Carl J; Cronk, Quentin C B

    2014-11-01

    As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  12. GeneChip expression profiling reveals the alterations of energy metabolism related genes in osteocytes under large gradient high magnetic fields.

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    Yang Wang

    Full Text Available The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF, which can provide three apparent gravity levels (μ-g, 1-g, and 2-g, was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84 were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis.

  13. The 3D structure of the apical complex and association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa.

    Science.gov (United States)

    Okamoto, Noriko; Keeling, Patrick J

    2014-01-01

    The apical complex is one of the defining features of apicomplexan parasites, including the malaria parasite Plasmodium, where it mediates host penetration and invasion. The apical complex is also known in a few related lineages, including several non-parasitic heterotrophs, where it mediates feeding behaviour. The origin of the apical complex is unclear, and one reason for this is that in apicomplexans it exists in only part of the life cycle, and never simultaneously with other major cytoskeletal structures like flagella and basal bodies. Here, we used conventional TEM and serial TEM tomography to reconstruct the three dimensional structure of the apical complex in Psammosa pacifica, a predatory relative of apicomplexans and dinoflagellates that retains the archetype apical complex and the flagellar apparatus simultaneously. The P. pacifica apical complex is associated with the gullet and consists of the pseudoconoid, micronemes, and electron dense vesicles. The pseudoconoid is a convex sheet consisting of eight short microtubules, plus a band made up of microtubules that originate from the flagellar apparatus. The flagellar apparatus consists of three microtubular roots. One of the microtubular roots attached to the posterior basal body is connected to bypassing microtubular strands, which are themselves connected to the extension of the pseudoconoid. These complex connections where the apical complex is an extension of the flagellar apparatus, reflect the ancestral state of both, dating back to the common ancestor of apicaomplexans and dinoflagellates.

  14. Transcriptional profiling of arbuscular mycorrhizal roots exposed to high levels of phosphate reveals the repression of cell cycle-related genes and secreted protein genes in Rhizophagus irregularis.

    Science.gov (United States)

    Sugimura, Yusaku; Saito, Katsuharu

    2017-02-01

    The development of arbuscular mycorrhiza (AM) is strongly suppressed under high-phosphate (Pi) conditions. To investigate AM fungal responses during the suppression of AM by high Pi, we performed an RNA-seq analysis of Rhizophagus irregularis colonizing Lotus japonicus roots at different levels of Pi (20, 100, 300, and 500 μM). AM fungal colonization decreased markedly under high-Pi conditions. In total, 163 fungal genes were differentially expressed among the four Pi treatments. Among these genes, a cell cycle-regulatory gene, cyclin-dependent kinase CDK1, and several DNA replication- and mitosis-related genes were repressed under high-Pi conditions. More than 20 genes encoding secreted proteins were also downregulated by high-Pi conditions, including the strigolactone-induced putative secreted protein 1 gene that enhances AM fungal colonization. In contrast, the expression of genes related to aerobic respiration and transport in R. irregularis were largely unaffected. Our data suggest that high Pi suppresses the expression of genes associated with fungal cell cycle progression or that encode secreted proteins that may be required for intercellular hyphal growth and arbuscule formation. However, high Pi has little effect on the transcriptional regulation of the primary metabolism or transport in preformed fungal structures.

  15. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

    KAUST Repository

    Lin, Hsiu Chin

    2013-12-12

    This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles. © 2013 © 2013 Taylor & Francis.

  16. Demonstrating a New Census of Infrared Galaxies with ALMA (DANCING-ALMA). I. FIR Size and Luminosity Relation at z = 0-6 Revealed with 1034 ALMA Sources

    Science.gov (United States)

    Fujimoto, Seiji; Ouchi, Masami; Shibuya, Takatoshi; Nagai, Hiroshi

    2017-11-01

    We present the large statistics of the galaxy effective radius R e in the rest-frame far-infrared (FIR) wavelength {R}{{e}({FIR})} obtained from 1627 Atacama Large Millimeter/submillimeter Array (ALMA) 1 mm band maps that become public by 2017 July. Our ALMA sample consists of 1034 sources with the star formation rate ˜ 100{--}1000 {M}⊙ {{yr}}-1 and the stellar mass ˜ {10}10{--}{10}11.5 {M}⊙ at z = 0-6. We homogeneously derive {R}{{e}({FIR})} and FIR luminosity L FIR of our ALMA sources via the uv-visibility method with the exponential disk model, carefully evaluating selection and measurement incompletenesses by realistic Monte-Carlo simulations. We find that there is a positive correlation between {R}{{e}({FIR})} and L FIR at the >99% significance level. The best-fit power-law function, {R}{{e}({FIR})}\\propto {L}{FIR}α , provides α =0.28+/- 0.07, and shows that {R}{{e}({FIR})} at a fixed L FIR decreases toward high redshifts. The best-fit α and the redshift evolution of {R}{{e}({FIR})} are similar to those of R e in the rest-frame UV (optical) wavelength {R}{{e}({UV})} ({R}{{e}({Opt}.)}) revealed by Hubble Space Telescope (HST) studies. We identify that our ALMA sources have significant trends of {R}{{e}({FIR})}≲ {R}{{e}({UV})} and {R}{{e}({Opt}.)}, which suggests that the dusty starbursts take place in compact regions. Moreover, {R}{{e}({FIR})} of our ALMA sources is comparable to {R}{{e}({Opt}.)} of quiescent galaxies at z ˜ 1-3 as a function of stellar mass, supporting the evolutionary connection between these two galaxy populations. We also investigate rest-frame UV and optical morphologies of our ALMA sources with deep HST images, and find that ˜30%-40% of our ALMA sources are classified as major mergers. This indicates that dusty starbursts are triggered by not only the major mergers but also the other mechanism(s).

  17. Using reflective learning opportunities to reveal and transform knowledge, attitudes, beliefs, and skills related to the occupation of sexual engagement impaired by disability

    Directory of Open Access Journals (Sweden)

    Rondalyn V. Whitney

    2017-03-01

    Full Text Available Sexuality is one area of human occupation that spans across the lifespan and is identified as an activity of daily living. Barriers to engagement in this occupation fall under the occupational therapists’ scope of practice. Teaching that fosters self-reflection about attitudes and perceptions has the power to shape the practice methodology of future practitioners. This paper presents a curriculum module that aims to go beyond basic delivery of content related to human sexuality to instead show how the teaching methodology developed competency in practitioners, changed perceptions that would serve as barriers to empathetic care, and followed the guidelines of best practice. The authors further present the setting of academia as a practice setting and, as such, one that must adhere to the same standards of evidence-based, science-driven protocols as clinical practice.

  18. Partial loss-of-function alleles reveal a role for GNOM in auxin transport-related, post-embryonic development of Arabidopsis

    DEFF Research Database (Denmark)

    Geldner, Niko; Richter, Sandra; Vieten, Anne

    2004-01-01

    The Arabidopsis GNOM gene encodes an ARF GDP/GTP exchange factor involved in embryonic axis formation and polar localisation of the auxin efflux regulator PIN1. To examine whether GNOM also plays a role in post-embryonic development and to clarify its involvement in auxin transport, we have...... characterised newly isolated weak gnom alleles as well as trans-heterozygotes of complementing strong alleles. These genotypes form a phenotypic series of GNOM activity in post-embryonic development, with auxin-related defects, especially in the maintenance of primary root meristem activity...... and in the initiation and organisation of lateral root primordia. Our results suggest a model for GNOM action mediating auxin transport in both embryogenesis and post-embryonic organ development....

  19. Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss

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    Guo Hu

    2016-01-01

    Full Text Available Excessive accumulation of carcass fat in farm animals, including fish, has a significant impact on meat quality and on the cost of feeding. Similar to farmed animals and humans, the liver can be considered one of the most important organs involved in lipid metabolism in rainbow trout (Oncorhynchus mykiss. RNA-seq based whole transcriptome sequencing was performed to liver tissue of rainbow trout with high and low carcass fat content in this study. In total 1,694 differentially expressed transcripts were identified, including many genes involved in lipid metabolism, such as L-FABP, adiponectin, PPAR-α, PPAR-β, and IGFBP1a. Evidence presented in this study indicated that lipid metabolic process in liver may be related to the difference of carcass fat content. The relevance of PPAR-α and PPAR-β as molecular markers for fat storage in liver should be worthy of further investigation.

  20. Screening of 336 single-nucleotide polymorphisms in 85 obesity-related genes revealed McKusick-Kaufman syndrome gene variants are associated with metabolic syndrome.

    Science.gov (United States)

    Hotta, Kikuko; Nakamura, Takahiro; Takasaki, Junichi; Takahashi, Hiroshi; Takahashi, Atsushi; Nakata, Yoshio; Kamohara, Seika; Kotani, Kazuaki; Komatsu, Ryoya; Itoh, Naoto; Mineo, Ikuo; Wada, Jun; Masuzaki, Hiroaki; Yoneda, Masato; Nakajima, Atsushi; Funahashi, Tohru; Miyazaki, Shigeru; Tokunaga, Katsuto; Hamaguchi, Kazuyuki; Tanaka, Kiyoji; Yamada, Kentaro; Hanafusa, Toshiaki; Oikawa, Shinichi; Yoshimatsu, Hironobu; Nakao, Kazuwa; Sakata, Toshiie; Matsuzawa, Yuji; Kamatani, Naoyuki; Nakamura, Yusuke

    2009-04-01

    Genetic factors are important in the development of metabolic syndrome. However, the genetic background of metabolic syndrome remains unclear. We screened polymorphisms in 85 obesity-related genes to determine which may be associated with metabolic syndrome. A total of 336 single-nucleotide polymorphisms (SNPs) in 85 genes selected from the JSNP database were genotyped. We conducted case-control association analyses using patients with metabolic syndrome (n=1080) and control individuals (n=528) who had no risk of the metabolic syndrome. Three SNPs in the McKusick-Kaufman syndrome (MKKS) gene were significantly related to metabolic syndrome by case-control association study; rs1545 (odds ratio (OR) adjusted for age and gender, 1.45; 95% confidence interval (CI), 1.21-1.74; P=0.000043 (additive model)); rs1547 (OR, 1.45; 95% CI, 1.21-1.74; P=0.000041); and rs2294901 (OR, 1.46; 95% CI, 1.22-1.75; P=0.000033). We selected five tag SNPs (rs2294901, rs221667, rs6133922, rs6077785 and rs6108572) in the MKKS gene. They were in one linkage disequilibrium (LD) block and rs6133922 (P=0.00042), rs6077785 (P=0.000013) and rs6108572 (P=0.000019) as well as rs2294901 were significantly associated with metabolic syndrome. TGAAA haplotype was protective against the metabolic syndrome (P=0.0074), and CCGTT haplotype was susceptible (P=0.00070) to the metabolic syndrome. Our data suggest that genetic variations at MKKS gene influence the risk of metabolic syndrome.

  1. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Directory of Open Access Journals (Sweden)

    Arce-Johnson Patricio

    2008-07-01

    Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

  2. Lg attenuation, frequency dependence and relative site response of the western United States as revealed by the EarthScope Transportable Array

    Science.gov (United States)

    Gallegos, Andrea; Ranasinghe, Nishath; Ni, James; Sandvol, Eric

    2017-06-01

    Lg attenuation of the western United States is estimated using regional waveforms recorded by EarthScope's Transportable Array, the Berkeley Digital Seismograph Network and the Caltech Regional Seismic Network. Lg attenuation is determined using the two-station method (TSM). 292 events ranging from magnitude 4 to 6.5 in a time range for the years between 2005 and 2010 are used. We have tomographically mapped variations in effective Lg Q at narrow bands with central frequencies of 0.5, 1, 2 and 3 Hz. The relative site responses of individual stations are determined using a reverse TSM at these central frequencies. Both the two-station and reverse TSMs have the advantage of effectively removing site and source effects without requiring a priori models while mapping lateral heterogeneities in the crust. Regions of high attenuation are found along the Snake River Plain, along the northern California-Oregon border, throughout the Basin and Range, Walker Lane, Wasatch Fault and the Rio Grande Rift. Regions of low attenuation are found in the Colorado Plateau, Rocky Mountains, central Nevada and the Columbia Plateau. Overall, Lg Q was found to have a power-law frequency dependence, with an increase in central frequency resulting in an increase in Q. Relative site responses were found to vary strongly with local geology. Hard rock areas such as the Sierra Nevada Mountains and the Snake River Plain show a consistent pattern of negative site response (i.e. deamplification), while areas with a higher degree of sediments, such as the grabens of the Basin and Range, show positive site response (i.e. amplification). Finally, site responses were found to vary with frequency, becoming less variable and more pronounced as frequency increases.

  3. Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus.

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    Wei Chi

    Full Text Available The natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus. How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male from the rice field eel to investigate changes in transcriptional level during the sex reversal process.Approximately 195 thousand unigenes were generated and over 44.4 thousand were functionally annotated. Comparative study between stages provided multiple differentially expressed genes in brain and gonad tissue. Overall 4668 genes were found to be of unequal abundance between gonad tissues, far more than that of the brain tissues (59 genes. These genes were enriched in several different signaling pathways. A number of 231 genes were found with different levels in gonad in each stage, with several reproduction-related genes included. A total of 19 candidate genes that could be most related to sex reversal were screened out, part of these genes' expression patterns were validated by RT-qPCR. The expression of spef2, maats1, spag6 and dmc1 were abundant in testis, but was barely detected in females, while the 17β-hsd12, zpsbp3, gal3 and foxn5 were only expressed in ovary.This study investigated the complexity of brain and gonad transcriptomes in three sex stages of the rice field eel. Integrated analysis of different gene expression and changes in signaling pathways, such as PI3K-Akt pathway, provided crucial data for further study of sex transformation mechanisms.

  4. Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus.

    Science.gov (United States)

    Chi, Wei; Gao, Yu; Hu, Qing; Guo, Wei; Li, Dapeng

    2017-01-01

    The natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus). How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male) from the rice field eel to investigate changes in transcriptional level during the sex reversal process. Approximately 195 thousand unigenes were generated and over 44.4 thousand were functionally annotated. Comparative study between stages provided multiple differentially expressed genes in brain and gonad tissue. Overall 4668 genes were found to be of unequal abundance between gonad tissues, far more than that of the brain tissues (59 genes). These genes were enriched in several different signaling pathways. A number of 231 genes were found with different levels in gonad in each stage, with several reproduction-related genes included. A total of 19 candidate genes that could be most related to sex reversal were screened out, part of these genes' expression patterns were validated by RT-qPCR. The expression of spef2, maats1, spag6 and dmc1 were abundant in testis, but was barely detected in females, while the 17β-hsd12, zpsbp3, gal3 and foxn5 were only expressed in ovary. This study investigated the complexity of brain and gonad transcriptomes in three sex stages of the rice field eel. Integrated analysis of different gene expression and changes in signaling pathways, such as PI3K-Akt pathway, provided crucial data for further study of sex transformation mechanisms.

  5. Vigilance task-related change in brain functional connectivity as revealed by wavelet phase coherence analysis of near-infrared spectroscopy signals

    Directory of Open Access Journals (Sweden)

    Wang Wei

    2016-08-01

    Full Text Available This study aims to assess the vigilance task-related change in connectivity in healthy adults using wavelet phase coherence (WPCO analysis of near-infrared spectroscopy signals (NIRS. NIRS is a non-invasive neuroimaging technique for assessing brain activity. Continuous recordings of the NIRS signals were obtained from the prefrontal cortex (PFC and sensorimotor cortical areas of 20 young healthy adults (24.9±3.3 years during a 10-min resting state and a 20-min vigilance task state. The vigilance task was used to simulate driving mental load by judging three random numbers (i.e., whether odd numbers. The task was divided into two sessions: the first 10 minutes (Task t1 and the second 10 minutes (Task t2. The WPCO of six channel pairs were calculated in five frequency intervals: 0.6–2 Hz (I, 0.145–0.6 Hz (II, 0.052–0.145 Hz (III, 0.021–0.052 Hz (IV, and 0.0095–0.021 Hz (V. The significant WPCO formed global connectivity (GC maps in intervals I and II and functional connectivity (FC maps in intervals III to V. Results show that the GC levels in interval I and FC levels in interval III were significantly lower in the Task t2 than in the resting state (p < 0.05, particularly between the left PFC and bilateral sensorimotor regions. Also, the reaction time shows an increase in Task t2 compared with that in Task t1. However, no significant difference in WPCO was found between Task t1 and resting state. The results showed that the change in FC at the range of 0.6-2 Hz was not attributed to the vigilance task pe se, but the interaction effect of vigilance task and time factors. The findings suggest that the decreased attention level might be partly attributed to the reduced GC levels between the left prefrontal region and sensorimotor area. The present results provide a new insight into the vigilance task-related brain activity.

  6. Urinary Metabolic Phenotyping Reveals Differences in the Metabolic Status of Healthy and Inflammatory Bowel Disease (IBD Children in Relation to Growth and Disease Activity

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    Francois-Pierre Martin

    2016-08-01

    Full Text Available Background: Growth failure and delayed puberty are well known features of children and adolescents with inflammatory bowel disease (IBD, in addition to the chronic course of the disease. Urinary metabonomics was applied in order to better understand metabolic changes between healthy and IBD children. Methods: 21 Pediatric patients with IBD (mean age 14.8 years, 8 males were enrolled from the Pediatric Gastroenterology Outpatient Clinic over two years. Clinical and biological data were collected at baseline, 6, and 12 months. 27 healthy children (mean age 12.9 years, 16 males were assessed at baseline. Urine samples were collected at each visit and subjected to 1H Nuclear Magnetic Resonance (NMR spectroscopy. Results: Using 1H NMR metabonomics, we determined that urine metabolic profiles of IBD children differ significantly from healthy controls. Metabolic differences include central energy metabolism, amino acid, and gut microbial metabolic pathways. The analysis described that combined urinary urea and phenylacetylglutamine—two readouts of nitrogen metabolism—may be relevant to monitor metabolic status in the course of disease. Conclusion: Non-invasive sampling of urine followed by metabonomic profiling can elucidate and monitor the metabolic status of children in relation to disease status. Further developments of omic-approaches in pediatric research might deliver novel nutritional and metabolic hypotheses.

  7. In silico analyses and global transcriptional profiling reveal novel putative targets for Pea3 transcription factor related to its function in neurons.

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    Başak Kandemir

    Full Text Available Pea3 transcription factor belongs to the PEA3 subfamily within the ETS domain transcription factor superfamily, and has been largely studied in relation to its role in breast cancer metastasis. Nonetheless, Pea3 plays a role not only in breast tumor, but also in other tissues with branching morphogenesis, including kidneys, blood vasculature, bronchi and the developing nervous system. Identification of Pea3 target promoters in these systems are important for a thorough understanding of how Pea3 functions. Present study particularly focuses on the identification of novel neuronal targets of Pea3 in a combinatorial approach, through curation, computational analysis and microarray studies in a neuronal model system, SH-SY5Y neuroblastoma cells. We not only show that quite a number of genes in cancer, immune system and cell cycle pathways, among many others, are either up- or down-regulated by Pea3, but also identify novel targets including ephrins and ephrin receptors, semaphorins, cell adhesion molecules, as well as metalloproteases such as kallikreins, to be among potential target promoters in neuronal systems. Our overall results indicate that rather than early stages of neurite extension and axonal guidance, Pea3 is more involved in target identification and synaptic maturation.

  8. Urinary 1H Nuclear Magnetic Resonance Metabolomic Fingerprinting Reveals Biomarkers of Pulse Consumption Related to Energy-Metabolism Modulation in a Subcohort from the PREDIMED study.

    Science.gov (United States)

    Madrid-Gambin, Francisco; Llorach, Rafael; Vázquez-Fresno, Rosa; Urpi-Sarda, Mireia; Almanza-Aguilera, Enrique; Garcia-Aloy, Mar; Estruch, Ramon; Corella, Dolores; Andres-Lacueva, Cristina

    2017-04-07

    Little is known about the metabolome fingerprint of pulse consumption. The study of robust and accurate biomarkers for pulse dietary assessment has great value for nutritional epidemiology regarding health benefits and their mechanisms. To characterize the fingerprinting of dietary pulses (chickpeas, lentils, and beans), spot urine samples from a subcohort from the PREDIMED study were stratified using a validated food frequency questionnaire. Urine samples of nonpulse consumers (≤4 g/day of pulse intake) and habitual pulse consumers (≥25 g/day of pulse intake) were analyzed using a 1H nuclear magnetic resonance (NMR) metabolomics approach combined with multi- and univariate data analysis. Pulse consumption showed differences through 16 metabolites coming from (i) choline metabolism, (ii) protein-related compounds, and (iii) energy metabolism (including lower urinary glucose). Stepwise logistic regression analysis was applied to design a combined model of pulse exposure, which resulted in glutamine, dimethylamine, and 3-methylhistidine. This model was evaluated by a receiver operating characteristic curve (AUC > 90% in both training and validation sets). The application of NMR-based metabolomics to reported pulse exposure highlighted new candidates for biomarkers of pulse consumption and the impact on energy metabolism, generating new hypotheses on energy modulation. Further intervention studies will confirm these findings.

  9. Revealing Origin of Decrease in Potency of Darunavir and Amprenavir against HIV-2 relative to HIV-1 Protease by Molecular Dynamics Simulations

    Science.gov (United States)

    Chen, Jianzhong; Liang, Zhiqiang; Wang, Wei; Yi, Changhong; Zhang, Shaolong; Zhang, Qinggang

    2014-11-01

    Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition, molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations were performed to investigate the effectiveness of the PR1 inhibitors DRV and APV against PR1/PR2. The rank of predicted binding free energies agrees with the experimental determined one. Moreover, our results show that two inhibitors bind less strongly to PR2 than to PR1, again in agreement with the experimental findings. The decrease in binding free energies for PR2 relative to PR1 is found to arise from the reduction of the van der Waals interactions induced by the structural adjustment of the triple mutant V32I, I47V and V82I. This result is further supported by the difference between the van der Waals interactions of inhibitors with each residue in PR2 and in PR1. The results from the principle component analysis suggest that inhibitor binding tends to make the flaps of PR2 close and the one of PR1 open. We expect that this study can theoretically provide significant guidance and dynamics information for the design of potent dual inhibitors targeting PR1/PR2.

  10. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer picea abies reveals extensive conservation as well as dynamic patterns

    Science.gov (United States)

    2013-01-01

    Background Members of the WUSCHEL-RELATED HOMEOBOX (WOX) gene family have important functions during all stages of plant development and have been implicated in the development of morphological novelties during evolution. Most studies have examined the function of these genes in angiosperms and very little is known from other plant species. Results In this study we examine the presence and expression of WOX genes in the conifer Picea abies. We have cloned 11 WOX genes from both mRNA and genomic DNA and examined their phylogenetic relationship to WOX genes from other species as well as their expression during somatic embryogenesis and in adult tissues. Conclusions Our study shows that all major radiations within the WOX gene family took place before the angiosperm-gymnosperm split and that there has been a recent expansion within the intermediate clade in the Pinaceae family. Furthermore, we show that the genes from the intermediate clade are preferentially expressed during embryo development in Picea abies. Our data also indicates that there are clear orthologs of both WUS and WOX5 present in the P. abies genome. PMID:23758772

  11. Structure of Yeast OSBP-Related Protein Osh1 Reveals Key Determinants for Lipid Transport and Protein Targeting at the Nucleus-Vacuole Junction.

    Science.gov (United States)

    Manik, Mohammad Kawsar; Yang, Huiseon; Tong, Junsen; Im, Young Jun

    2017-04-04

    Yeast Osh1 belongs to the oxysterol-binding protein (OSBP) family of proteins and contains multiple targeting modules optimized for lipid transport at the nucleus-vacuole junction (NVJ). The key determinants for NVJ targeting and the role of Osh1 at NVJs have remained elusive because of unknown lipid specificities. In this study, we determined the structures of the ankyrin repeat domain (ANK), and OSBP-related domain (ORD) of Osh1, in complex with Nvj1 and ergosterol, respectively. The Osh1 ANK forms a unique bi-lobed structure that recognizes a cytosolic helical segment of Nvj1. We discovered that Osh1 ORD binds ergosterol and phosphatidylinositol 4-phosphate PI(4)P in a competitive manner, suggesting counter-transport function of the two lipids. Ergosterol is bound to the hydrophobic pocket in a head-down orientation, and the structure of the PI(4)P-binding site in Osh1 is well conserved. Our results suggest that Osh1 performs non-vesicular transport of ergosterol and PI(4)P at the NVJ. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Revealing the neural networks associated with processing of natural social interaction and the related effects of actor-orientation and face-visibility.

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    Saggar, Manish; Shelly, Elizabeth Walter; Lepage, Jean-Francois; Hoeft, Fumiko; Reiss, Allan L

    2014-01-01

    Understanding the intentions and desires of those around us is vital for adapting to a dynamic social environment. In this paper, a novel event-related functional Magnetic Resonance Imaging (fMRI) paradigm with dynamic and natural stimuli (2s video clips) was developed to directly examine the neural networks associated with processing of gestures with social intent as compared to nonsocial intent. When comparing social to nonsocial gestures, increased activation in both the mentalizing (or theory of mind) and amygdala networks was found. As a secondary aim, a factor of actor-orientation was included in the paradigm to examine how the neural mechanisms differ with respect to personal engagement during a social interaction versus passively observing an interaction. Activity in the lateral occipital cortex and precentral gyrus was found sensitive to actor-orientation during social interactions. Lastly, by manipulating face-visibility we tested whether facial information alone is the primary driver of neural activation differences observed between social and nonsocial gestures. We discovered that activity in the posterior superior temporal sulcus (pSTS) and fusiform gyrus (FFG) was partially driven by observing facial expressions during social gestures. Altogether, using multiple factors associated with processing of natural social interaction, we conceptually advance our understanding of how social stimuli is processed in the brain and discuss the application of this paradigm to clinical populations where atypical social cognition is manifested as a key symptom. © 2013.

  13. Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response

    Directory of Open Access Journals (Sweden)

    Sakaki Yoshiyuki

    2007-12-01

    Full Text Available Abstract Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs. Results The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. Conclusion The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome.

  14. Tick (Ixodes ricinus) abundance and seasonality at recreational sites in the UK: hazards in relation to fine-scale habitat types revealed by complementary sampling methods.

    Science.gov (United States)

    Dobson, Andrew D M; Taylor, Jennifer L; Randolph, Sarah E

    2011-06-01

    The seasonal risk to humans of picking up Ixodes ricinus ticks in different habitats at 3 recreational sites in the UK was assessed. A comprehensive range of vegetation types was sampled at 3-weekly intervals for 2 years, using standard blanket-dragging complemented by woollen leggings and square 'heel flags'. Ticks were found in all vegetation types sampled, including short grass close to car parks, but highest densities were consistently found in plots with trees present. Blankets picked up the greatest number of ticks, but heel flags provided important complementary counts of the immature stages in bracken plots; they showed clearly that the decline in tick numbers on blankets in early summer was due to the seasonal growth of vegetation that lifted the blanket clear of the typical questing height, but in reality ticks remained abundant through the summer. Leggings picked up only 11% of the total nymphs and 22% of total adults counted, but this still represented a significant hazard to humans. These results should prompt a greater awareness of the fine-scale distribution of this species in relation to human activities that determines the most likely zones of contact between humans and ticks. Risk communication may then be designed accordingly. Copyright © 2011 Elsevier GmbH. All rights reserved.

  15. Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change.

    Directory of Open Access Journals (Sweden)

    Kai J Miller

    2016-01-01

    Full Text Available The link between object perception and neural activity in visual cortical areas is a problem of fundamental importance in neuroscience. Here we show that electrical potentials from the ventral temporal cortical surface in humans contain sufficient information for spontaneous and near-instantaneous identification of a subject's perceptual state. Electrocorticographic (ECoG arrays were placed on the subtemporal cortical surface of seven epilepsy patients. Grayscale images of faces and houses were displayed rapidly in random sequence. We developed a template projection approach to decode the continuous ECoG data stream spontaneously, predicting the occurrence, timing and type of visual stimulus. In this setting, we evaluated the independent and joint use of two well-studied features of brain signals, broadband changes in the frequency power spectrum of the potential and deflections in the raw potential trace (event-related potential; ERP. Our ability to predict both the timing of stimulus onset and the type of image was best when we used a combination of both the broadband response and ERP, suggesting that they capture different and complementary aspects of the subject's perceptual state. Specifically, we were able to predict the timing and type of 96% of all stimuli, with less than 5% false positive rate and a ~20ms error in timing.

  16. TMS-EEG reveals hemispheric asymmetries in top-down influences of posterior intraparietal cortex on behavior and visual event-related potentials.

    Science.gov (United States)

    Koivisto, Mika; Grassini, Simone; Hurme, Mikko; Salminen-Vaparanta, Niina; Railo, Henry; Vorobyev, Victor; Tallus, Jussi; Paavilainen, Teemu; Revonsuo, Antti

    2017-11-11

    Clinical data and behavioral studies using transcranial magnetic stimulation (TMS) suggest right-hemisphere dominance for top-down modulation of visual processing in humans. We used concurrent TMS-EEG to directly test for hemispheric differences in causal influences of the right and left intraparietal cortex on visual event-related potentials (ERPs). We stimulated the left and right posterior part of intraparietal sulcus (IPS1) while the participants were viewing and rating the visibility of bilaterally presented Gabor patches. Subjective visibility ratings showed that TMS of right IPS shifted the visibility toward the right hemifield, while TMS of left IPS did not have any behavioral effect. TMS of right IPS, but not left one, reduced the amplitude of posterior N1 potential, 180-220 ms after stimulus-onset. The attenuation of N1 occurred bilaterally over the posterior areas of both hemispheres. Consistent with previous TMS-fMRI studies, this finding suggests that the right IPS has top-down control on the neural processing in visual cortex. As N1 most probably reflects reactivation of early visual areas, the current findings support the view that the posterior parietal cortex in the right hemisphere amplifies recurrent interactions in ventral visual areas during the time-window that is critical for conscious perception. Copyright © 2017. Published by Elsevier Ltd.

  17. Spatio-temporal variation in small mammal species richness, relative abundance and body mass reveal changes in a coastal wetland ecosystem in Ghana.

    Science.gov (United States)

    Ofori, Benjamin Y; Attuquayefio, Daniel K; Owusu, Erasmus H; Musah, Yahaya; Ntiamoa-Baidu, Yaa

    2016-06-01

    Coastal wetlands in Ghana are under severe threat of anthropogenic drivers of habitat degradation and climate change, thereby increasing the need for assessment and monitoring to inform targeted and effective conservation of these ecosystems. Here, we assess small mammal species richness, relative abundance and body mass in three habitats at the Muni-Pomadze Ramsar site of Ghana, and compare these to baseline data gathered in 1997 to evaluate changes in the wetland ecosystem. Small mammals were live-trapped using Sherman collapsible and pitfall traps. We recorded 84 individuals of 10 species in 1485 trap-nights, whereas the baseline study recorded 45 individuals of seven species in 986 trap-nights. The overall trap-success was therefore greater in the present study (5.66 %) than the baseline study (4.56 %). The species richness increased from one to four in the forest, and from zero to eight in the thicket, but decreased from six to four in the grassland. The total number of individuals increased in all habitats, with the dominant species in the grassland shifting from Lemniscomys striatus to Mastomys erythroleucus. Three species, Malacomys edwardsi, Grammomys poensis and Praomys tullbergi are the first records for the Muni-Pomadze Ramsar site. Generally, the average body mass of individual species in the grassland was lower in the present study. The considerable changes in small mammal community structure suggest changes in the wetland ecosystem. The conservation implications of our findings are discussed.

  18. Cell surface expression of MR1B, a splice variant of the MHC class I-related molecule MR1, revealed with antibodies.

    Science.gov (United States)

    Yamaguchi, Hisateru; Tsukamoto, Kentaro; Hashimoto, Keiichiro

    2014-01-10

    The major histocompatibility complex (MHC) class I-related molecule, MR1, is highly conserved in mammals and can present bacteria-derived vitamin B metabolites to mucosal-associated invariant T (MAIT) cells, possibly having important defense function in the microbial infection. MR1B is a splice variant of MR1 and possesses an intriguing domain structure with only two extracellular domains resembling some NKG2D ligand molecules. Thus far, cell surface expression of MR1B could not be analyzed with flow cytometry due to a lack of appropriate antibodies reactive with MR1B. Here we clarified the expression of MR1B recombinant protein on the cell surface of the transfected cells by flow cytometry analyses using the antiserum against MR1. Consistently, MR1B tagged with FLAG peptide at the N-terminus also could be detected with anti-FLAG monoclonal antibodies. Our result showed that MR1B can be recognized on the cell surface by macromolecules such as antibodies, indicating its potential of interaction with certain receptor(s). We discuss possibility of interaction of MR1B and/or the full-length MR1 with some receptor(s) other than αβ T cell receptor (TCR) of MAIT cells based on the highly conserved characteristic residues of the ligand-binding domains of MR1 and its MAIT cells αβTCR footprints. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs

    Science.gov (United States)

    Cau, Andrea; Beyrand, Vincent; Voeten, Dennis F. A. E.; Fernandez, Vincent; Tafforeau, Paul; Stein, Koen; Barsbold, Rinchen; Tsogtbaatar, Khishigjav; Currie, Philip J.; Godefroit, Pascal

    2017-12-01

    Maniraptora includes birds and their closest relatives among theropod dinosaurs. During the Cretaceous period, several maniraptoran lineages diverged from the ancestral coelurosaurian bauplan and evolved novel ecomorphologies, including active flight, gigantism, cursoriality and herbivory. Propagation X-ray phase-contrast synchrotron microtomography of a well-preserved maniraptoran from Mongolia, still partially embedded in the rock matrix, revealed a mosaic of features, most of them absent among non-avian maniraptorans but shared by reptilian and avian groups with aquatic or semiaquatic ecologies. This new theropod, Halszkaraptor escuilliei gen. et sp. nov., is related to other enigmatic Late Cretaceous maniraptorans from Mongolia in a novel clade at the root of Dromaeosauridae. This lineage adds an amphibious ecomorphology to those evolved by maniraptorans: it acquired a predatory mode that relied mainly on neck hyperelongation for food procurement, it coupled the obligatory bipedalism of theropods with forelimb proportions that may support a swimming function, and it developed postural adaptations convergent with short-tailed birds.

  20. Identification of the dichotomous role of age-related LCK in calorie restriction revealed by integrative analysis of cDNA microarray and interactome.

    Science.gov (United States)

    Park, Daeui; Lee, Eun Kyeong; Jang, Eun Jee; Jeong, Hyoung Oh; Kim, Byoung-Chul; Ha, Young Mi; Hong, Seong Eui; Yu, Byung Pal; Chung, Hae Young

    2013-08-01

    Among the many experimental paradigms used for the investigation of aging, the calorie restriction (CR) model has been proven to be the most useful in gerontological research. Exploration of the mechanisms underlying CR has produced a wealth of data. To identify key molecules controlled by aging and CR, we integrated data from 84 mouse and rat cDNA microarrays with a protein-protein interaction network. On the basis of this integrative analysis, we selected three genes that are upregulated in aging but downregulated by CR and two genes that are downregulated in aging but upregulated by CR. One of these key molecules is lymphocyte-specific protein tyrosine kinase (LCK). To further confirm this result on LCK, we performed a series of experiments in vitro and in vivo using kidneys obtained from aged ad libitum-fed and CR rats. Our major significant findings are as follows: (1) identification of LCK as a key molecule using integrative analysis; (2) confirmation that the age-related increase in LCK was modulated by CR and that protein tyrosine kinase activity was decreased using a LCK-specific inhibitor; and (3) upregulation of LCK leads to NF-κB activation in a ONOO(-) generation-dependent manner, which is modulated by CR. These results indicate that LCK could be considered a target attenuated by the anti-aging effects of CR. Integrative analysis of cDNA microarray and interactome data are powerful tools for identifying target molecules that are involved in the aging process and modulated by CR.

  1. Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation.

    Science.gov (United States)

    Lonjou, Christine; Damiola, Francesca; Moissonnier, Monika; Durand, Geoffroy; Malakhova, Irina; Masyakin, Vladimir; Le Calvez-Kelm, Florence; Cardis, Elisabeth; Byrnes, Graham; Kesminiene, Ausrele; Lesueur, Fabienne

    2017-05-12

    Genetic factors may influence an individual's sensitivity to ionising radiation and therefore modify his/her risk of developing papillary thyroid carcinoma (PTC). Previously, we reported that common single nucleotide polymorphisms (SNPs) within the DNA damage recognition gene ATM contribute to PTC risk in Belarusian children exposed to fallout from the Chernobyl power plant accident. Here we explored in the same population the contribution of a panel of DNA repair-related SNPs in genes acting downstream of ATM. The association of 141 SNPs located in 43 DNA repair genes was examined in 75 PTC cases and 254 controls from the Gomel region in Belarus. All subjects were younger than 15 years at the time of the Chernobyl accident. Conditional logistic regressions accounting for radiation dose were performed with PLINK using the additive allelic inheritance model, and a linkage disequilibrium (LD)-based Bonferroni correction was used for correction for multiple testing. The intronic SNP rs2296675 in MGMT was associated with an increased PTC risk [per minor allele odds ratio (OR) 2.54 95% CI 1.50, 4.30, P per allele = 0.0006, P corr.= 0.05], and gene-wide association testing highlighted a possible role for ERCC5 (P Gene = 0.01) and PCNA (P Gene = 0.05) in addition to MGMT (P Gene = 0.008). These findings indicate that several genes acting in distinct DNA repair mechanisms contribute to PTC risk. Further investigation is needed to decipher the functional properties of the methyltransferase encoded by MGMT and to understand how alteration of such functions may lead to the development of the most common type of thyroid cancer.

  2. The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation.

    Science.gov (United States)

    Shao, Qiang; Gao, Yi Qin

    2011-10-07

    Molecular dynamics simulations using the integrated tempering sampling method were performed for the folding of wild-type B domain of protein A (BdpA). Starting from random and stretched structures, these simulations allow us to fold this protein into the native-like structure frequently, achieving very small backbone (1.7 Å) and all heavy-atom root-mean-square deviation (2.6 Å). Therefore, the method used here increases the efficiency of configuration sampling and thermodynamics characterization by molecular dynamics simulation. Although inconsistency exists between the calculation and experiments for the absolute stabilities, as a limitation of the force field parameters, the calculated order of helix stability (H3 > H2 > H1) is consistent with that determined by experiments for individual separate helices. The lowest free energy folding pathway of BdpA was found to start with a barrierless and non-cooperative structural collapse from the entirely extended (E) state, which leads to a physiologically unfolded (P) state consisting of multiple stable structures with few native inter-helical hydrophobic interactions formed. In the P state, only H3 is fully structured. The final formation of H1 (and to a lesser extent, H2) in the folded (F) state requires the packing of the inter-helical hydrophobic contacts. In addition, it was found that stabilities of backbone hydrogen bonds are significantly affected by their positions relative to the inter-helical hydrophobic core. As temperature increases, the stability of the hydrogen bonds exposed to the solvent tends to increase while that of the hydrogen bonds buried within the hydrophobic core decreases. Finally, we discuss implications of this study on the general folding mechanism of proteins. © 2011 American Institute of Physics

  3. Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity

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    Rachel Waller

    2018-01-01

    Full Text Available Amyotrophic lateral sclerosis (ALS is a clinical subtype of motor neurone disease (MND, a fatal neurodegenerative disease involving the loss of both the upper and lower motor neurones from the motor cortex, brainstem, and spinal cord. Identifying specific disease biomarkers would help to not only improve diagnostic delay but also to classify disease subtypes, monitor response to therapeutic drugs and track disease progression. miRNAs are small non-coding RNA responsible for regulating gene expression and ultimately protein expression and have been used as biomarkers for many cancers and neurodegenerative disorders. Investigating the detection of miRNAs in cerebrospinal fluid (CSF, the fluid that bathes the central nervous system (CNS is a prime target for identifying potential biomarkers for ALS. This is the first study to investigate the expression of miRNAs in the CSF of ALS patients using small RNA sequencing. We detected 11 differentially expressed miRNAs in the CSF of sporadic ALS (sALS patients related to neural and glial activity. Additionally, miRNAs involved in glucose metabolism and the regulation of oxidative stress were also identified. Detecting the presence of potential CSF derived miRNA biomarkers in sALS could open up a whole new area of knowledge to help gain a better understanding of disease pathophysiology. Additionally, with further investigation, the tracking of CSF miRNA over the disease course could be used to follow the disease progression and monitor the effect of novel therapeutics that could be personalized to an individual disease phenotype.

  4. Analysis of plant leaf metabolites reveals no common response to insect herbivory by Pieris rapae in three related host-plant species.

    Science.gov (United States)

    Riach, A C; Perera, M V L; Florance, H V; Penfield, S D; Hill, J K

    2015-05-01

    Studying the biochemical responses of different plant species to insect herbivory may help improve our understanding of the evolution of defensive metabolites found in host plants and their role in plant-herbivore interactions. Untargeted metabolic fingerprints measured as individual mass features were used to compare metabolite reactions in three Brassicales host-plant species (Cleome spinosa, Brassica oleracea, and Lunaria annua) to larval herbivore attack (Pieris rapae; Lepidoptera). Principal component analyses of metabolic fingerprints were able to distinguish among the three plant species and between uneaten control plants and plants that had been eaten. A large number of mass features (1186, 13% of mass features measured in control plants) were common to the three plant species. However, there were few similarities in the mass features that were induced (i.e. changed in abundance) following herbivory. Of the 87 and 68 induced mass features in B. oleracea and C. spinosa, respectively, there were only three that were induced in both plant species. By contrast, L. annua only had one mass feature induced by herbivory, and this was not induced in the other two plant species. The growth of the P. rapae larvae was poorer on the host plant L. annua than on B. oleracea and C. spinosa. The absence of common metabolites among the plants meant these induced responses could not be related to the performance of the herbivore. Thus, the response to herbivory by the same herbivore in these three host plants has evolved to be idiosyncratic in terms of the specific metabolites induced. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  5. Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup.

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    M Chehani Alles

    Full Text Available BACKGROUND: Breast cancers lacking the estrogen receptor (ER can be distinguished from other breast cancers on the basis of poor prognosis, high grade, distinctive histopathology and unique molecular signatures. These features further distinguish estrogen receptor negative (ER- tumor subtypes, but targeted therapy is currently limited to tumors over-expressing the ErbB2 receptor. METHODOLOGY/PRINCIPAL FINDINGS: To uncover the pathways against which future therapies could be developed we undertook a meta-analysis of gene expression from five large microarray datasets relative to ER status. A measure of association with ER status was calculated for every Affymetrix HG-U133A probe set and the pathways that distinguished ER- tumors were defined by testing for enrichment of biologically defined gene sets using Gene Set Enrichment Analysis (GSEA. As expected, the expression of the direct transcriptional targets of the ER was muted in ER- tumors, but the expression of genes indirectly regulated by estrogen was enhanced. We also observed enrichment of independent MYC- and E2F-driven transcriptional programs. We used a cell model of estrogen and MYC action to define the interaction between estrogen and MYC transcriptional activity in breast cancer. We found that the basal subgroup of ER- breast cancer showed a strong MYC transcriptional response that reproduced the indirect estrogen response seen in estrogen receptor positive (ER+ breast cancer cells. CONCLUSIONS/SIGNIFICANCE: Increased transcriptional activity of MYC is a characteristic of basal breast cancers where it mimics a large part of an estrogen response in the absence of the ER, suggesting a mechanism by which these cancers achieve estrogen-independence and providing a potential therapeutic target for this poor prognosis sub group of breast cancer.

  6. Cytological and transcriptional dynamics analysis of host plant revealed stage-specific biological processes related to compatible rice-Ustilaginoidea virens interaction.

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    Jinquan Chao

    Full Text Available Rice false smut, a fungal disease caused by Ustilaginoidea virens is becoming a severe detriment to rice production worldwide. However, little is known about the molecular response of rice to attacks by the smut pathogen. In this article, we define the initial infection process as having three stages: initial colonization on the pistil (stage 1, S1, amplification on the anther (stage 2, S2 and sporulation in the anther chambers (stage 3, S3. Based on the transcriptome of rice hosts in response to U. virens in two separate years, we identified 126, 204, and 580 specific regulated genes in their respective stages S1, S2, and S3, respectively, by excluding common expression patterns in other openly biotic/abiotic databases using bioinformatics. As the disease progresses, several stage-specific biological processes (BP terms were distinctively enriched: "Phosphorylation" in stage S1, "PCD" in S2, and "Cell wall biogenesis" in S3, implying a concise signal cascade indicative of the tactics that smut pathogens use to control host rice cells during infection. 113 regulated genes were coexpressed among the three stages. They shared highly conserved promoter cis-element in the promoters in response to the regulation of WRKY and Myb for up-regulation, and ABA and Ca2+ for down regulation, indicating their potentially critical roles in signal transduction during rice-U. virens interaction. We further analyzed seven highly regulated unique genes; four were specific to pollen development, implying that pollen-related genes play critical roles in the establishment of rice susceptibility to U. virens. To my knowledge, this is the first report about probing of molecular response of rice to smut pathogen infection, which will greatly expand our understanding of the molecular events surrounding infection by rice false smut.

  7. Comparative Genomics of Mycoplasma bovis Strains Reveals That Decreased Virulence with Increasing Passages Might Correlate with Potential Virulence-Related Factors

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    Muhammad A. Rasheed

    2017-05-01

    Full Text Available Mycoplasma bovis is an important cause of bovine respiratory disease worldwide. To understand its virulence mechanisms, we sequenced three attenuated M. bovis strains, P115, P150, and P180, which were passaged in vitro 115, 150, and 180 times, respectively, and exhibited progressively decreasing virulence. Comparative genomics was performed among the wild-type M. bovis HB0801 (P1 strain and the P115, P150, and P180 strains, and one 14.2-kb deleted region covering 14 genes was detected in the passaged strains. Additionally, 46 non-sense single-nucleotide polymorphisms and indels were detected, which confirmed that more passages result in more mutations. A subsequent collective bioinformatics analysis of paralogs, metabolic pathways, protein-protein interactions, secretory proteins, functionally conserved domains, and virulence-related factors identified 11 genes that likely contributed to the increased attenuation in the passaged strains. These genes encode ascorbate-specific phosphotransferase system enzyme IIB and IIA components, enolase, L-lactate dehydrogenase, pyruvate kinase, glycerol, and multiple sugar ATP-binding cassette transporters, ATP binding proteins, NADH dehydrogenase, phosphate acetyltransferase, transketolase, and a variable surface protein. Fifteen genes were shown to be enriched in 15 metabolic pathways, and they included the aforementioned genes encoding pyruvate kinase, transketolase, enolase, and L-lactate dehydrogenase. Hydrogen peroxide (H2O2 production in M. bovis strains representing seven passages from P1 to P180 decreased progressively with increasing numbers of passages and increased attenuation. However, eight mutants specific to eight individual genes within the 14.2-kb deleted region did not exhibit altered H2O2 production. These results enrich the M. bovis genomics database, and they increase our understanding of the mechanisms underlying M. bovis virulence.

  8. Heightened biological uptake of polybrominated diphenyl ethers relative to polychlorinated biphenyls near-source revealed by sediment and plankton profiles along a coastal transect in British Columbia.

    Science.gov (United States)

    Desforges, Jean-Pierre W; Dangerfield, Neil; Shaw, Patrick D; Ross, Peter S

    2014-06-17

    Polychlorinated biphenyl (PCB) and polybrominated diphenyl ether (PBDE) concentrations and profiles in paired sediment-plankton samples were determined along a 500 km transect in coastal British Columbia, Canada. PCB and PBDE levels in sediment were both greater in the industrialized Strait of Georgia than in remote northern sites and exhibited parallel spatial trends. In plankton, recent-use PBDE levels were higher near-source, while levels of legacy PCBs were uniform across sites. Principal component analysis of 95 PCB congeners illustrated the influence of proximity to source (i.e., latitude) on congener patterns for both matrices (sediment, r(2) = 0.52, p = 0.012; plankton, r(2) = 0.59, p = 0.016). The PCB pattern in plankton grew lighter with latitude, but the opposite pattern in sediments suggested that temperature-related fractionation, sediment processes, and basin-wide oceanography had divergent effects on each matrix. Biota-sediment accumulation factors (BSAFs) were greater for PBDEs than PCBs, but spatial profiles were similar; PCBs and PBDEs were near equilibrium in remote atmospherically driven sites (BSAF = 1.7 and 1.3) but accumulated preferentially in sediments at source-driven sites (BSAF = 0.2 and 0.4). The influences of particle-binding and hydrophobicity on the aquatic fate of PCBs and PBDEs was evident by the strong influence of log KOW on congener-specific BSAFs (PCBs, r(2) = 0.18 p < 0.001; PBDEs, r(2) = 0.61 p < 0.001). While biotic uptake of PCBs has become spatially uniform in coastal BC because of dilution over time, biomagnification of PBDEs remains higher in industrialized waters.

  9. STOP-EVENT-RELATED POTENTIALS FROM INTRACRANIAL ELECTRODES REVEAL A KEY ROLE OF PREMOTOR AND MOTOR CORTICES IN STOPPING ONGOING MOVEMENTS

    Directory of Open Access Journals (Sweden)

    Maurizio eMattia

    2012-06-01

    Full Text Available In humans, the ability to withhold manual motor responses seems to rely on a right-lateralized frontal–basal ganglia–thalamic network, including the pre-supplementary motor area and the inferior frontal gyrus. These areas should drive subthalamic nuclei to implement movement inhibition via the hyperdirect pathway. The output of this network is expected to influence those cortical areas underlying limb movement preparation and initiation, i.e. premotor (PMA and primary motor (M1 cortices. Electroencephalographic (EEG studies have shown an enhancement of the N200/P300 complex in the event-related potentials (ERPs when a planned reaching movement is successfully stopped after the presentation of an infrequent stop-signal. PMA and M1 have been suggested as possible neural sources of this ERP complex but, due to the limited spatial resolution of scalp EEG, it is not yet clear which cortical areas contribute to its generation. To elucidate the role of motor cortices, we recorded epicortical ERPs from the lateral surface of the fronto-temporal lobes of five pharmacoresistant epileptic patients performing a reaching version of the countermanding task while undergoing presurgical monitoring. We consistently found a stereotyped ERP complex on a single-trial level when a movement was successfully cancelled. These ERPs were selectively expressed in M1, PMA and Brodmann's area (BA 9 and their onsets preceded the end of the stop process, suggesting a causal involvement in this executive function. Such ERPs also occurred in unsuccessful-stop trials, that is, when subjects moved despite the occurrence of a stop-signal, mostly when they had long reaction times. These findings support the hypothesis that motor cortices are the final target of the inhibitory command elaborated by the frontal–basal ganglia–thalamic network.

  10. 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

  11. The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation

    Directory of Open Access Journals (Sweden)

    Yingxin Zhang

    2017-10-01

    Full Text Available Transposable elements (TEs in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4% of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like

  12. Magnetic resonance imaging at 7T reveals common events in age-related sarcopenia and in the homeostatic response to muscle sterile injury.

    Directory of Open Access Journals (Sweden)

    Antonio Esposito

    Full Text Available Skeletal muscle remodeling in response to various noxae physiologically includes structural changes and inflammatory events. The possibility to study those phenomena in-vivo has been hampered by the lack of validated imaging tools. In our study, we have relied on multiparametric magnetic resonance imaging for quantitative monitoring of muscle changes in mice experiencing age-related sarcopenia or active regeneration after sterile acute injury of tibialis anterior muscle induced by cardiotoxin (CTX injection. The extent of myofibrils' necrosis, leukocyte infiltration, and regeneration have been evaluated and compared with parameters from magnetic resonance imaging: T2-mapping (T2 relaxation time; T2-rt, diffusion-tensor imaging (fractional anisotropy, F.A. and diffusion weighted imaging (apparent diffusion coefficient, ADC. Inflammatory leukocytes within the perimysium and heterogeneous size of fibers characterized aged muscles. They displayed significantly increased T2-rt (P<0.05 and F.A. (P<0.05 compared with young muscles. After acute damage T2-rt increased in otherwise healthy young muscles with a peak at day 3, followed by a progressive decrease to basal values. F.A. dropped 24 hours after injury and afterward increased above the basal level in the regenerated muscle (from day 7 to day 15 returning to the basal value at the end of the follow up period. The ADC displayed opposite kinetics. T2-rt positively correlated with the number of infiltrating leucocytes retrieved by immunomagnetic bead sorting from the tissue (r = 0.92 and with the damage/infiltration score (r = 0.88 while F.A. correlated with the extent of tissue regeneration evaluated at various time points after injury (r = 0.88. Our results indicate that multiparametric MRI is a sensitive and informative tool for monitoring inflammatory and structural muscle changes in living experimental animals; particularly, it allows identifying the increase of T2-rt and F.A. as common events

  13. Computer-based comparison of structural features of envelope protein of Alkhurma hemorrhagic fever virus with the homologous proteins of two closest viruses.

    Science.gov (United States)

    Mohabatkar, Hassan

    2011-06-01

    The aim of this study was prediction of epitopes and medically important structural properties of protein E of Alkhurma hemorrhagic fever virus (AHFV) and comparing these features with two closely relates viruses, i.e. Kyasanur Forest disease virus (KFDV) and Tick-borne encephalitis virus (TBEV) by bioinformatics tools. Prediction of evolutionary distance, localization, sequence of signal peptides, C, N O glycosylation sites, transmembrane helices (TMHs), cysteine bond positions and B cell and T cell epitopes of E proteins were performed. 2D-MH, Virus-PLoc, Signal-CF, EnsembleGly, MemBrain, DiANNA, BCPREDS and MHCPred servers were applied for the prediction. According to the results, the evolutionary distance of E protein of AHFV and two other viruses was almost equal. In all three proteins of study, residues 1-35 were predicted as signal sequences and one asparagine was predicted to be glycosylated. Results of prediction of transmembrane helices showed one TMH at position 444-467 and the other one at position 476-490. Twelve cysteines were potentially involved to form six disulfide bridges in the proteins. Four parts were predicted as B cell epitopes in E protein of AHFV. One epitope was conserved between three proteins of study. The only conserved major histocompatibility complex (MHC) binding epitope between three viruses was for DRB0401 allele. As there are not much experimental data available about AHFV, computer-aided study and comparison of E protein of this virus with two closely related flaviviruses can help in better understanding of medical properties of the virus.

  14. Towards abolition of immunogenic structures in insect cells: characterization of a honey-bee (Apis mellifera) multi-gene family reveals both an allergy-related core α1,3-fucosyltransferase and the first insect Lewis-histo-blood-group-related antigen-synthesizing enzyme

    Science.gov (United States)

    Rendić, Dubravko; Klaudiny, Jaroslav; Stemmer, Ute; Schmidt, Julia; Paschinger, Katharina; Wilson, Iain B. H.

    2006-01-01

    Glycoproteins from honey-bee (Apis mellifera), such as phospholipase A2 and hyaluronidase, are well-known major bee-venom allergens. They carry N-linked oligosaccharide structures with two types of α1,3-fucosylation: the modification by α1,3-fucose of the innermost core GlcNAc, which constitutes an epitope recognized by IgE from some bee-venom-allergic patients, and an antennal Lewis-like GalNAcβ1,4(Fucα1,3)GlcNAc moiety. We now report the cloning and expression of two cDNAs encoding the relevant active α1,3-FucTs (α1,3-fucosyltransferases). The first sequence, closest to that of fruitfly (Drosophila melanogaster) FucTA, was found to be a core α1,3-FucT (EC 2.4.1.214), as judged by several enzyme and biochemical assays. The second cDNA encoded an enzyme, most related to Drosophila FucTC, that was shown to be capable of generating the Lex [Galβ1-4(Fucα1-3)GlcNAc] epitope in vitro and is the first Lewis-type α1,3-FucT (EC 2.4.1.152) to be described in insects. The transcription levels of these two genes in various tissues were examined: FucTA was found to be predominantly expressed in the brain tissue and venom glands, whereas FucTC transcripts were detected at highest levels in venom and hypopharyngeal glands. Very low expression of a third homologue of unknown function, FucTB, was also observed in various tissues. The characterization of these honey-bee gene products not only accounts for the observed α1,3-fucosylation of bee-venom glycoproteins, but is expected to aid the identification and subsequent down-regulation of the FucTs in insect cell lines of biotechnological importance. PMID:17029591

  15. Towards abolition of immunogenic structures in insect cells: characterization of a honey-bee (Apis mellifera) multi-gene family reveals both an allergy-related core alpha1,3-fucosyltransferase and the first insect Lewis-histo-blood-group-related antigen-synthesizing enzyme.

    Science.gov (United States)

    Rendić, Dubravko; Klaudiny, Jaroslav; Stemmer, Ute; Schmidt, Julia; Paschinger, Katharina; Wilson, Iain B H

    2007-02-15

    Glycoproteins from honey-bee (Apis mellifera), such as phospholipase A2 and hyaluronidase, are well-known major bee-venom allergens. They carry N-linked oligosaccharide structures with two types of alpha1,3-fucosylation: the modification by alpha1,3-fucose of the innermost core GlcNAc, which constitutes an epitope recognized by IgE from some bee-venom-allergic patients, and an antennal Lewis-like GalNAcbeta1,4(Fucalpha1,3)GlcNAc moiety. We now report the cloning and expression of two cDNAs encoding the relevant active alpha1,3-FucTs (alpha1,3-fucosyltransferases). The first sequence, closest to that of fruitfly (Drosophila melanogaster) FucTA, was found to be a core alpha1,3-FucT (EC 2.4.1.214), as judged by several enzyme and biochemical assays. The second cDNA encoded an enzyme, most related to Drosophila FucTC, that was shown to be capable of generating the Le(x) [Galbeta1-4(Fucalpha1-3)GlcNAc] epitope in vitro and is the first Lewis-type alpha1,3-FucT (EC 2.4.1.152) to be described in insects. The transcription levels of these two genes in various tissues were examined: FucTA was found to be predominantly expressed in the brain tissue and venom glands, whereas FucTC transcripts were detected at highest levels in venom and hypopharyngeal glands. Very low expression of a third homologue of unknown function, FucTB, was also observed in various tissues. The characterization of these honey-bee gene products not only accounts for the observed alpha1,3-fucosylation of bee-venom glycoproteins, but is expected to aid the identification and subsequent down-regulation of the FucTs in insect cell lines of biotechnological importance.

  16. Drug-related problem classification systems.

    Science.gov (United States)

    van Mil, J W Foppe; Westerlund, L O Tommy; Hersberger, Kurt E; Schaefer, Marion A

    2004-05-01

    To provide an overview of and critically appraise classifications of drug-related problems (DRPs) for use during the pharmaceutical care process and research in pharmacy. A literature search was conducted using MEDLINE and Yahoo (January 2003) and manually. The search terms included DRP, drug-related problem, drug-therapy problem, and medicine-related problem. English- and German-language articles on pharmaceutical care and DRPs were reviewed. Most classifications of DRPs were identified through searching publications on pharmaceutical care and DRPs. Fourteen classifications with different focuses were found. Some classifications were hierarchical, categorized into main groups and subgroups. Various terminologies and definitions for DRPs were revealed, as well as guidelines for an optimal DRP classification. Classifications were assessed according to a clear definition, published validation method, and results reflecting process and outcomes, usability in pharmaceutical care practice, and a hierarchical structure with main groups and subgroups. Finding DRP classifications by computerized search of the biomedical literature with the help of PubMed proved to be difficult. No classification could be found that met all of our criteria for an optimal system. Few classifications have been validated. Three have been tested as to their usability in practice and internal consistency. The Pharmaceutical Care Network Europe system Version 4 comes closest to the defined requirements.

  17. Phylogeny of Darwin's finches as revealed by mtDNA sequences.

    Science.gov (United States)

    Sato, A; O'hUigin, C; Figueroa, F; Grant, P R; Grant, B R; Tichy, H; Klein, J

    1999-04-27

    Darwin's finches comprise a group of passerine birds first collected by Charles Darwin during his visit to the Galápagos Archipelago. The group, a textbook example of adaptive radiation (the diversification of a founding population into an array of species differentially adapted to diverse environmental niches), encompasses 14 currently recognized species, of which 13 live on the Galápagos Islands and one on the Cocos Island in the Pacific Ocean. Although Darwin's finches have been studied extensively by morphologists, ecologists, and ethologists, their phylogenetic relationships remain uncertain. Here, sequences of two mtDNA segments, the cytochrome b and the control region, have been used to infer the evolutionary history of the group. The data reveal the Darwin's finches to be a monophyletic group with the warbler finch being the species closest to the founding stock, followed by the vegetarian finch, and then by two sister groups, the ground and the tree finches. The Cocos finch is related to the tree finches of the Galápagos Islands. The traditional classification of ground finches into six species and tree finches into five species is not reflected in the molecular data. In these two groups, ancestral polymorphisms have not, as yet, been sorted out among the cross-hybridizing species.

  18. Phylogeny of Darwin’s finches as revealed by mtDNA sequences

    Science.gov (United States)

    Sato, Akie; O’hUigin, Colm; Figueroa, Felipe; Grant, Peter R.; Grant, B. Rosemary; Tichy, Herbert; Klein, Jan

    1999-01-01

    Darwin’s finches comprise a group of passerine birds first collected by Charles Darwin during his visit to the Galápagos Archipelago. The group, a textbook example of adaptive radiation (the diversification of a founding population into an array of species differentially adapted to diverse environmental niches), encompasses 14 currently recognized species, of which 13 live on the Galápagos Islands and one on the Cocos Island in the Pacific Ocean. Although Darwin’s finches have been studied extensively by morphologists, ecologists, and ethologists, their phylogenetic relationships remain uncertain. Here, sequences of two mtDNA segments, the cytochrome b and the control region, have been used to infer the evolutionary history of the group. The data reveal the Darwin’s finches to be a monophyletic group with the warbler finch being the species closest to the founding stock, followed by the vegetarian finch, and then by two sister groups, the ground and the tree finches. The Cocos finch is related to the tree finches of the Galápagos Islands. The traditional classification of ground finches into six species and tree finches into five species is not reflected in the molecular data. In these two groups, ancestral polymorphisms have not, as yet, been sorted out among the cross-hybridizing species. PMID:10220425

  19. Growth hormone deficiency due to sports-related head trauma is associated with impaired cognitive performance in amateur boxers and kickboxers as revealed by P300 auditory event-related potentials.

    Science.gov (United States)

    Tanriverdi, Fatih; Suer, Cem; Yapislar, Hande; Kocyigit, Ismail; Selcuklu, Ahmet; Unluhizarci, Kursad; Casanueva, Felipe F; Kelestimur, Fahrettin

    2013-05-01

    It has been recently reported that boxing and kickboxing may cause pituitary dysfunction, GH deficiency in particular. The strong link between poor cognitive performance and GH deficiency due to causes other than head trauma and the improvement of cognitive function after GH replacement therapy have been previously shown. P300 auditory event-related potential (ERP) measure is widely used to evaluate cognitive performance. In this study, we investigated the relation between the GH-IGF-I axis and cognitive performance in boxers and kickboxers. Forty-one actively competing or retired male boxers (n: 27) and kickboxers (n: 14) with a mean age of 29·04 ± 9·30 year and 14 age- and education-matched healthy male controls were included in the study. For neuropsychological tests, the mini-mental state examination (MMSE) and Quality of Life Assessment of GH Deficiency in Adults (QoL-AGHDA) questionnaires were administered. Moreover, cognitive performance was evaluated according to P300 ERPs. Nine of 41 (21·9%) athletes had GH deficiency. P300 amplitudes were lower at all electrode sites in the GH-deficient group than in controls, and the differences were statistically significant at Fz and Oz electrode sites (P P300 amplitudes were lower at all electrode sites in the GH-deficient group; these differences were statistically significant at Fz, Pz and Cz electrode sites (P P300 latencies, and there were significant positive correlations between IGF-I levels vs P300 amplitudes (P relation between the P300 ERPs and the GH-IGF-I axis in boxers and kickboxers. © 2012 Blackwell Publishing Ltd.

  20. Mahalanobis Distance Based Iterative Closest Point

    DEFF Research Database (Denmark)

    Hansen, Mads Fogtmann; Blas, Morten Rufus; Larsen, Rasmus

    2007-01-01

    a fast optimization. Initially, the covariance matrices are set to the identity matrix, and all shapes are aligned to a randomly selected shape (equivalent to standard ICP). From this point the algorithm iterates between the steps: (a) obtain mean shape and new estimates of the covariance matrices from...... the notion of a mahalanobis distance map upon a point set with associated covariance matrices which in addition to providing correlation weighted distance implicitly provides a method for assigning correspondence during alignment. This distance map provides an easy formulation of the ICP problem that permits...... the aligned shapes, (b) align shapes to the mean shape. Three different methods for estimating the mean shape with associated covariance matrices are explored in the paper. The proposed methods are validated experimentally on two separate datasets (IMM face dataset and femur-bones). The superiority of ICP...

  1. Enological characterization of Spanish Saccharomyces kudriavzevii strains, one of the closest relatives to parental strains of winemaking and brewing Saccharomyces cerevisiae × S. kudriavzevii hybrids.

    Science.gov (United States)

    Peris, D; Pérez-Través, L; Belloch, C; Querol, A

    2016-02-01

    Wine fermentation and innovation have focused mostly on Saccharomyces cerevisiae strains. However, recent studies have shown that other Saccharomyces species can also be involved in wine fermentation or are useful for wine bouquet, such as Saccharomyces uvarum and Saccharomyces paradoxus. Many interspecies hybrids have also been isolated from wine fermentation, such as S. cerevisiae × Saccharomyces kudriavzevii hybrids. In this study, we explored the genetic diversity and fermentation performance of Spanish S. kudriavzevii strains, which we compared to other S. kudriavzevii strains. Fermentations of red and white grape musts were performed, and the phenotypic differences between Spanish S. kudriavzevii strains under different temperature conditions were examined. An ANOVA analysis suggested striking similarity between strains for glycerol and ethanol production, although a high diversity of aromatic profiles among fermentations was found. The sources of these phenotypic differences are not well understood and require further investigation. Although the Spanish S. kudriavzevii strains showed desirable properties, particularly must fermentations, the quality of their wines was no better than those produced with a commercial S. cerevisiae. We suggest hybridization or directed evolution as methods to improve and innovate wine. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation.

    Science.gov (United States)

    Beaton, E D; Stevenson, Bradley S; King-Sharp, Karen J; Stamps, Blake W; Nunn, Heather S; Stuart, Marilyne

    2016-01-01

    Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth's biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the

  3. Origin of Bannerman's Turaco Tauraco bannermani in relation to ...

    African Journals Online (AJOL)

    We determined the systematic relationships and approximate divergence time of Bannerman's Turaco Tauraco bannermani and used this information to test whether the origin and distribution of this species and its closest relatives are associated with the effects of historical climate change on forest habitats in West Africa.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24...... and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native...... Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from...

  5. Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice

    Directory of Open Access Journals (Sweden)

    Maria Camila Rebolledo

    2016-09-01

    Full Text Available Number of spikelets per panicle (NSP is a key trait to increase yield potential in rice (O. sativa. The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN and secondary (SBL and SBN branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i the genetic control of panicle architecture and NSP in different environments and (ii the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS based on the genotyping of the diversity panel, providing 83,374 SNPs.Accessions sown under direct seeding in one environement had reduced Panicle Length (PL, NSP, PBN, PBL, SBN and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL was not significantly correlated with variables related to number of branches (PBN and SBN , suggesting independent genetic control.Twenty- three GWAS sites were detected with P-values ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported.The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi

  6. Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure.

    Science.gov (United States)

    Nimusiima, Jean; Köberl, Martina; Tumuhairwe, John Baptist; Kubiriba, Jerome; Staver, Charles; Berg, Gabriele

    2015-12-10

    Africa is among the continents where the battle over genetically modified crops is currently being played out. The impact of GM in Africa could potentially be very positive. In Uganda, researchers have developed transgenic banana lines resistant to banana Xanthomonas wilt. The transgenic lines expressing hrap and pflp can provide a timely solution to the pandemic. However, the impact of the transgenes expression on non-target microorganisms has not yet been investigated. To study this effect, transgenic and control lines were grown under field conditions and their associated microbiome was investigated by 16S rRNA gene profiling combining amplicon sequencing and molecular fingerprinting. Three years after sucker planting, no statistically significant differences between transgenic lines and their non-modified predecessors were detected for their associated bacterial communities. The overall gammaproteobacterial rhizosphere microbiome was highly dominated by Xanthomonadales, while Pseudomonadales and Enterobacteriales were accumulated in the pseudostem. Shannon indices revealed much higher diversity in the rhizosphere than in the pseudostem endosphere. However, the expression of the transgenes did not result in changes in the diversity of Gammaproteobacteria, the closest relatives of the target pathogen. In this field experiment, the expression of the resistance genes appears to have no consequences for non-target rhizobacteria and endophytes.

  7. Revealing and Concealing in Antiquity

    DEFF Research Database (Denmark)

    Secrecy and the act of concealing and revealing knowledge effectually segregate the initiated and the uninitiated. The act of sharing or hiding knowledge plays a central role in all human relations private or public, political or religious. This volume explores the concept of secrecy and its impl...

  8. The Two-Dimensional Analogue of General Relativity

    OpenAIRE

    Lemos, José P. S.; Sá, Paulo M.

    1993-01-01

    General Relativity in three or more dimensions can be obtained by taking the limit $\\omega\\rightarrow\\infty$ in the Brans-Dicke theory. In two dimensions General Relativity is an unacceptable theory. We show that the two-dimensional closest analogue of General Relativity is a theory that also arises in the limit $\\omega\\rightarrow\\infty$ of the two-dimensional Brans-Dicke theory.

  9. Chimpanzee genomic diversity reveals ancient admixture with bonobos

    DEFF Research Database (Denmark)

    de Manuel, Marc; Kuhlwilm, Martin; Frandsen, Peter

    2016-01-01

    Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor...... of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another......, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution....

  10. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

    Directory of Open Access Journals (Sweden)

    Xue-Feng Ma

    Full Text Available We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS, identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7, presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

  11. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  12. Two-component signal transduction in Bacillus cereus and closely related bacteria

    NARCIS (Netherlands)

    Been, de M.W.H.J.

    2009-01-01

    Bacillus cereus is a Gram-positive pathogen that is recognised as an important cause of food-borne disease worldwide. Within the genus Bacillus, B. cereus and its closest relatives form a homogeneous subdivision that has been termed the B. cereus group. This group includes B. anthracis, a pathogen

  13. Garlic (Allium sativum L.) and its wild relatives from Central Asia: evaluation for fertility potential

    NARCIS (Netherlands)

    Kamenetsky, R.; London Safir, I.; Baizerman, M.; Khassanov, F.; Kik, C.; Rabinowitch, H.D.

    2004-01-01

    Garlic (Allium sativum L.) a popular condiment, is completely sterile, and thus is propagated only vegetatively. According to modern taxonomy, A. sativum and its closest wild relative A. longicuspis form a species complex. The collection of a large number of accessions of these taxa is the only

  14. Comparisons of Transcriptional Profiles of Gut Genes between Cry1Ab-Resistant and Susceptible Strains of Ostrinia nubilalis Revealed Genes Possibly Related to the Adaptation of Resistant Larvae to Transgenic Cry1Ab Corn

    Directory of Open Access Journals (Sweden)

    Jianxiu Yao

    2017-01-01

    Full Text Available A microarray developed on the basis of 2895 unique transcripts from larval gut was used to compare gut gene expression profiles between a laboratory-selected Cry1Ab-resistant (R strain and its isoline susceptible (S strain of the European corn borer (Ostrinia nubilalis after the larvae were fed the leaves of transgenic corn (MON810 expressing Cry1Ab or its non-transgenic isoline for 6 h. We revealed 398 gut genes differentially expressed (i.e., either up- or down-regulated genes with expression ratio ≥2.0 in S-strain, but only 264 gut genes differentially expressed in R-strain after being fed transgenic corn leaves. Although the percentages of down-regulated genes among the total number of differentially expressed genes (50% in S-strain and 45% in R-strain were similar between the R- and S-strains, the expression ratios of down-regulated genes were much higher in S-strain than in R-strain. We revealed that 17 and 9 significantly up- or down-regulated gut genes from S and R-strain, respectively, including serine proteases and aminopeptidases. These genes may be associated with Cry1Ab toxicity by degradation, binding, and cellular defense. Overall, our study suggests enhanced adaptation of Cry1Ab-resistant larvae on transgenic Cry1Ab corn as revealed by lower number and lower ratios of differentially expressed genes in R-strain than in S-strain of O. nubilalis.

  15. Comparisons of Transcriptional Profiles of Gut Genes between Cry1Ab-Resistant and Susceptible Strains of Ostrinia nubilalis Revealed Genes Possibly Related to the Adaptation of Resistant Larvae to Transgenic Cry1Ab Corn.

    Science.gov (United States)

    Yao, Jianxiu; Zhu, Yu-Cheng; Lu, Nanyan; Buschman, Lawrent L; Zhu, Kun Yan

    2017-01-30

    A microarray developed on the basis of 2895 unique transcripts from larval gut was used to compare gut gene expression profiles between a laboratory-selected Cry1Ab-resistant (R) strain and its isoline susceptible (S) strain of the European corn borer (Ostrinia nubilalis) after the larvae were fed the leaves of transgenic corn (MON810) expressing Cry1Ab or its non-transgenic isoline for 6 h. We revealed 398 gut genes differentially expressed (i.e., either up- or down-regulated genes with expression ratio ≥2.0) in S-strain, but only 264 gut genes differentially expressed in R-strain after being fed transgenic corn leaves. Although the percentages of down-regulated genes among the total number of differentially expressed genes (50% in S-strain and 45% in R-strain) were similar between the R- and S-strains, the expression ratios of down-regulated genes were much higher in S-strain than in R-strain. We revealed that 17 and 9 significantly up- or down-regulated gut genes from S and R-strain, respectively, including serine proteases and aminopeptidases. These genes may be associated with Cry1Ab toxicity by degradation, binding, and cellular defense. Overall, our study suggests enhanced adaptation of Cry1Ab-resistant larvae on transgenic Cry1Ab corn as revealed by lower number and lower ratios of differentially expressed genes in R-strain than in S-strain of O. nubilalis.

  16. Determination of structure of the MinD-ATP complex reveals the orientation of MinD on the membrane and the relative location of the binding sites for MinE and MinC

    Science.gov (United States)

    Wu, Wei; Park, Kyung-Tae; Holyoak, Todd; Lutkenhaus, Joe

    2011-01-01

    Summary The three Min proteins spatially regulate Z ring positioning in E. coli and are dynamically associated with the membrane. MinD binds to vesicles in the presence of ATP and can recruit MinC or MinE. Biochemical and genetic evidence indicate the binding sites for these two proteins on MinD overlap. Here we solved the structure of a hydrolytic-deficient mutant of MinD truncated for the C-terminal amphipathic helix involved in binding to the membrane. The structure solved in the presence of ATP is a dimer and reveals the face of MinD abutting the membrane. Using a combination of random and extensive site-directed mutagenesis additional residues important for MinE and MinC binding were identified. The location of these residues on the MinD structure confirms that the binding sites overlap and reveals that the binding sites are at the dimer interface and exposed to the cytosol. The location of the binding sites at the dimer interface offers a simple explanation for the ATP-dependency of MinC and MinE binding to MinD. PMID:21231967

  17. 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...

  18. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  19. Mysterious Blob Galaxies Revealed

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2Figure 3 This image composite shows a giant galactic blob (red, figure 2) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow, figure 3). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images like the one shown in figure 2, reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together (figure 3). Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile.

  20. To Reveal Thy Heart Perchance to Reveal the World

    Directory of Open Access Journals (Sweden)

    Robert B. Faux

    2005-05-01

    Full Text Available Ronald PELIAS, a professor of speech communications, employs a variety of writing methods as examples of alternative ways to do research and to share with the reader a seldom seen and seldom considered aspect of academic life: Heart. In the early chapters of the book, PELIAS sets out to establish a way to place his Heart in the foreground; baring his emotional vulnerability, his humanness, his being in the world. Later chapters of the book encompass an autoethnographic study of academic life in which the previously revealed Heart is placed in context. In this review essay I discuss PELIAS' book in relation to the larger literature on autoethnography and subjectivist research; I follow this by discussing the need for and usefulness of such alternative methods using PELIAS' autoethnography of academic life as a context. URN: urn:nbn:de:0114-fqs050279

  1. Prospectively surveying health-related quality of life and symptom relief in a lot-based sample of medical cannabis-using patients in urban Washington State reveals managed chronic illness and debility.

    Science.gov (United States)

    Aggarwal, S K; Carter, G T; Sullivan, M D; Zumbrunnen, C; Morrill, R; Mayer, J D

    2013-09-01

    To characterize health-related quality of life (HRQoL) in medical cannabis patients. Short Form 36 (SF-36) Physical Health Component Score and Mental Health Component Score (MCS) surveys as well has CDC (Centers for Disease Control) HRQoL-14 surveys were completed by 37 qualified patients. Mean SF-36 PCS and MCS, normalized at 50, were 37.4 and 44.2, respectively. Eighty percent of participants reported activity/functional limitations secondary to impairments or health problems. Patients reported using medical cannabis to treat a wide array of symptoms across multiple body systems with relief ratings consistently in the 7-10/10 range. The HRQoL results in this sample of medical cannabis-using patients are comparable with published norms in other chronically ill populations. Data presented provide insight into medical cannabis-using patients' self-rated health, HRQoL, disease incidences, and cannabis-related symptom relief.

  2. The duration of disgusted and fearful faces is judged longer and shorter than that of neutral faces: the attention-related time distortions as revealed by behavioral and electrophysiological measurements

    Directory of Open Access Journals (Sweden)

    Dandan eZhang

    2014-08-01

    Full Text Available Time perception has been shown to be altered by emotions. This study employed event-related potentials (ERPs to examine the effects of two threat-related emotions on the judgment of time intervals in the range of 490-910 ms. We demonstrated that disgust and fear have distinct influences on time perception. At the behavioral level, disgusted faces were estimated longer and fearful faces were estimated shorter (i.e., the generalization gradient for the disgusted faces was shifted left while the generalization gradient for the fearful faces was shifted right when compared with neutral faces. Accordingly, the contingent negative variation, an online ERP index of timing, displayed larger area in disgust and smaller area in fear conditions when compared with neutral condition (disgust = 1.94 ± 2.35 μV•s, neutral = 1.40 ± 2.5 μV•s, and fear = 1.00 ± 2.26 μV•s. These findings indicated that specific neural mechanisms may underlie the attention effects of different subtypes of threat-related emotions on timing; compared with neutral faces, fearful faces are likely to attract more attentional resources while disgusted faces may attract less attentional resources for emotional processing. The major contribution of the current study is to provide neural correlates of fear vs. disgust divergence in the aspect of time perception and to demonstrate beyond the behavioral level that the categorization of threat-related emotions should be refined so to highlight the adaptability of the human defense system.

  3. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

    Directory of Open Access Journals (Sweden)

    Dragana Dobrijevic

    Full Text Available The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

  4. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

    Science.gov (United States)

    Dobrijevic, Dragana; Abraham, Anne-Laure; Jamet, Alexandre; Maguin, Emmanuelle; van de Guchte, Maarten

    2016-01-01

    The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

  5. Analysis of variations in the glutamate receptor, N-methyl D-aspartate 2A (GRIN2A gene reveals their relative importance as genetic susceptibility factors for heroin addiction.

    Directory of Open Access Journals (Sweden)

    Bin Zhao

    Full Text Available The glutamate receptor, N-methyl D-aspartate 2A (GRIN2A gene that encodes the 2A subunit of the N-methyl D-aspartate (NMDA receptor was recently shown to be involved in the development of opiate addiction. Genetic polymorphisms in GRIN2A have a plausible role in modulating the risk of heroin addiction. An association of GRIN2A single-nucleotide polymorphisms (SNPs with heroin addiction was found earlier in African Americans. To identify markers that contribute to the genetic susceptibility to heroin addiction, we examined the potential association between heroin addiction and forty polymorphisms of the GRIN2A gene using the MassARRAY system and GeneScan in this study. The frequency of the (GT26 repeats (rs3219790 in the heroin addiction group was significantly higher than that in the control group (χ(2 = 5.360, P = 0.021. The allele frequencies of three polymorphisms (rs1102972, rs1650420, and rs3104703 in intron 3 were strongly associated with heroin addiction (P<0.001, 0.0002, and <0.001, after Bonferroni correction. Three additional SNPs from the same intron (rs1071502, rs6497730, and rs1070487 had nominally significant P values for association (P<0.05, but did not pass the threshold value. Haplotype analysis revealed that the G-C-T-C-C-T-A (block 6 and T-T (block 10 haplotypes of the GRIN2A gene displayed a protective effect (P = <0.001 and 0.003. These findings point to a role for GRIN2A polymorphisms in heroin addiction among the Han Chinese from Shaanxi province, and may be informative for future genetic or neurobiological studies on heroin addiction.

  6. 13C based proteinogenic amino acid (PAA and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP pathway in response to agitation and temperature related stresses

    Directory of Open Access Journals (Sweden)

    Kamalrul Azlan Azizan

    2017-07-01

    Full Text Available Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C and agitation (with and without agitation at 150 rpm. Collectively, the concentrations of proteinogenic amino acids (PAAs and free fatty acids (FAAs were compared, and Pearson correlation analysis (r was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA. Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA from pyruvate (PYR reaction in all conditions suggested the activation of pyruvate carboxylate (pycA in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall

  7. An international survey and modified Delphi process revealed editors' perceptions, training needs, and ratings of competency-related statements for the development of core competencies for scientific editors of biomedical journals.

    Science.gov (United States)

    Galipeau, James; Cobey, Kelly D; Barbour, Virginia; Baskin, Patricia; Bell-Syer, Sally; Deeks, Jonathan; Garner, Paul; Shamseer, Larissa; Sharon, Straus; Tugwell, Peter; Winker, Margaret; Moher, David

    2017-01-01

    Background: Scientific editors (i.e., those who make decisions on the content and policies of a journal) have a central role in the editorial process at biomedical journals. However, very little is known about the training needs of these editors or what competencies are required to perform effectively in this role. Methods: We conducted a survey of perceptions and training needs among scientific editors from major editorial organizations around the world, followed by a modified Delphi process in which we invited the same scientific editors to rate the importance of competency-related statements obtained from a previous scoping review. Results: A total of 148 participants completed the survey of perceptions and training needs. At least 80% of participants agreed on six of the 38 skill and expertise-related statements presented to them as being important or very important to their role as scientific editors. At least 80% agreed on three of the 38 statements as necessary skills they perceived themselves as possessing (well or very well).  The top five items on participants' list of top training needs were training in statistics, research methods, publication ethics, recruiting and dealing with peer reviewers, and indexing of journals. The three rounds of the Delphi were completed by 83, 83, and 73 participants, respectively, which ultimately produced a list of 23 "highly rated" competency-related statements and another 86 "included" items. Conclusion: Both the survey and the modified Delphi process will be critical for understanding knowledge and training gaps among scientific editors when designing curriculum around core competencies in the future.

  8. An international survey and modified Delphi process revealed editors’ perceptions, training needs, and ratings of competency-related statements for the development of core competencies for scientific editors of biomedical journals

    Science.gov (United States)

    Galipeau, James; Cobey, Kelly D.; Barbour, Virginia; Baskin, Patricia; Bell-Syer, Sally; Deeks, Jonathan; Garner, Paul; Shamseer, Larissa; Sharon, Straus; Tugwell, Peter; Winker, Margaret; Moher, David

    2017-01-01

    Background: Scientific editors (i.e., those who make decisions on the content and policies of a journal) have a central role in the editorial process at biomedical journals. However, very little is known about the training needs of these editors or what competencies are required to perform effectively in this role. Methods: We conducted a survey of perceptions and training needs among scientific editors from major editorial organizations around the world, followed by a modified Delphi process in which we invited the same scientific editors to rate the importance of competency-related statements obtained from a previous scoping review. Results: A total of 148 participants completed the survey of perceptions and training needs. At least 80% of participants agreed on six of the 38 skill and expertise-related statements presented to them as being important or very important to their role as scientific editors. At least 80% agreed on three of the 38 statements as necessary skills they perceived themselves as possessing (well or very well).  The top five items on participants’ list of top training needs were training in statistics, research methods, publication ethics, recruiting and dealing with peer reviewers, and indexing of journals. The three rounds of the Delphi were completed by 83, 83, and 73 participants, respectively, which ultimately produced a list of 23 “highly rated” competency-related statements and another 86 “included” items. Conclusion: Both the survey and the modified Delphi process will be critical for understanding knowledge and training gaps among scientific editors when designing curriculum around core competencies in the future. PMID:28979768

  9. Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Sekizuka

    Full Text Available Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898. Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1, in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32% and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%, as well as isolates of other countries (Malaysia, France, United Kingdom and United States. The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC, suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.

  10. An international survey and modified Delphi process revealed editors’ perceptions, training needs, and ratings of competency-related statements for the development of core competencies for scientific editors of biomedical journals [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    James Galipeau

    2017-09-01

    Full Text Available Background: Scientific editors (i.e., those who make decisions on the content and policies of a journal have a central role in the editorial process at biomedical journals. However, very little is known about the training needs of these editors or what competencies are required to perform effectively in this role. Methods: We conducted a survey of perceptions and training needs among scientific editors from major editorial organizations around the world, followed by a modified Delphi process in which we invited the same scientific editors to rate the importance of competency-related statements obtained from a previous scoping review. Results: A total of 148 participants completed the survey of perceptions and training needs. At least 80% of participants agreed on six of the 38 skill and expertise-related statements presented to them as being important or very important to their role as scientific editors. At least 80% agreed on three of the 38 statements as necessary skills they perceived themselves as possessing (well or very well.  The top five items on participants’ list of top training needs were training in statistics, research methods, publication ethics, recruiting and dealing with peer reviewers, and indexing of journals. The three rounds of the Delphi were completed by 83, 83, and 73 participants, respectively, which ultimately produced a list of 23 “highly rated” competency-related statements and another 86 “included” items. Conclusion: Both the survey and the modified Delphi process will be critical for understanding knowledge and training gaps among scientific editors when designing curriculum around core competencies in the future.

  11. The Differential Gene Expression Pattern of Mycobacterium tuberculosis in Response to Capreomycin and PA-824 versus First-Line TB Drugs Reveals Stress- and PE/PPE-Related Drug Targets

    Directory of Open Access Journals (Sweden)

    Li M. Fu

    2009-01-01

    Full Text Available Tuberculosis is a leading infectious disease causing millions of deaths each year. How to eradicate mycobacterial persistence has become a central research focus for developing next-generation TB drugs. Yet, the knowledge in this area is fundamentally limited and only a few drugs, notably capreomycin and PA-824, have been shown to be active against non-replicating persistent TB bacilli. In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. Our study has identified 42 genes specifically induced by capreomycin and PA-824. Many of these genes are related to stress responses. In terms of the distribution of identified genes in a specific category relative to the whole genome, only the categories of PE/PPE and conserved hypotheticals have statistical significance. Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. Further biological elucidation of their roles in mycobacterial persistence is warranted.

  12. Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

    DEFF Research Database (Denmark)

    Bergseng, Elin; Dørum, Siri; Arntzen, Magnus Ø.

    2014-01-01

    Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. The α- or β-chain sharing HLA molecules DQ2.5, DQ2.2, and DQ7.5 display different risks for the disease...... established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine...... at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease....

  13. Combined analysis of circulating β-endorphin with gene polymorphisms in OPRM1, CACNAD2 and ABCB1 reveals correlation with pain, opioid sensitivity and opioid-related side effects.

    Science.gov (United States)

    Rhodin, Annica; Grönbladh, Alfhild; Ginya, Harumi; Nilsson, Kent W; Rosenblad, Andreas; Zhou, Qin; Enlund, Mats; Hallberg, Mathias; Gordh, Torsten; Nyberg, Fred

    2013-02-12

    Opioids are associated with wide inter-individual variability in the analgesic response and a narrow therapeutic index. This may be partly explained by the presence of single nucleotide polymorphisms (SNPs) in genes encoding molecular entities involved in opioid metabolism and receptor activation. This paper describes the investigation of SNPs in three genes that have a functional impact on the opioid response: OPRM1, which codes for the μ-opioid receptor; ABCB1 for the ATP-binding cassette B1 transporter enzyme; and the calcium channel complex subunit CACNA2D2. The genotyping was combined with an analysis of plasma levels of the opioid peptide β-endorphin in 80 well-defined patients with chronic low back pain scheduled for spinal fusion surgery, and with differential sensitivity to the opioid analgesic remifentanil. This patient group was compared with 56 healthy controls. The plasma β-endorphin levels were significantly higher in controls than in pain patients.A higher incidence of opioid-related side effects and sex differences was found in patients with the minor allele of the ABCB1 gene. Further, a correlation between increased opioid sensitivity and the major CACNA2D2 allele was confirmed. A tendency of a relationship between opioid sensitivity and the minor allele of OPRM1 was also found. Although the sample cohort in this study was limited to 80 patients it appears that it was possible to observe significant correlations between polymorphism in relevant genes and various items related to pain sensitivity and opioid response. Of particular interest is the new finding of a correlation between increased opioid sensitivity and the major CACNA2D2 allele. These observations may open for improved strategies in the clinical treatment of chronic pain with opioids.

  14. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Kateryna V Zhalnina

    Full Text Available The activity of ammonia-oxidizing archaea (AOA leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

  15. Novel bacterial endosymbionts of Acanthamoeba spp. related to the Paramecium caudatum symbiont Caedibacter caryophilus.

    Science.gov (United States)

    Horn, M; Fritsche, T R; Gautom, R K; Schleifer, K H; Wagner, M

    1999-08-01

    Acanthamoebae are increasingly being recognized as hosts for obligate bacterial endosymbionts, most of which are presently uncharacterized. In this study, the phylogeny of three Gram-negative, rod-shaped endosymbionts and their Acanthamoeba host cells was analysed by the rRNA approach. Comparative analyses of 16S rDNA sequences retrieved from amoebic cell lysates revealed that the endosymbionts of Acanthamoeba polyphaga HN-3, Acanthamoeba sp. UWC9 and Acanthamoeba sp. UWE39 are related to the Paramecium caudatum endosymbionts Caedibacter caryophilus, Holospora elegans and Holospora obtusa. With overall 16S rRNA sequence similarities to their closest relative, C. caryophilus, of between 87% and 93%, these endosymbionts represent three distinct new species. In situ hybridization with fluorescently labelled endosymbiont-specific 16S rRNA-targeted probes demonstrated that the retrieved 16S rDNA sequences originated from the endosymbionts and confirmed their intracellular localization. We propose to classify provisionally the endosymbiont of Acanthamoeba polyphaga HN-3 as 'Candidatus Caedibacter acanthamoebae', the endosymbiont of Acanthamoeba sp. strain UWC9 as 'Candidatus Paracaedibacter acanthamoebae' and the endosymbiont of Acanthamoeba sp. strain UWE39 as 'Candidatus Paracaedibacter symbiosus'. The phylogeny of the Acanthamoeba host cells was analysed by comparative sequence analyses of their 18S rRNA. Although Acanthamoeba polyphaga HN-3 clearly groups together with most of the known Acanthamoeba isolates (18S rRNA sequence type 4), Acanthamoeba sp. UWC9 and UWE39 exhibit sp. UWC9 and Acanthamoeba sp. UWE39.

  16. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

    Science.gov (United States)

    Kiu, Raymond; Caim, Shabhonam; Alexander, Sarah; Pachori, Purnima; Hall, Lindsay J.

    2017-01-01

    Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen. PMID:29312194

  17. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

    Directory of Open Access Journals (Sweden)

    Raymond Kiu

    2017-12-01

    Full Text Available Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc, enterotoxin (cpe, and Perfringolysin O (pfo or pfoA, although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56 of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet and anti-defensins genes (mprF were consistently detected in silico (tet: 75%; mprF: 100%. However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  18. Whole blood transcriptional profiling reveals deregulation of oxidative and antioxidative defence genes in myelofibrosis and related neoplasms. Potential implications of downregulation of Nrf2 for genomic instability and disease progression.

    Directory of Open Access Journals (Sweden)

    Hans Carl Hasselbalch

    Full Text Available The Philadelphia-negative chronic myeloproliferative neoplasms - essential thrombocythemia (ET, polycythemia vera (PV, and myelofibrosis (MF (MPNs - have recently been shown to be associated with chronic inflammation, oxidative stress and accumulation of reactive oxygen species (ROS. Using whole blood transcriptional profiling, we report that several oxidative stress and anti-oxidative stress genes are significantly deregulated in MPNs. Among the twenty most up- and downregulated genes, ATOX1, DEFB122, GPX8, PRDX2, PRDX6, PTGS1, and SEPP1 were progressively upregulated from ET over PV to PMF, whereas AKR1B1, CYBA, SIRT2, TTN, and UCP2 were progressively downregulated in ET, PV and PMF (all FDR <0.05. The gene Nrf2, encoding the transcription factor nuclear factor erythroid 2-related factor 2 (NFE2L2 or Nrf2 was significantly downregulated in all MPNs. Nrf2 has a key role in the regulation of the oxidative stress response and modulates both migration and retention of hematopoietic stem cells (HSCs in their niche. The patogenetic importance of Nrf2 depletion in the context of expansion of the hematopoietic progenitor pool in MPNs is discussed with particular focus upon the implications of concomitant downregulation of Nrf2 and CXCR4 for stem cell mobilization.

  19. Integrity of H1 helix in prion protein revealed by molecular dynamic simulations to be especially vulnerable to changes in the relative orientation of H1 and its S1 flank.

    Science.gov (United States)

    Tseng, Chih-Yuan; Yu, Chun-Ping; Lee, H C

    2009-06-01

    In the template-assistance model, normal prion protein (PrPC), the pathogenic cause of prion diseases such as Creutzfeldt-Jakob in human, bovine spongiform encephalopathy in cow, and scrapie in sheep, converts to infectious prion (PrPSc) through an autocatalytic process triggered by a transient interaction between PrPC and PrPSc. Conventional studies suggest the S1-H1-S2 region in PrPC to be the template of S1-S2 beta-sheet in PrPSc, and the conformational conversion of PrPC into PrPSc may involve an unfolding of H1 in PrPC and its refolding into the beta-sheet in PrPSc. Here we conduct a series of simulation experiments to test the idea of transient interaction of the template-assistance model. We find that the integrity of H1 in PrPC is vulnerable to a transient interaction that alters the native dihedral angles at residue Asn(143), which connects the S1 flank to H1, but not to interactions that alter the internal structure of the S1 flank, nor to those that alter the relative orientation between H1 and the S2 flank.

  20. The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Card, G L; Peterson, N A; Smith, C A; Rupp, B; Schick, B M; Baker, E N

    2005-02-15

    Mycobacterium tuberculosis, the cause of TB, is a devastating human pathogen. The emergence of multi-drug resistance in recent years has prompted a search for new drug targets and for a better understanding of mechanisms of resistance. Here we focus on the gene product of an open reading frame from M. tuberculosis, Rv1347c, which is annotated as a putative aminoglycoside N-acetyltransferase. The Rv1347c protein does not show this activity, however, and we show from its crystal structure, coupled with functional and bioinformatic data, that its most likely role is in the biosynthesis of mycobactin, the M. tuberculosis siderophore. The crystal structure of Rv1347c was determined by MAD phasing from selenomethionine-substituted protein and refined at 2.2 {angstrom} resolution (R = 0.227, R{sub free} = 0.257). The protein is monomeric, with a fold that places it in the GCN5-related N-acetyltransferase (GNAT) family of acyltransferases. Features of the structure are an acylCoA binding site that is shared with other GNAT family members, and an adjacent hydrophobic channel leading to the surface that could accommodate long-chain acyl groups. Modeling the postulated substrate, the N{sup {var_epsilon}}-hydroxylysine side chain of mycobactin, into the acceptor substrate binding groove identifies two residues at the active site, His130 and Asp168, that have putative roles in substrate binding and catalysis.

  1. Specific-detection of clinical samples, systematic functional investigations, and transcriptome analysis reveals that splice variant MUC4/Y contributes to the malignant progression of pancreatic cancer by triggering malignancy-related positive feedback loops signaling.

    Science.gov (United States)

    Zhu, Yi; Zhang, Jing-Jing; Xie, Kun-Ling; Tang, Jie; Liang, Wen-Biao; Zhu, Rong; Zhu, Yan; Wang, Bin; Tao, Jin-Qiu; Zhi, Xiao-Fei; Li, Zheng; Gao, Wen-Tao; Jiang, Kui-Rong; Miao, Yi; Xu, Ze-Kuan

    2014-11-04

    MUC4 plays important roles in the malignant progression of human pancreatic cancer. But the huge length of MUC4 gene fragment restricts its functional and mechanism research. As one of its splice variants, MUC4/Y with coding sequence is most similar to that of the full-length MUC4 (FL-MUC4), together with alternative splicing of the MUC4 transcript has been observed in pancreatic carcinomas but not in normal pancreas. So we speculated that MUC4/Y might be involved in malignant progression similarly to FL-MUC4, and as a research model of MUC4 in pancreatic cancer. The conjecture was confirmed in the present study. MUC4/Y expression was detected by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) using gene-specific probe in the clinic samples. The effects of MUC4/Y were observed by serial in vitro and in vivo experiments based on stable over-expressed cell model. The underlying mechanisms were investigated by sequence-based transcriptome analysis and verified by qRT-PCR, Western blot and enzyme-linked immunosorbent assays. The detection of clinical samples indicates that MUC4/Y is significantly positive-correlated with tumor invasion and distant metastases. Based on stable forced-expressed pancreatic cancer PANC-1 cell model, functional studies show that MUC4/Y enhances malignant activity in vitro and in vivo, including proliferation under low-nutritional-pressure, resistance to apoptosis, motility, invasiveness, angiogenesis, and distant metastasis. Mechanism studies indicate the novel finding that MUC4/Y triggers malignancy-related positive feedback loops for concomitantly up-regulating the expression of survival factors to resist adverse microenvironment and increasing the expression of an array of cytokines and adhesion molecules to affect the tumor milieu. In light of the enormity of the potential regulatory circuitry in cancer afforded by MUC4 and/or MUC4/Y, repressing MUC4 transcription, inhibiting post

  2. Crater Lake revealed

    Science.gov (United States)

    Ramsey, David W.; Dartnell, Peter; Bacon, Charles R.; Robinson, Joel E.; Gardner, James V.

    2003-01-01

    Around 500,000 people each year visit Crater Lake National Park in the Cascade Range of southern Oregon. Volcanic peaks, evergreen forests, and Crater Lake’s incredibly blue water are the park’s main attractions. Crater Lake partially fills the caldera that formed approximately 7,700 years ago by the eruption and subsequent collapse of a 12,000-foot volcano called Mount Mazama. The caldera-forming or climactic eruption of Mount Mazama drastically changed the landscape all around the volcano and spread a blanket of volcanic ash at least as far away as southern Canada. Prior to the climactic event, Mount Mazama had a 400,000 year history of cone building activity like that of other Cascade volcanoes such as Mount Shasta. Since the climactic eruption, there have been several less violent, smaller postcaldera eruptions within the caldera itself. However, relatively little was known about the specifics of these eruptions because their products were obscured beneath Crater Lake’s surface. As the Crater Lake region is still potentially volcanically active, understanding past eruptive events is important to understanding future eruptions, which could threaten facilities and people at Crater Lake National Park and the major transportation corridor east of the Cascades. Recently, the lake bottom was mapped with a high-resolution multibeam echo sounder. The new bathymetric survey provides a 2m/pixel view of the lake floor from its deepest basins virtually to the shoreline. Using Geographic Information Systems (GIS) applications, the bathymetry data can be visualized and analyzed to shed light on the geology, geomorphology, and geologic history of Crater Lake.

  3. 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

  4. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    KAUST Repository

    Liu, Huanle

    2017-10-06

    Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world\\'s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

  5. Palaeoseismicity in relation to basin tectonics as revealed from soft ...

    Indian Academy of Sciences (India)

    Tillite of Antarctica (Krishnan 1982). The Talchir formation is overlain successively by Barakar formation, Barren Measure formation and Raniganj formation, from bottom to top. The. Talchir formation has a conformable contact with the overlying sandstones of the Barakar forma- tion which, in turn, pass conformably into the.

  6. Giraffe genome sequence reveals clues to its unique morphology and physiology

    Science.gov (United States)

    Agaba, Morris; Ishengoma, Edson; Miller, Webb C.; McGrath, Barbara C.; Hudson, Chelsea N.; Bedoya Reina, Oscar C.; Ratan, Aakrosh; Burhans, Rico; Chikhi, Rayan; Medvedev, Paul; Praul, Craig A.; Wu-Cavener, Lan; Wood, Brendan; Robertson, Heather; Penfold, Linda; Cavener, Douglas R.

    2016-01-01

    The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions. PMID:27187213

  7. Assessing the relative importance of correlates of loneliness in later life: Gaining insight using recursive partitioning

    DEFF Research Database (Denmark)

    Ejlskov, Linda; Wulff, Jesper; Bøggild, Henrik

    2017-01-01

    study the MRC National Survey of Health and Development. RESULTS: Positive mental well-being, personal mastery, identifying the spouse as the closest confidant, being extrovert and informal social contact were the most important correlates of lower loneliness levels. Participation in organised groups...... and demographic correlates were poor identifiers of loneliness. The regression tree suggested that loneliness was not raised among those with poor mental wellbeing if they identified their partner as closest confidante and had frequent social contact. CONCLUSION: Recursive partitioning can identify which...... the characteristics and assessing the relative importance of correlates of loneliness in older adults. METHOD: Using exploratory regression trees and random forests, we examined combinations and the relative importance of 42 correlates in relation to loneliness at age 68 among 2453 participants from the birth cohort...

  8. Phylogenetic analysis of three genes of Penguinpox virus corresponding to Vaccinia virus G8R (VLTF-1, A3L (P4b and H3L reveals that it is most closely related to Turkeypox virus, Ostrichpox virus and Pigeonpox virus

    Directory of Open Access Journals (Sweden)

    Williamson Anna-Lise

    2009-05-01

    Full Text Available Abstract Phylogenetic analysis of three genes of Penguinpox virus, a novel Avipoxvirus isolated from African penguins, reveals its relationship to other poxviruses. The genes corresponding to Vaccinia virus G8R (VLTF-1, A3L (P4b and H3L were sequenced and phylogenetic trees (Neighbour-Joining and UPGMA constructed from MUSCLE nucleotide and amino acid alignments of the equivalent sequences from several different poxviruses. Based on this analysis, PEPV was confirmed to belong to the genus Avipoxvirus, specifically, clade A, subclade A2 and to be most closely related to Turkeypox virus (TKPV, Ostrichpox virus (OSPVand Pigeonpox virus (PGPV.

  9. The Closest M-Dwarf Quadruple System to the Sun

    Science.gov (United States)

    2013-12-24

    calibrated using at least 10 photometric standard stars per night from Landolt (1992) and Graham (1982). All images were obtained at an airmass of...mass Online-only material: color figure 1. INTRODUCTION Although the processes involved in single star formation have a wide variety of observational and...theoretical constraints (e.g., McKee & Ostriker 2007), the complex physics involved in the formation of binary and especially multiple star systems

  10. Mexico, Our Closest Neighbor: Three Elementary Teachers' Perspectives

    Science.gov (United States)

    Field, Sherry L.; Bauml, Michelle; LeCompte, Karon; Alleman, Janet

    2009-01-01

    The authors describe how three elementary teachers working in very different parts of the United States teach about Mexico. These teachers' practices allow them to enhance the traditional social studies curriculum, help children learn about themselves and other people, and increase children's capacities for global citizenship. (Contains 1 figure.)

  11. Yarrowia divulgata f.a., sp. nov., a yeast species from animal-related and marine sources.

    Science.gov (United States)

    Nagy, Edina; Niss, Marete; Dlauchy, Dénes; Arneborg, Nils; Nielsen, Dennis Sandris; Péter, Gábor

    2013-12-01

    Five yeast strains, phenotypically indistinguishable from Yarrowia lipolytica and Yarrowia deformans, were recovered from different animal-related samples. One strain was isolated from a bacon processing plant in Denmark, two strains from chicken liver in the USA, one strain from chicken breast in Hungary and one from minced beef in Hungary. Comparisons of the sequences of their large subunit rRNA gene D1/D2 domain and the internal transcribed spacer (ITS) regions revealed that, despite their phenotypic similarity, they represent a novel yeast species of the Yarrowia clade with Y. deformans being the genotypically closest relative (LSU rRNA gene D1/D2 and ITS region similarity of 97.0 and 93.7 %, respectively). Yarrowia divulgata f.a., sp. nov. is proposed to accommodate these strains with F6-17(T) ( = CBS 11013(T) = CCUG 56725(T)) as the type strain. Some D1/D2 sequences of yeasts from marine habitats were found in the GenBank database that were identical to those of the strains of Y. divulgata f.a., sp. nov. Unfortunately, these strains were not available for our study.

  12. Mating type locus of Chinese black truffles reveals heterothallism and the presence of cryptic species within the T. indicum species complex.

    Directory of Open Access Journals (Sweden)

    Beatrice Belfiori

    Full Text Available Tuber spp. are filamentous ascomycetes which establish symbiosis with the roots of trees and shrub species. By virtue of this symbiosis they produce hypogeous ascocarps, known as truffles. Filamentous ascomycetes can reproduce by homothallism or heterothallism depending on the structure and organization of their mating type locus. The first mating type locus in a truffle species has been recently characterized in Tuber melanosporum and it has been shown that this fungus, endemic in Europe, is heterothallic. The availability of sequence information for T. melanosporum mating type genes is seminal to cloning their orthologs from other Tuber species and assessing their reproductive mode. Here we report on the organization of the mating type region in T. indicum, the black truffle species present in Asia, which is the closest relative to T. melanosporum and is characterized by an high level of morphological and genetic variability. The present study shows that T. indicum is also heterothallic. Examination of Asiatic black truffles belonging to different genetic classes, sorted according to the sequence polymorphism of the internal transcribed spacer rDNA region, has revealed sequence variations and rearrangements in both coding and non-coding regions of the mating type locus, to suggest the existence of cryptic species within the T. indicum complex. The presence of transposable elements within or linked to the mating type region suggests a role of these elements in generating the genotypic diversity present among T. indicum strains. Overall, comparative analyses of the mating type locus have thus allowed us to tackle taxonomical and phylogenetic issues within black truffles and make inferences about the evolution of T. melanosporum-T. indicum lineage. Our results are not only of fundamental but also of applied relevance as T. indicum produces edible fruit bodies that are imported also into Europe and thus may represent a biological threat for T

  13. A spectrophotometer-based diffusivity assay reveals that diffusion hindrance of small molecules in extracellular matrix gels used in 3D cultures is dominated by viscous effects.

    Science.gov (United States)

    Galgoczy, Roland; Pastor, Isabel; Colom, Adai; Giménez, Alicia; Mas, Francesc; Alcaraz, Jordi

    2014-08-01

    The design of 3D culture studies remains challenging due to the limited understanding of extracellular matrix (ECM)-dependent hindered diffusion and the lack of simple diffusivity assays. To address these limitations, we set up a cost-effective diffusivity assay based on a Transwell plate and the spectrophotometer of a Microplate Reader, which are readily accessible to cell biology groups. The spectrophotometer-based assay was used to assess the apparent diffusivity D of FITC-dextrans with molecular weight (4-70kDa) spanning the physiological range of signaling factors in a panel of acellular ECM gels including Matrigel, fibrin and type I collagen. Despite their technical differences, D data exhibited ∼15% relative difference with respect to FRAP measurements. Our results revealed that diffusion hindrance of small particles is controlled by the enhanced viscosity of the ECM gel in conformance with the Stokes-Einstein equation rather than by geometrical factors. Moreover, we provided a strong rationale that the enhanced ECM viscosity is largely contributed to by unassembled ECM macromolecules. We also reported that gels with the lowest D exhibited diffusion hindrance closest to the large physiologic hindrance of brain tissue, which has a typical pore size much smaller than ECM gels. Conversely, sparse gels (≤1mg/ml), which are extensively used in 3D cultures, failed to reproduce the hindered diffusion of tissues, thereby supporting that dense (but not sparse) ECM gels are suitable tissue surrogates in terms of macromolecular transport. Finally, the consequences of reduced diffusivity in terms of optimizing the design of 3D culture experiments were addressed in detail. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing.

    Science.gov (United States)

    Rehm, Peter; Meusemann, Karen; Borner, Janus; Misof, Bernhard; Burmester, Thorsten

    2014-08-01

    Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. [Vulvar oedema revealing systemic mastocytosis].

    Science.gov (United States)

    Deveza, E; Locatelli, F; Girardin, M; Valmary-Degano, S; Daguindau, E; Aubin, F; Humbert, P; Pelletier, F

    2015-11-01

    Systemic mastocytosis is characterised by abnormal proliferation of mast cells in various organs. We report an original case of systemic mastocytosis revealed by vulvar oedema. A 24-year-old patient was examined in the dermatology department for vulvar oedema appearing during sexual intercourse. She presented vasomotor dysfunction of the lower limbs, urticaria on the trunk on exertion, diarrhoea and bone pains. Laboratory tests showed serum tryptase of 29.7μg and plasma histamine at twice the normal value. Myelogram results showed infiltration by dysmorphic mast cells. Screening for c-kit D816V mutation was positive. Duodenal biopsies revealed mast-cell clusters with aggregation involving over 15 mast cells. CD2 staining was inconclusive and CD25 staining could not be done. Trabecular osteopenia was found, and we thus made a diagnosis of indolent systemic mastocytosis (ISM variant Ia) as per the WHO 2008 criteria. Symptomatic treatment was initiated (antiH1, H2, antileukotrienes) and clinical and laboratory follow-up was instituted. The cutaneous signs leading to diagnosis in this patient of systemic mastocytosis involving several organs were seemingly minimal signs associated with mastocyte degranulation. This is the third recorded case of mastocytosis revealed by vulvar oedema and the first case revealing systemic involvement. The two previously reported cases of vulvar oedema revealed cutaneous mastocytosis alone. Mastocytosis, whether systemic or cutaneous, must be included among the differential diagnoses considered in the presence of vulvar oedema. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  16. How gender affects patterns of social relations and their impact on health: a comparison of one or multiple sources of support from "close persons".

    Science.gov (United States)

    Fuhrer, R; Stansfeld, S A

    2002-03-01

    Numerous studies have reported gender differences in the effects of social relations on morbidity and mortality. When studying health and associated factors, one cannot ignore that sex differences exist and methods that are not "gender-fair" may lead to erroneous conclusions. This paper presents a critical analysis of the health/social relations association from a measurement perspective, including the definitions of people's networks and how they differ by gender. Findings from the Whitehall II Study of Civil Servants illustrate that women report more close persons in their primary networks, and are less likely to nominate their spouse as the closest person, but both men and women report the same proportion of women among their four closest persons. Women have a wider range of sources of emotional support. To date, most epidemiological studies have habitually analysed support provided by the closest person or confidant(e). We compared the health effects of social support when measured for the closest person only and when information from up to four close persons was incorporated into a weighted index. Information from up to four close persons offered a more accurate portrayal of support exchanged, and gender differences were attenuated, if not eliminated, when this support index was used to predict physical and psychological health.

  17. Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance

    Directory of Open Access Journals (Sweden)

    Yang Li

    2017-01-01

    Full Text Available Pseudomonas sp. QTF5 was isolated from the continuous permafrost near the bitumen layers in the Qiangtang basin of Qinghai-Tibetan Plateau in China (5,111 m above sea level. It is psychrotolerant and highly and widely tolerant to heavy metals and has the ability to metabolize benzoic acid and salicylic acid. To gain insight into the genetic basis for its adaptation, we performed whole genome sequencing and analyzed the resistant genes and metabolic pathways. Based on 120 published and annotated genomes representing 31 species in the genus Pseudomonas, in silico genomic DNA-DNA hybridization (<54% and average nucleotide identity calculation (<94% revealed that QTF5 is closest to Pseudomonas lini and should be classified into a novel species. This study provides the genetic basis to identify the genes linked to its specific mechanisms for adaptation to extreme environment and application of this microorganism in environmental conservation.

  18. [Cervicofacial cellulitis revealing cutaneous lymphomas].

    Science.gov (United States)

    Benbouzid, M A; Bencheikh, R; Benhammou, A; El Edghiri, H; Boulaich, M; Essakali, L; Kzadri, M

    2007-06-01

    The cervicofacial localization of cutaneous lymphomas is rare. These lymphomas usually present as a long-lasting and treatment-refractory papule or nodule. Lymphomas can also be revealed by cervicofacial cellulitis. We report 2 cases of cervicofacial cellulitis revealing a cutaneous lymphoma. The diagnosis was proved by multiple biopsies, performed because there was no clinical improvement in spite of an aggressive and adequate antibiotherapy. Our 2 patients were treated by radio and chemotherapy. Cutaneous lymphomas are lymphocytic proliferations stemming from cutaneous lymphoid tissue, without nodal, medullary, or visceral localization. Their clinical presentation is quite polymorphic, and cellulitis is one of the modes of revelation, especially forehead and neck localization. They have no portal of entry and are resistant to treatment. The diagnosis relies on histology, and biopsies must be performed if there is a suspicion of lymphoma. The treatment is radio and chemotherapy, and the evolution depends on the tumoral stage.

  19. Decision Making and Revealed Preference

    DEFF Research Database (Denmark)

    de la Rosa, Leonidas Enrique

    If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis. ....... Given advances in evolutionary psychology and neuroscience, I propose one way to model those evolutionary pressures that will hopefully prove useful in expanding normative economics.......If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis...

  20. Urticarial vasculitis reveals unsuspected thyroiditis.

    Science.gov (United States)

    Ferreira, Olga; Mota, Alberto; Baudrier, Teresa; Azevedo, Filomena

    2012-01-01

    A 38-year-old woman presented with erythematous, violaceous plaques with a serpiginous and unusual appearance located on the left shoulder, left thigh, and right buttock, evolving for 5 days, which eventually became generalized. A skin biopsy revealed leukocytoclastic vasculitis and a diagnosis of urticarial vasculitis was made. The complete blood count, biochemistry, complement levels, and other immunological test results were unremarkable. However, antithyroid antibody titers were increased. Despite having normal thyroid function tests and an absence of specific symptoms, the patient underwent a thyroid ultrasound, which revealed features of thyroiditis, and was subsequently referred to an endocrinologist. Several diseases can be associated with urticarial vasculitis, namely infections and autoimmune connective-tissue disorders such as systemic lupus erythematosus and Sjögren syndrome. Thyroiditis is an uncommon association.

  1. Gene genealogies, cryptic species, and molecular evolution in the human pathogen Coccidioides immitis and relatives (Ascomycota, Onygenales).

    Science.gov (United States)

    Koufopanou, V; Burt, A; Szaro, T; Taylor, J W

    2001-07-01

    Previous genealogical analyses of population structure in Coccidioides immitis revealed the presence of two cryptic and sexual species in this pathogenic fungus but did not clarify their origin and relationships with respect to other taxa. By combining the C. immitis data with those of two of its closest relatives, the free-living saprophytes Auxarthron zuffianum and Uncinocarpus reesii, we show that the C. immitis species complex is monophyletic, indicating a single origin of pathogenicity. Cryptic species also were found in both A. zuffianum and U. reesii, indicating that they can be found in both pathogenic and free-living fungi. Our study, together with a few others, indicates that the current list of known fungal species might be augmented by a factor of at least two. However, at least in the C. immitis, A. zuffianum, and U. reesii complexes, cryptic species represent subdivisions at the tips of deep monophyletic clades and thus well within the existing framework of generic classification. An analysis of silent and expressed divergence and polymorphism values between and within the taxa identified by genealogical concordance did not reveal faster evolution in C. immitis as a consequence of adaptation to the pathogenic habit, nor did it show positive Darwinian evolution in a region of a dioxygenase gene (tcrP gene coding for 4-HPPD) known to cause antigenic responses in humans. Instead, the data suggested relative stasis, indicative of purifying selection against mostly deleterious mutations. Two introns in the same gene fragment were considerably more divergent than exons and were unalignable between species complexes but had very low polymorphism within taxa.

  2. Strategy for Identification of Bacillus cereus and Bacillus thuringiensis Strains Closely Related to Bacillus anthracis†

    Science.gov (United States)

    Daffonchio, Daniele; Raddadi, Noura; Merabishvili, Maya; Cherif, Ameur; Carmagnola, Lorenzo; Brusetti, Lorenzo; Rizzi, Aurora; Chanishvili, Nina; Visca, Paolo; Sharp, Richard; Borin, Sara

    2006-01-01

    Bacillus cereus strains that are genetically closely related to B. anthracis can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these “near neighbors” are of great interest for the study of B. anthracis virulence mechanisms, as well as to prevent the use of such strains for B. anthracis-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of B. anthracis based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of B. anthracis. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of B. anthracis was screened in 126 B. cereus group strains of different origin. Two B. cereus strains and one B. thuringiensis strain showed RSI-PCR profiles identical to that of B. anthracis. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to B. anthracis. The strict relationship with B. anthracis was confirmed by multilocus sequence typing (MLST) of four other independent loci: cerA, plcR, AC-390, and SG-749. The relationship to B. anthracis of the three strains described by MLST was comparable and even higher to that of four B. cereus strains associated with periodontitis in humans and previously reported as the closest known strains to B. anthracis. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to B. anthracis. PMID:16461679

  3. Hyposplenism revealed by Plasmodium malariae infection.

    Science.gov (United States)

    Hommel, Benjamin; Galloula, Alexandre; Simon, Anne; Buffet, Pierre

    2013-08-02

    Hyposplenism, due to splenectomy, inherited red blood cell disorders or acquired conditions such as celiac disease, has an important impact on the severity of malaria, especially in non-immune patients. Conversely, that malaria may reveal functional hyposplenism has not been described previously. A 31-year old gardener was diagnosed with an uncomplicated attack of Plasmodium malariae 11 years after leaving the endemic area. In addition to trophozoites and schizonts, thick and thin smears also showed Howell-Jolly bodies, pointing to functional hyposplenism. This was later confirmed by the presence of a calcified spleen in the context of S/β + sickle-cell syndrome in a patient previously unaware of this condition. Malaria may reveal hyposplenism. Although Howell-Jolly bodies are morphologically similar to nuclei of young Plasmodium trophozoite, distinction on smears is based on the absence of cytoplasm and irregular size of Howell-Jolly bodies. In the patient reported here, hyposplenism was revealed by the occurrence of P. malariae infection relatively late in life. Timely diagnosis of hyposplenism resulted in the implementation of appropriate measures to prevent overwhelming infection with capsulated bacteria. This observation highlights the importance of diagnosing hyposplenism in patients with malaria despite the morphological similarities between ring nuclei and Howell-Jolly bodies on thick smears.

  4. Transparency masters for mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1980-01-01

    Transparency Masters for Mathematics Revealed focuses on master diagrams that can be used for transparencies for an overhead projector or duplicator masters for worksheets. The book offers information on a compilation of master diagrams prepared by John R. Stafford, Jr., audiovisual supervisor at the University of Missouri at Kansas City. Some of the transparencies are designed to be shown horizontally. The initial three masters are number lines and grids that can be used in a mathematics course, while the others are adaptations of text figures which are slightly altered in some instances. The

  5. Relativity made relatively easy

    CERN Document Server

    Steane, Andrew M

    2012-01-01

    Relativity Made Relatively Easy presents an extensive study of Special Relativity and a gentle (but exact) introduction to General Relativity for undergraduate students of physics. Assuming almost no prior knowledge, it allows the student to handle all the Relativity needed for a university course, with explanations as simple, thorough, and engaging as possible.The aim is to make manageable what would otherwise be regarded as hard; to make derivations as simple as possible and physical ideas as transparent as possible. Lorentz invariants and four-vectors are introduced early on, but tensor not

  6. Communication Games Reveal Preparation Contextuality

    Science.gov (United States)

    Hameedi, Alley; Tavakoli, Armin; Marques, Breno; Bourennane, Mohamed

    2017-12-01

    A communication game consists of distributed parties attempting to jointly complete a task with restricted communication. Such games are useful tools for studying limitations of physical theories. A theory exhibits preparation contextuality whenever its predictions cannot be explained by a preparation noncontextual model. Here, we show that communication games performed in operational theories reveal the preparation contextuality of that theory. For statistics obtained in a particular family of communication games, we show a direct correspondence with correlations in spacelike separated events obeying the no-signaling principle. Using this, we prove that all mixed quantum states of any finite dimension are preparation contextual. We report on an experimental realization of a communication game involving three-level quantum systems from which we observe a strong violation of the constraints of preparation noncontextuality.

  7. Plan competitions reveal entrepreneurial talent

    Energy Technology Data Exchange (ETDEWEB)

    Madison, Alison L.

    2011-05-15

    Monthly economic diversity column for Tri-City Herald business section. Excerpt below: There’s something to be said for gaining valuable real-world experience in a structured, nurturing environment. Take for instance learning to scuba dive in the comfort of my resort pool rather than immediately hanging out with sharks while I figure out little things like oxygen tanks and avoiding underwater panic attacks. Likewise, graduate students are getting some excellent, supportive real-world training through university business plan competitions. These competitions are places where smart minds, new technologies, months of preparation and coaching, and some healthy pre-presentation jitters collide to reveal not only solid new business ideas, but also some promising entrepreneurial talent. In fact, professionals from around our region descend upon college campuses every spring to judge these events, which help to bridge the gap between academics and the real technology and business-driven economy.

  8. Revealing Non-Covalent Interactions

    Science.gov (United States)

    Johnson, Erin R.; Keinan, Shahar; Mori-Sánchez, Paula; Contreras-García, Julia; Cohen, Aron J.; Yang, Weitao

    2010-01-01

    Molecular structure does not easily identify the intricate non-covalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. Our approach reveals underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of non-bonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands. PMID:20394428

  9. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    Science.gov (United States)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS. PMID:25560234

  10. SCHEMA Designed Variants of Human Arginase I & II Reveal Sequence Elements Important to Stability and Catalysis

    Science.gov (United States)

    Romero, Philip A.; Stone, Everett; Lamb, Candice; Chantranupong, Lynne; Krause, Andreas; Miklos, Alex; Hughes, Randall A.; Fechtel, Blake; Ellington, Andrew D.; Arnold, Frances H.; Georgiou, George

    2012-01-01

    Arginases catalyze the divalent cation-dependent hydrolysis of L-arginine to urea and L-ornithine. There is significant interest in using arginase as a therapeutic anti-neogenic agent against L-arginine auxotrophic tumors and in enzyme replacement therapy for treating hyperargininemia. Both therapeutic applications require enzymes with sufficient stability under physiological conditions. To explore sequence elements that contribute to arginase stability we used SCHEMA-guided recombination to design a library of chimeric enzymes composed of sequence fragments from the two human isozymes Arginase I and II. We then developed a novel active learning algorithm that selects sequences from this library that are both highly informative and functional. Using high-throughput gene synthesis and our two-step active learning algorithm, we were able to rapidly create a small but highly informative set of seven enzymatically active chimeras that had an average variant distance of 40 mutations from the closest parent arginase. Within this set of sequences, linear regression was used to identify the sequence elements that contribute to the long-term stability of human arginase under physiological conditions. This approach revealed a striking correlation between the isoelectric point and the long-term stability of the enzyme to deactivation under physiological conditions. PMID:22737599

  11. Hubble Images Reveal Jupiter's Auroras

    Science.gov (United States)

    1996-01-01

    These images, taken by the Hubble Space Telescope, reveal changes in Jupiter's auroral emissions and how small auroral spots just outside the emission rings are linked to the planet's volcanic moon, Io. The images represent the most sensitive and sharply-detailed views ever taken of Jovian auroras.The top panel pinpoints the effects of emissions from Io, which is about the size of Earth's moon. The black-and-white image on the left, taken in visible light, shows how Io and Jupiter are linked by an invisible electrical current of charged particles called a 'flux tube.' The particles - ejected from Io (the bright spot on Jupiter's right) by volcanic eruptions - flow along Jupiter's magnetic field lines, which thread through Io, to the planet's north and south magnetic poles. This image also shows the belts of clouds surrounding Jupiter as well as the Great Red Spot.The black-and-white image on the right, taken in ultraviolet light about 15 minutes later, shows Jupiter's auroral emissions at the north and south poles. Just outside these emissions are the auroral spots. Called 'footprints,' the spots are created when the particles in Io's 'flux tube' reach Jupiter's upper atmosphere and interact with hydrogen gas, making it fluoresce. In this image, Io is not observable because it is faint in the ultraviolet.The two ultraviolet images at the bottom of the picture show how the auroral emissions change in brightness and structure as Jupiter rotates. These false-color images also reveal how the magnetic field is offset from Jupiter's spin axis by 10 to 15 degrees. In the right image, the north auroral emission is rising over the left limb; the south auroral oval is beginning to set. The image on the left, obtained on a different date, shows a full view of the north aurora, with a strong emission inside the main auroral oval.The images were taken by the telescope's Wide Field and Planetary Camera 2 between May 1994 and September 1995.This image and other images and data

  12. Closely related intertidal and deep-sea Halomonhystera species have distinct fatty acid compositions

    Science.gov (United States)

    Van Campenhout, Jelle; Vanreusel, Ann

    2017-01-01

    The deep-sea free-living nematode Halomonhystera hermesi, dominant in the sulphidic sediments of the Håkon Mosby mud volcano (1280 m, Barent sea slope), is part of the mainly estuarine Halomonhystera disjuncta species complex consisting of five cryptic species (GD1-GD5). Cryptic species have a very similar morphology raising questions on their specific environmental differences. This study analyzed total fatty acid (FA) compositions of H. hermesi and GD1, one of H. hermesi's closest relatives. Additionally, we experimentally investigated the effect of a temperature reduction, salinity increase and sulphide concentrations on GD1's FA composition. Because nematodes are expected to have low amounts of storage FA, total FA compositions most likely reflect FA contents of cellular membranes. The deep-sea nematode H. hermesi had significantly lower saturation levels and increased highly unsaturated fatty acid (HUFAs) proportions due to the presence of docosahexanoic acid (DHA—22:6ω3) and higher eicosapentaenoic acid (EPA—20:5ω3) proportions. HUFAs were absent in H. hermesi's food source indicating the ability and need for this nematode to synthesize HUFAs in a deep-sea environment. Our experimental data revealed that only a decrease in temperature resulted in lower saturated fatty acids proportions, indicating that the FA content of H. hermesi is most likely a response to temperature but not to sulphide concentrations or salinity differences. In experimental nematodes, EPA proportions were low and DHA was absent indicating that other factors than temperature, salinity and sulphides mediate the presence of these HUFAs in H. hermesi.

  13. Tadpole begging reveals high quality.

    Science.gov (United States)

    Dugas, M B; Strickler, S A; Stynoski, J L

    2017-05-01

    Parents can benefit from allocating limited resources nonrandomly among offspring, and offspring solicitation (i.e. begging) is often hypothesized to evolve because it contains information valuable to choosy parents. We tested the predictions of three 'honest begging' hypotheses - Signal of Need, Signal of Quality and Signal of Hunger - in the tadpoles of a terrestrial frog (Oophaga pumilio). In this frog, mothers provision tadpoles with trophic eggs, and when mothers visit, tadpoles perform a putative begging signal by stiffening their bodies and vibrating rapidly. We assessed the information content of intense tadpole begging with an experimental manipulation of tadpole condition (need/quality) and food deprivation (hunger). This experiment revealed patterns consistent with the Signal of Quality hypothesis and directly counter to predictions of Signal of Need and Signal of Hunger. Begging effort and performance were higher in more developed and higher condition tadpoles and declined with food deprivation. Free-living mothers were unlikely to feed tadpoles of a nonbegging species experimentally cross-fostered with their own, and allocated larger meals to more developed tadpoles and those that vibrated at higher speed. Mother O. pumilio favour their high-quality young, and because their concurrent offspring are reared in separate nurseries, must do so by making active allocation decisions. Our results suggest that these maternal choices are based at least in part on offspring signals, indicating that offspring solicitation can evolve to signal high quality. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  14. Near earth propagation: physics revealed

    Science.gov (United States)

    Wert, R.; Goroch, A.; Worthington, E.; Wong, V.

    2007-04-01

    Both the military and consumer sectors are pursuing distributed networked systems and sensors. A major stumbling block to deployment of these sensors will be the radio frequency (RF) propagation environment within a few wavelengths of the earth. Increasing transmit power (battery consumption) is not a practical solution to the problem. This paper will discuss some of the physical phenomena related to the near earth propagation (NEP) problem. When radiating near the earth the communications link is subjected to a list of physical impairments. On the list are the expected Fresnel region encroachment and multipath reflections. Additionally, radiation pattern changes and near earth boundary layer perturbations exist. A significant amount of data has been collected on NEP. Disturbances in the NEP atmosphere can have a time varying attenuation related to the time of day and these discoveries will be discussed. Solutions, or workarounds, to the near earth propagation problem hinge on dynamic adaptive RF elements. Adaptive RF elements will allow the distributed sensor to direct energy, beam form, impedance correct, increase communication efficiency, and decrease battery consumption. Small electrically controllable elements are under development to enable antenna impedance matching in a dynamic environment. Additionally, small dynamic beam forming arrays are under development to focus RF energy in the direction of need. With an increased understanding of the near earth propagation problem, distributed autonomous networked sensors can become a reality within a few centimeters of the earth.

  15. Geotrichum silvicola sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces.

    Science.gov (United States)

    Pimenta, Raphael S; Alves, Priscila D D; Corrêa, Ary; Lachance, Marc-André; Prasad, G S; Rajaram; Sinha, B R R P; Rosa, Carlos A

    2005-01-01

    Four strains of an asexual arthroconidial yeast species were isolated from Drosophila flies in two Atlantic rain forest sites in Brazil and two strains from oak tasar silkworm larvae (Antheraea proylei) in India. Analysis of the sequences of the D1/D2 large subunit rRNA gene showed that this yeast represented a novel species of the genus Geotrichum, described as Geotrichum silvicola sp. nov. The novel species was related to the ascogenous genus Galactomyces. The closest relatives of Geotrichum silvicola were Galactomyces sp. strain NRRL Y-6418 and Galactomyces geotrichum. The type culture of Geotrichum silvicola is UFMG-354-2T (=CBS 9194T=NRRL Y-27641T).

  16. Focus groups reveal consumer ambivalence.

    Science.gov (United States)

    1983-01-01

    According to qualitative research, Salvadoreans are ambivalent about the use of contraceptives. Since complete responsibility for management of the CSM project was accepted by the Association Demografica Salvadorena (ADS), the agency which operates the contraceptive social marketing project in El Salvador, in November 1980, the need for decisions in such areas as product price increases, introduction of new condom brands, promotion of the vaginal foaming tablet, and assessment of product sales performance had arisen. The ICSMP funded market research, completed during 1983, was intended to provide the data on which such decisions by ADS could be based. The qualitative research involved 8 focus groups, comprised of men and women, aged 18-45, contraceptive users and nonusers, from the middle and lower socioeconomic strata of the city of San Salvador and other suburban areas. In each group a moderator led discussion of family planning and probed respondents for specific attitudes, knowledge, and behavior regarding the use of contraceptives. To assess attitudes at a more emotional level, moderators asked respondents to "draw" their ideas on certain issues. A marked discrepancy was revealed between respondents' intellectual responses to the issues raised in group discussion, as opposed to their feelings expressed in the drawings. Intellectually, participants responded very positively to family planning practice, but when they were asked to draw their perceptions, ambivalent feelings emerged. Drawings of both the user and the nonuser convey primarily negative aspects for either choice. The user is tense and moody toward her children; the nonuser loses her attractiveness and "dies." Figures also show drawings of some of the attitudes of single and married male participants. 1 drawing shows an incomplete and a complete circle, symbolizing a sterilized man (incomplete) and a nonsterilized man (complete). Another picture depicts a chained man who has lost his freedom

  17. What Facial Appearance Reveals Over Time: When Perceived Expressions in Neutral Faces Reveal Stable Emotion Dispositions.

    Science.gov (United States)

    Adams, Reginald B; Garrido, Carlos O; Albohn, Daniel N; Hess, Ursula; Kleck, Robert E

    2016-01-01

    It might seem a reasonable assumption that when we are not actively using our faces to express ourselves (i.e., when we display nonexpressive, or neutral faces), those around us will not be able to read our emotions. Herein, using a variety of expression-related ratings, we examined whether age-related changes in the face can accurately reveal one's innermost affective dispositions. In each study, we found that expressive ratings of neutral facial displays predicted self-reported positive/negative dispositional affect, but only for elderly women, and only for positive affect. These findings meaningfully replicate and extend earlier work examining age-related emotion cues in the face of elderly women (Malatesta et al., 1987a). We discuss these findings in light of evidence that women are expected to, and do, smile more than men, and that the quality of their smiles predicts their life satisfaction. Although ratings of old male faces did not significantly predict self-reported affective dispositions, the trend was similar to that found for old female faces. A plausible explanation for this gender difference is that in the process of attenuating emotional expressions over their lifetimes, old men reveal less evidence of their total emotional experiences in their faces than do old women.

  18. Revealing Nanostructures through Plasmon Polarimetry.

    Science.gov (United States)

    Kleemann, Marie-Elena; Mertens, Jan; Zheng, Xuezhi; Cormier, Sean; Turek, Vladimir; Benz, Felix; Chikkaraddy, Rohit; Deacon, William; Lombardi, Anna; Moshchalkov, Victor V; Vandenbosch, Guy A E; Baumberg, Jeremy J

    2017-01-24

    Polarized optical dark-field spectroscopy is shown to be a versatile noninvasive probe of plasmonic structures that trap light to the nanoscale. Clear spectral polarization splittings are found to be directly related to the asymmetric morphology of nanocavities formed between faceted gold nanoparticles and an underlying gold substrate. Both experiment and simulation show the influence of geometry on the coupled system, with spectral shifts Δλ = 3 nm from single atoms. Analytical models allow us to identify the split resonances as transverse cavity modes, tightly confined to the nanogap. The direct correlation of resonance splitting with atomistic morphology allows mapping of subnanometre structures, which is crucial for progress in extreme nano-optics involving chemistry, nanophotonics, and quantum devices.

  19. Age-related effects in the neocortical organization of chimpanzees

    DEFF Research Database (Denmark)

    Autrey, Michelle M; Reamer, Lisa A; Mareno, Mary Catherine

    2014-01-01

    Among primates, humans exhibit the most profound degree of age-related brain volumetric decline in particular regions, such as the hippocampus and the frontal lobe. Recent studies have shown that our closest living relatives, the chimpanzees, experience little to no volumetric decline in gray...... and white matter over the adult lifespan. However, these previous studies were limited with a small sample of chimpanzees of the most advanced ages. In the present study, we sought to further test for potential age-related decline in cortical organization in chimpanzees by expanding the sample size of aged...... chimpanzees. We used the BrainVisa software to measure total brain volume, gray and white matter volumes, gray matter thickness, and gyrification index in a cross-sectional sample of 219 captive chimpanzees (8-53 years old), with 38 subjects being 40 or more years of age. Mean depth and cortical fold opening...

  20. Revealing conceptual understanding of international business

    NARCIS (Netherlands)

    Ashley, S.; Schaap, H.; Bruijn, E. de

    2017-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students’ conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual

  1. Revealing conceptual understanding of international business

    NARCIS (Netherlands)

    Ashley, S.M.; Schaap, H.; de Bruijn, E.

    2016-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students’ conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual

  2. Puerto Rico Revealed Preference Survey Data 2004

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Revealed preference models provide insights into recreational angler behavior and the economic value of recreational fishing trips. Revealed preference data is...

  3. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.

    Science.gov (United States)

    Almeida, Pedro; Barbosa, Raquel; Bensasson, Douda; Gonçalves, Paula; Sampaio, José Paulo

    2017-04-01

    In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives. © 2017 John Wiley & Sons Ltd.

  4. Organization of the sleep-related neural systems in the brain of the river hippopotamus (Hippopotamus amphibius): A most unusual cetartiodactyl species.

    Science.gov (United States)

    Dell, Leigh-Anne; Patzke, Nina; Spocter, Muhammad A; Bertelsen, Mads F; Siegel, Jerome M; Manger, Paul R

    2016-07-01

    This study provides the first systematic analysis of the nuclear organization of the neural systems related to sleep and wake in the basal forebrain, diencephalon, midbrain, and pons of the river hippopotamus, one of the closest extant terrestrial relatives of the cetaceans. All nuclei involved in sleep regulation and control found in other mammals, including cetaceans, were present in the river hippopotamus, with no specific nuclei being absent, but novel features of the cholinergic system, including novel nuclei, were present. This qualitative similarity relates to the cholinergic, noradrenergic, serotonergic, and orexinergic systems and is extended to the γ-aminobutyric acid (GABA)ergic elements of these nuclei. Quantitative analysis reveals that the numbers of pontine cholinergic (259,578) and noradrenergic (127,752) neurons, and hypothalamic orexinergic neurons (68,398) are markedly higher than in other large-brained mammals. These features, along with novel cholinergic nuclei in the intralaminar nuclei of the dorsal thalamus and the ventral tegmental area of the midbrain, as well as a major expansion of the hypothalamic cholinergic nuclei and a large laterodorsal tegmental nucleus of the pons that has both parvocellular and magnocellular cholinergic neurons, indicates an unusual sleep phenomenology for the hippopotamus. Our observations indicate that the hippopotamus is likely to be a bihemispheric sleeper that expresses REM sleep. The novel features of the cholinergic system suggest the presence of an undescribed sleep state in the hippopotamus, as well as the possibility that this animal could, more rapidly than other mammals, switch cortical electroencephalographic activity from one state to another. J. Comp. Neurol. 524:2036-2058, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  5. Genetic diversity of taraxacum germplasm revealed by sequence ...

    African Journals Online (AJOL)

    Genetic diversity of taraxacum germplasm revealed by sequence-related amplified polymorphism (SRAP) analysis. ... African Journal of Biotechnology ... The genetic relationships analyzed with un-weighed pairgroup method with arithmetic mean (UPMGA) showed that 11 population of taraxacum were grouped into three ...

  6. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

    KAUST Repository

    Tian, Renmao

    2014-08-29

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge.

    Science.gov (United States)

    Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Bajic, Vladimir; Qian, Pei-Yuan

    2014-11-01

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. The great divides: Ardipithecus ramidus reveals the postcrania of our last common ancestors with African apes.

    Science.gov (United States)

    Lovejoy, C Owen; Suwa, Gen; Simpson, Scott W; Matternes, Jay H; White, Tim D

    2009-10-02

    Genomic comparisons have established the chimpanzee and bonobo as our closest living relatives. However, the intricacies of gene regulation and expression caution against the use of these extant apes in deducing the anatomical structure of the last common ancestor that we shared with them. Evidence for this structure must therefore be sought from the fossil record. Until now, that record has provided few relevant data because available fossils were too recent or too incomplete. Evidence from Ardipithecus ramidus now suggests that the last common ancestor lacked the hand, foot, pelvic, vertebral, and limb structures and proportions specialized for suspension, vertical climbing, and knuckle-walking among extant African apes. If this hypothesis is correct, each extant African ape genus must have independently acquired these specializations from more generalized ancestors who still practiced careful arboreal climbing and bridging. African apes and hominids acquired advanced orthogrady in parallel. Hominoid spinal invagination is an embryogenetic mechanism that reoriented the shoulder girdle more laterally. It was unaccompanied by substantial lumbar spine abbreviation, an adaptation restricted to vertical climbing and/or suspension. The specialized locomotor anatomies and behaviors of chimpanzees and gorillas therefore constitute poor models for the origin and evolution of human bipedality.

  9. Bone growth marks reveal protracted growth in New Zealand kiwi (Aves, Apterygidae)

    Science.gov (United States)

    Bourdon, Estelle; Castanet, Jacques; de Ricqlès, Armand; Scofield, Paul; Tennyson, Alan; Lamrous, Hayat; Cubo, Jorge

    2009-01-01

    The presence of bone growth marks reflecting annual rhythms in the cortical bone of non-avian tetrapods is now established as a general phenomenon. In contrast, ornithurines (the theropod group including modern birds and their closest relatives) usually grow rapidly in less than a year, such that no annual rhythms are expressed in bone cortices, except scarce growth marks restricted to the outer cortical layer. So far, cyclical growth in modern birds has been restricted to the Eocene Diatryma, the extant parrot Amazona amazonica and the extinct New Zealand (NZ) moa (Dinornithidae). Here we show the presence of lines of arrested growth in the long bones of the living NZ kiwi (Apteryx spp., Apterygidae). Kiwis take 5–6 years to reach full adult body size, which indicates a delayed maturity and a slow reproductive cycle. Protracted growth probably evolved convergently in moa and kiwi sometime since the Middle Miocene, owing to the severe climatic cooling in the southwest Pacific and the absence of mammalian predators. PMID:19515655

  10. Revealing Conceptual Understanding of International Business

    Science.gov (United States)

    Ashley, Sue; Schaap, Harmen; de Bruijn, Elly

    2017-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students' conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual understanding in higher education. Essays and concept…

  11. [Cholangitis revealing an intrahepatic Osler's disease].

    Science.gov (United States)

    Asma, Kochlef; Dalila, Gargouri; Olfa, Bousnina; Malika, Romani; Afef, Kilani; Najet, BelHadg; Jamel, Kharrat; Abdeljabbar, Gorbel; Sarra, Shili; Chiraz, Jemli; Mohamed, Habib Daghfous; Slim, Khlifi; Anis, Ben Maamer; Abdelmajid, Letaïef

    2005-08-01

    Osler Weber Rendu Disease is an hereditary haemorrhagic télangectasia habitually revealed by reccurent bleeding (epistaxis). Hepatic involvement in Osler disease is found in 8 to 31%, manifested by cholestasis. We report an original observation of a cholangitis revealing Osler disease.

  12. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.

    Science.gov (United States)

    Wattam, Alice R; Williams, Kelly P; Snyder, Eric E; Almeida, Nalvo F; Shukla, Maulik; Dickerman, A W; Crasta, O R; Kenyon, R; Lu, J; Shallom, J M; Yoo, H; Ficht, T A; Tsolis, R M; Munk, C; Tapia, R; Han, C S; Detter, J C; Bruce, D; Brettin, T S; Sobral, Bruno W; Boyle, Stephen M; Setubal, João C

    2009-06-01

    The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact beta-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the "domino theory" of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.

  13. VISTA Reveals the Secret of the Unicorn

    Science.gov (United States)

    2010-10-01

    . The width of VISTA's field of view is equivalent to about 80 light-years at this distance. Since the dust is largely transparent at infrared wavelengths, many young stars that cannot be seen in visible-light images become apparent. The most massive of these stars are less than ten million years old. The new image was created from exposures taken in three different parts of the near-infrared spectrum. In molecular clouds like Monoceros R2, the low temperatures and relatively high densities allow molecules to form, such as hydrogen, which under certain conditions emit strongly in the near infrared. Many of the pink and red structures that appear in the VISTA image are probably the glows from molecular hydrogen in outflows from young stars. Monoceros R2 has a dense core, no more than two light-years in extent, which is packed with very massive young stars, as well as a cluster of bright infrared sources, which are typically new-born massive stars still surrounded by dusty discs. This region lies at the centre of the image, where a much higher concentration of stars is visible on close inspection and where the prominent reddish features probably indicate emission from molecular hydrogen. The rightmost of the bright clouds in the centre of the picture is NGC 2170, the brightest reflection nebula in this region. In visible light, the nebulae appear as bright, light blue islands in a dark ocean, while in the infrared frenetic factories are revealed in their interiors where hundreds of massive stars are coming into existence. NGC 2170 is faintly visible through a small telescope and was discovered by William Herschel from England in 1784. Stars form in a process that typically lasts few million years and which takes place inside large clouds of interstellar gas and dust, hundreds of light-years across. Because the interstellar dust is opaque to visible light, infrared and radio observations are crucial in the understanding of the earliest stages of the stellar evolution. By

  14. Genetic characterization of the unique short segment of phocid herpesvirus type 1 reveals close relationships among alphaherpesviruses of hosts of the order Carnivora.

    Science.gov (United States)

    Martina, B E E; Harder, T C; Osterhaus, A D M E

    2003-06-01

    To further characterize phocid herpesvirus type 1 (PhHV-1) at the molecular level, a cluster of genes comprising the complete unique short (Us) region of PhHV-1 has been cloned and sequenced. Within this region, ORFs were detected that code for the equivalent of the Us 2- protein of herpes simplex virus (HSV), a putative protein kinase, and for the glycoprotein equivalents gG, gD, gI and gE. In addition, two small ORFs downstream of gE, homologous to the Us 8.5 and Us 9 proteins of HSV were identified. Comparative analysis of the ORF encoding the gD equivalent of PhHV-1 identified the corresponding proteins of the alphaherpesviruses canine herpesvirus and, to lesser degree, feline herpesvirus as the closest relatives.

  15. Spectrum of MHC Class II Variability in Darwin’s Finches and Their Close Relatives

    Science.gov (United States)

    Sato, Akie; Tichy, Herbert; Grant, Peter R.; Grant, B. Rosemary; Sato, Tetsuji; O’hUigin, Colm

    2011-01-01

    The study describes >400 major histocompatibility complex (MHC) class II B exon 2 and 114 intron 2 sequences of 36 passerine bird species, 13 of which belong to the group of Darwin’s finches (DFs) and the remaining 23 to close or more distant relatives of DFs in Central and South America. The data set is analyzed by a combination of judiciously selected statistical methods. The analysis reveals that reliable information concerning MHC organization, including the assignment of sequences to loci, and evolution, as well as the process of species divergence, can be obtained in the absence of genomic sequence data, if the analysis is taken several steps beyond the standard phylogenetic tree construction approach. The main findings of the present study are these: The MHC class II B region of the passerine birds is as elaborate in its organization, divergence, and genetic diversity as the MHC of the eutherian mammals, specifically the primates. Hence, the reported simplicity of the fowl MHC is an oddity. With the help of appropriate markers, the divergence of the MHC genes can be traced deep in the phylogeny of the bird taxa. Transspecies polymorphism is rampant at many of the bird MHC loci. In this respect, the DFs behave as if they were a single, genetically undifferentiated population. There is thus far no indication of alleles that could be considered species, genus, or even DF group specific. The implication of these findings is that DFs are in the midst of adaptive radiations, in which morphological differentiation into species is running ahead of genetic differentiation in genetic systems such as the MHC or the mitochondrial DNA. The radiations are so young that there has not been enough time to sort out polymorphisms at most of the loci among the morphologically differentiating species. These findings parallel those on Lake Victoria haplochromine fishes. Several of the DF MHC allelic lineages can be traced back to the MHC genes of the species Tiaris obscura

  16. Reconstructing relational information.

    Science.gov (United States)

    Horecka, Kevin M; Dulas, Michael R; Schwarb, Hillary; Lucas, Heather D; Duff, Melissa; Cohen, Neal J

    2018-02-01

    Hippocampal involvement in learning and remembering relational information has an extensive history, often focusing specifically on spatial information. In humans, spatial reconstruction (SR) paradigms are a powerful tool for evaluating an individuals' spatial-relational memory. In SR tasks, participants study locations of items in space and subsequently reconstruct the studied display after a short delay. Previous work has revealed that patients with hippocampal damage are impaired both in overall placement accuracy as well as on a specific measure of relational memory efficacy, "swaps" (i.e., when the relative location of two items is reversed). However, the necessity of the hippocampus for other types of spatial-relational information involved in reconstruction behaviors (e.g., where in the environment and relative to which other items an item was located) have not yet been investigated systematically. In this work, three patients with hippocampal damage and nine healthy matched comparison participants performed an SR task. An analysis framework was developed to independently assess three first-order types of relations: (1) memory for the binding of specific item identities to locations, (2) memory for arrangement of items in relation to each other or the environment bounds, regardless of memory for the item identity, and (3) higher-order, compound relational errors (i.e., errors involving multiple pieces of relational information). Reconstruction errors were evaluated to determine the degree to which patients and comparisons differed (or not) on each type of spatial-relational information. Data revealed that the primary group difference in performance was for identity-location information. However, when the locations of items were evaluated without regarding the identities, no group difference was found in the number of item placements to studied locations. The present work provides a principled approach to analysis of SR data and clarifies our understanding of

  17. Passive seismology reveals biannual calving periodicity

    Science.gov (United States)

    Bartholomaus, T. C.; Larsen, C. F.; West, M. E.; Oneel, S.

    2013-12-01

    Iceberg calving is a large and variable component of the total mass loss from marine-terminating glaciers worldwide. However, the processes that control the size and variability of calving fluxes are poorly understood. Even more basic descriptions of iceberg calving, such as its seasonality, are uncertain. Here, we present nearly two years of automatically-estimated calving fluxes at Yahtse Glacier, a tidewater glacier whose terminus flows at ~7 km/yr towards the Gulf of Alaska. At the terminus, ice losses to calving and submarine melt total approximately 1.5 km^3/yr. In order to identify temporal variability in this mean rate, we develop a statistical model of calving size based on characteristics of calving-generated icequakes. These characteristics include 4 amplitude-based variables and 5 variables related to the shape of the icequake envelope. We build our model by combining automatically-detected icequakes (O'Neel et al., 2007) located at the terminus of Yahtse Glacier (Jones et al., 2013) with a training set of 1400 icequakes produced by visually-observed calving events (Bartholomaus et al., 2012). In each of the models tested (regression trees, multinomia