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  • 1
    Journal cover
    Public Library of Science (PLoS)
    Online: 1.2003 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 2
    Journal cover
    Public Library of Science (PLoS) | PubMed Central
    Online: 1.2009 –
    Publisher: Public Library of Science (PLoS) , PubMed Central
    Electronic ISSN: 2157-3999
    Topics: Medicine , Natural Sciences in General
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  • 3
    Journal cover
    Public Library of Science (PLoS)
    Online: 1.2005 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 4
    Journal cover
    Public Library of Science (PLoS)
    Online: 1.2005 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 5
    Journal cover
    Public Library of Science (PLoS)
    Online: 1.2010 –
    Publisher: Public Library of Science (PLoS)
    Topics: Biology
    Keywords: Biodiversität ; Biodiversität
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  • 6
    Publication Date: 2016-10-12
    Description: The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the “stilt-legged” horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species.
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  • 7
    Publication Date: 2016-09-23
    Description: © 2005 Sullivan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 3 (2005): e144, doi:10.1371/journal.pbio.0030144.
    Description: The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish ‘‘core’’ genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of ‘‘cyanobacterial’’ genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent ‘‘signature’’ cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments.
    Description: This research was supported by the US DOE under grant numbers DEFG02– 99ER62814 and DE-FG02–02ER63445, and the National Science Foundation under grant number OCE-9820035 (to SWC).
    Keywords: Oceanic cyanobacteria ; Prochlorococcus phages
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
    Publication Date: 2016-09-23
    Description: This is an open-access article distributed under the terms of the Creative Commons Public Domain dedication. The definitive version was published in PLoS Biology 4 (2006): e383, doi:10.1371/journal.pbio.0040383.
    Description: Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
    Description: This work was performed under the auspices of the United States Department of Energy by Lawrence Livermore National Laboratory, University of California, under contract W-7405-ENG-48. Genome closure was funded in part by a University of South Florida Innovative Teaching Grant (to KMS). KMS, SKF, and CAK gratefully acknowledge support from the United States Department of Agriculture Higher Education Challenge Grants Program (Award # 20053841115876). SMS kindly acknowledges support through a fellowship received from the Hanse Wissenschaftskolleg in Delmenhorst, Germany (http://www.h-w-k.de). MH was supported by a Woods Hole Oceanographic Institution postdoctoral scholarship.
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2016-09-22
    Description: © 2006 Parfrey et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Genetics 2 (2006): e220, doi:10.1371/journal.pgen.0020220.
    Description: Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six ‘‘supergroups.’’ The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.
    Description: This work is supported by the National Science Foundation Assembling the Tree of Life grant (043115) to DB, DJP, and LAK.
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2016-09-22
    Description: © 2006 Bordenstein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Pathogens 2(2006): e43, doi:10.1371/journal.ppat.0020043.
    Description: By manipulating arthropod reproduction worldwide, the heritable endosymbiont Wolbachia has spread to pandemic levels. Little is known about the microbial basis of cytoplasmic incompatibility (CI) except that bacterial densities and percentages of infected sperm cysts associate with incompatibility strength. The recent discovery of a temperate bacteriophage (WO-B) of Wolbachia containing ankyrin-encoding genes and virulence factors has led to intensifying debate that bacteriophage WO-B induces CI. However, current hypotheses have not considered the separate roles that lytic and lysogenic phage might have on bacterial fitness and phenotype. Here we describe a set of quantitative approaches to characterize phage densities and its associations with bacterial densities and CI. We enumerated genome copy number of phage WO-B and Wolbachia and CI penetrance in supergroup A- and B-infected males of the parasitoid wasp Nasonia vitripennis. We report several findings: (1) variability in CI strength for A-infected males is positively associated with bacterial densities, as expected under the bacterial density model of CI, (2) phage and bacterial densities have a significant inverse association, as expected for an active lytic infection, and (3) CI strength and phage densities are inversely related in A-infected males; similarly, males expressing incomplete CI have significantly higher phage densities than males expressing complete CI. Ultrastructural analyses indicate that approximately 12% of the A Wolbachia have phage particles, and aggregations of these particles can putatively occur outside the Wolbachia cell. Physical interactions were observed between approximately 16% of the Wolbachia cells and spermatid tails. The results support a low to moderate frequency of lytic development in Wolbachia and an overall negative density relationship between bacteriophage and Wolbachia. The findings motivate a novel phage density model of CI in which lytic phage repress Wolbachia densities and therefore reproductive parasitism. We conclude that phage, Wolbachia, and arthropods form a tripartite symbiotic association in which all three are integral to understanding the biology of this widespread endosymbiosis. Clarifying the roles of lytic and lysogenic phage development in Wolbachia biology will effectively structure inquiries into this research topic.
    Description: This work was supported by grants from the NASA Astrobiology Institute (NNA04CC04A) and National Institutes of Health (R01 GM62626-01) to JJW, and by the Marine Biological Laboratory's Program in Global Infectious Diseases, funded by the Ellison Medical Foundation, to SRB.
    Repository Name: Woods Hole Open Access Server
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  • 11
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    Public Library of Science (PLoS)
    Publication Date: 2016-09-22
    Description: © 2004 Jennifer J. Wernegreen. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 2 (2004): e68, doi:10.1371/journal.pbio.0020068.
    Description: Symbiosis, an interdependent relationship between two species, is an important driver of evolutionary novelty and ecological diversity. Microbial symbionts in particular have been major evolutionary catalysts throughout the 4 billion years of life on earth and have largely shaped the evolution of complex organisms. Endosymbiosis is a specifi c type of symbiosis in which one—typically microbial—partner lives within its host and represents the most intimate contact between interacting organisms. Mitochondria and chloroplasts, for example, result from endosymbiotic events of lasting significance that extended the range of acceptable habitats for life. The wide distribution of intracellular bacteria across diverse hosts and marine and terrestrial habitats testifies to the continued importance of endosymbiosis in evolution. Among multicellular organisms, insects as a group form exceptionally diverse associations with microbial associates, including bacteria that live exclusively within host cells and undergo maternal transmission to offspring. These microbes have piqued the interest of evolutionary biologists because they represent a wide spectrum of evolutionary strategies, ranging from obligate mutualism to reproductive parasitism (Buchner 1965; Ishikawa 2003) (Box 1; Table 1).
    Description: JJW gratefully acknowledges the support of the National Institutes of Health (R01 GM62626-01), the National Science Foundation (DEB 0089455), the National Aeronautics and Space Administration Astrobiology Institute (NNA04CC04A), and the Josephine Bay Paul and C. Michael Paul Foundation.
    Keywords: Endosymbiosis ; Endosymbiosis manipulation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 12
    Publication Date: 2018-11-09
    Description: Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions.
    Type: Article , PeerReviewed
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  • 13
    Publication Date: 2015-02-06
    Description: by Natalya Lukoyanova, Stephanie C. Kondos, Irene Farabella, Ruby H. P. Law, Cyril F. Reboul, Tom T. Caradoc-Davies, Bradley A. Spicer, Oded Kleifeld, Daouda A. K. Traore, Susan M. Ekkel, Ilia Voskoboinik, Joseph A. Trapani, Tamas Hatfaludi, Katherine Oliver, Eileen M. Hotze, Rodney K. Tweten, James C. Whisstock, Maya Topf, Helen R. Saibil, Michelle A. Dunstone Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ∼70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 14
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-06
    Description: by Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 15
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-06
    Description: by Yushi Zhang, Yongqiang Li, Jianhua Deng, Zhigang Ji, Hongyan Yu, Hanzhong Li Objective To evaluate the clinical efficacy of sorafenib as preoperative neoadjuvant therapy in patients with high risk renal cell carcinoma (RCC). Materials and Methods Clinical data of 18 patients with high risk RCC who received surgery done successfully after preoperative neoadjuvant therapy with sorafenib in Peking Union Medical College Hospital (PUMCH) from April 2007 to October 2013 have been reviewed and analyzed in this study. Results Among the 18 patients there were 13 male and 5 female, with a median age of 54.6 years. The objective response rate (ORR) of the operation on the selected patients is very high (94.4%), including 4 cases (22.2%) of partial response (PR) and 13 cases (72.2%) of stable disease (SD). After preoperative sorafenib treatment, the average tumor size of the 18 patients decreased from 7.8 cm (ranging from 3.6 to 19.2 cm) to 6.2 cm (ranging from 2.4 to 16.8 cm), and the median value of average tumor CT value decreased from 61HU to 52 HU. Among the 5 patients who had IVC tumor thrombi, the grades of tumor thrombi in 2 patients who were grade II before sorafenib treatment became grade I and grade 0 respectively, 2 patients of grade III both became grade II. Conclusion Preoperative neoadjuvant therapy with sorafenib for high risk RCC patients can significantly decrease primary tumor volume as well as tumor thrombus, which could help the nephron-sparing surgery (NSS) or radical nephrectomy to be done successfully.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 16
    Publication Date: 2015-02-06
    Description: by The PLOS ONE Staff
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 17
    Publication Date: 2015-02-14
    Description: by Eric Lowet, Mark Roberts, Avgis Hadjipapas, Alina Peter, Jan van der Eerden, Peter De Weerd Fine-scale temporal organization of cortical activity in the gamma range (∼25–80Hz) may play a significant role in information processing, for example by neural grouping (‘binding’) and phase coding. Recent experimental studies have shown that the precise frequency of gamma oscillations varies with input drive (e.g. visual contrast) and that it can differ among nearby cortical locations. This has challenged theories assuming widespread gamma synchronization at a fixed common frequency. In the present study, we investigated which principles govern gamma synchronization in the presence of input-dependent frequency modulations and whether they are detrimental for meaningful input-dependent gamma-mediated temporal organization. To this aim, we constructed a biophysically realistic excitatory-inhibitory network able to express different oscillation frequencies at nearby spatial locations. Similarly to cortical networks, the model was topographically organized with spatially local connectivity and spatially-varying input drive. We analyzed gamma synchronization with respect to phase-locking, phase-relations and frequency differences, and quantified the stimulus-related information represented by gamma phase and frequency. By stepwise simplification of our models, we found that the gamma-mediated temporal organization could be reduced to basic synchronization principles of weakly coupled oscillators, where input drive determines the intrinsic (natural) frequency of oscillators. The gamma phase-locking, the precise phase relation and the emergent (measurable) frequencies were determined by two principal factors: the detuning (intrinsic frequency difference, i.e. local input difference) and the coupling strength. In addition to frequency coding, gamma phase contained complementary stimulus information. Crucially, the phase code reflected input differences, but not the absolute input level. This property of relative input-to-phase conversion, contrasting with latency codes or slower oscillation phase codes, may resolve conflicting experimental observations on gamma phase coding. Our modeling results offer clear testable experimental predictions. We conclude that input-dependency of gamma frequencies could be essential rather than detrimental for meaningful gamma-mediated temporal organization of cortical activity.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 18
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-14
    Description: by W. Maartin Strauss, Robyn S. Hetem, Duncan Mitchell, Shane K. Maloney, Leith C. R. Meyer, Andrea Fuller In artiodactyls, arterial blood destined for the brain can be cooled through counter-current heat exchange within the cavernous sinus via a process called selective brain cooling. We test the hypothesis that selective brain cooling, which results in lowered hypothalamic temperature, contributes to water conservation in sheep. Nine Dorper sheep, instrumented to provide measurements of carotid blood and brain temperature, were dosed with deuterium oxide (D 2 O), exposed to heat for 8 days (40◦C for 6-h per day) and deprived of water for the last five days (days 3 to 8). Plasma osmolality increased and the body water fraction decreased over the five days of water deprivation, with the sheep losing 16.7% of their body mass. Following water deprivation, both the mean 24h carotid blood temperature and the mean 24h brain temperature increased, but carotid blood temperature increased more than did brain temperature resulting in increased selective brain cooling. There was considerable inter-individual variation in the degree to which individual sheep used selective brain cooling. In general, sheep spent more time using selective brain cooling, and it was of greater magnitude, when dehydrated compared to when they were euhydrated. We found a significant positive correlation between selective brain cooling magnitude and osmolality (an index of hydration state). Both the magnitude of selective brain cooling and the proportion of time that sheep spent selective brain cooling were negatively correlated with water turnover. Sheep that used selective brain cooling more frequently, and with greater magnitude, lost less water than did conspecifics using selective brain cooling less efficiently. Our results show that a 50kg sheep can save 2.6L of water per day (~60% of daily water intake) when it employs selective brain cooling for 50% of the day during heat exposure. We conclude that selective brain cooling has a water conservation function in artiodactyls.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 19
    Publication Date: 2015-02-14
    Description: by Piklu Roy Chowdhury, Ian G. Charles, Steven P. Djordjevic In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains bla TEM-1 , strAB , sul2 , tet(A) A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn 21 /Tn 1721 hybrid backbone. Within the hybrid backbone, a Tn 6029 -family transposon, identified here as Tn 6029C abuts the sul1 gene in the 3´-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS 26 -mediated events created two novel transposons identified here as Tn 6029D and Tn 6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 20
    Publication Date: 2015-02-14
    Description: by Chun-Ting Hsu, Arthur M. Jacobs, Ulrike Altmann, Markus Conrad Literature containing supra-natural, or magical events has enchanted generations of readers. When reading narratives describing such events, readers mentally simulate a text world different from the real one. The corresponding violation of world-knowledge during this simulation likely increases cognitive processing demands for ongoing discourse integration, catches readers’ attention, and might thus contribute to the pleasure and deep emotional experience associated with ludic immersive reading. In the present study, we presented participants in an MR scanner with passages selected from the Harry Potter book series, half of which described magical events, while the other half served as control condition. Passages in both conditions were closely matched for relevant psycholinguistic variables including, e.g., emotional valence and arousal, passage-wise mean word imageability and frequency, and syntactic complexity. Post-hoc ratings showed that readers considered supra-natural contents more surprising and more strongly associated with reading pleasure than control passages. In the fMRI data, we found stronger neural activation for the supra-natural than the control condition in bilateral inferior frontal gyri, bilateral inferior parietal lobules, left fusiform gyrus, and left amygdala. The increased activation in the amygdala (part of the salience and emotion processing network) appears to be associated with feelings of surprise and the reading pleasure, which supra-natural events, full of novelty and unexpectedness, brought about. The involvement of bilateral inferior frontal gyri likely reflects higher cognitive processing demand due to world knowledge violations, whereas increased attention to supra-natural events is reflected in inferior frontal gyri and inferior parietal lobules that are part of the fronto-parietal attention network.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 21
    Publication Date: 2015-02-14
    Description: by John P. Didion, Andrew P. Morgan, Amelia M.-F. Clayshulte, Rachel C. Mcmullan, Liran Yadgary, Petko M. Petkov, Timothy A. Bell, Daniel M. Gatti, James J. Crowley, Kunjie Hua, David L. Aylor, Ling Bai, Mark Calaway, Elissa J. Chesler, John E. French, Thomas R. Geiger, Terry J. Gooch, Theodore Garland, Alison H. Harrill, Kent Hunter, Leonard McMillan, Matt Holt, Darla R. Miller, Deborah A. O'Brien, Kenneth Paigen, Wenqi Pan, Lucy B. Rowe, Ginger D. Shaw, Petr Simecek, Patrick F. Sullivan, Karen L Svenson, George M. Weinstock, David W. Threadgill, Daniel Pomp, Gary A. Churchill, Fernando Pardo-Manuel de Villena Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 – 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d ) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation ( R2d2WSBdel1 ) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1 , the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1 , thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 22
    Publication Date: 2015-02-14
    Description: by Julia K. Boehm, Ying Chen, David R. Williams, Carol Ryff, Laura D. Kubzansky Socioeconomic status is associated with health disparities, but underlying psychosocial mechanisms have not been fully identified. Dispositional optimism may be a psychosocial process linking socioeconomic status with health. We hypothesized that lower optimism would be associated with greater social disadvantage and poorer social mobility. We also investigated whether life satisfaction and positive affect showed similar patterns. Participants from the Midlife in the United States study self-reported their optimism, satisfaction, positive affect, and socioeconomic status (gender, race/ethnicity, education, occupational class and prestige, income). Social disparities in optimism were evident. Optimistic individuals tended to be white and highly educated, had an educated parent, belonged to higher occupational classes with more prestige, and had higher incomes. Findings were generally similar for satisfaction, but not positive affect. Greater optimism and satisfaction were also associated with educational achievement across generations. Optimism and life satisfaction are consistently linked with socioeconomic advantage and may be one conduit by which social disparities influence health.
    Electronic ISSN: 1932-6203
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  • 23
    Publication Date: 2015-02-14
    Description: by Eun Sung Kim, Ji Hyun Shin, So Jung Park, Yoon Kyung Jo, Jae-Sung Kim, Il-Hwan Kang, Jung-Bum Nam, Doo-Young Chung, Yoonchul Cho, EunJoo H. Lee, Jong Wook Chang, Dong-Hyung Cho Primary cilia are conserved cellular organelles that regulate diverse signaling pathways. Autophagy is a complex process of cellular degradation and recycling of cytoplasmic proteins and organelles, and plays an important role in cellular homeostasis. Despite its potential importance, the role of autophagy in ciliogenesis is largely unknown. In this study, we identified sertraline as a regulator of autophagy and ciliogenesis. Sertraline, a known antidepressant, induced the growth of cilia and blocked the disassembly of cilia in htRPE cells. Following treatment of sertraline, there was an increase in the number of cells with autophagic puncta and LC3 protein conversion. In addition, both a decrease of ATG5 expression and the treatment of an autophagy inhibitor resulted in the suppression of the sertraline-induced activation of autophagy in htRPE cells. Interestingly, we found that genetic and chemical inhibition of autophagy attenuated the growth of primary cilia in htRPE cells. Taken together, our results suggest that the inhibition of autophagy suppresses sertraline-induced ciliogenesis.
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  • 24
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-14
    Description: by Ronny Uzana, Galit Eisenberg, Sharon Merims, Shoshana Frankenburg, Aviad Pato, Eitan Yefenof, Roni Engelstein, Tamar Peretz, Arthur Machlenkin, Michal Lotem Trogocytosis is a contact-dependent unidirectional transfer of membrane fragments between immune effector cells and their targets, initially detected in T cells following interaction with professional antigen presenting cells (APC). Previously, we have demonstrated that trogocytosis also takes place between melanoma-specific cytotoxic T lymphocytes (CTLs) and their cognate tumors. In the present study, we took this finding a step further, focusing on the ability of melanoma membrane-imprinted CD8 + T cells to act as APCs (CD8 + T-APCs). We demonstrate that, following trogocytosis, CD8 + T-APCs directly present a variety of melanoma derived peptides to fraternal T cells with the same TCR specificity or to T cells with different TCRs. The resulting T cell-T cell immune synapse leads to (1) Activation of effector CTLs, as determined by proliferation, cytokine secretion and degranulation; (2) Fratricide (killing) of CD8 + T-APCs by the activated CTLs. Thus, trogocytosis enables cross-reactivity among CD8 + T cells with interchanging roles of effectors and APCs. This dual function of tumor-reactive CTLs may hint at their ability to amplify or restrict reactivity against the tumor and participate in modulation of the anti-cancer immune response.
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  • 25
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-14
    Description: by Philipp Mitteroecker, Sonja Windhager, Gerd B. Müller, Katrin Schaefer In studies of social inference and human mate preference, a wide but inconsistent array of tools for computing facial masculinity has been devised. Several of these approaches implicitly assumed that the individual expression of sexually dimorphic shape features, which we refer to as maleness, resembles facial shape features perceived as masculine. We outline a morphometric strategy for estimating separately the face shape patterns that underlie perceived masculinity and maleness, and for computing individual scores for these shape patterns. We further show how faces with different degrees of masculinity or maleness can be constructed in a geometric morphometric framework. In an application of these methods to a set of human facial photographs, we found that shape features typically perceived as masculine are wide faces with a wide inter-orbital distance, a wide nose, thin lips, and a large and massive lower face. The individual expressions of this combination of shape features—the masculinity shape scores—were the best predictor of rated masculinity among the compared methods ( r = 0.5). The shape features perceived as masculine only partly resembled the average face shape difference between males and females (sexual dimorphism). Discriminant functions and Procrustes distances to the female mean shape were poor predictors of perceived masculinity.
    Electronic ISSN: 1932-6203
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  • 26
    Publication Date: 2015-02-14
    Description: by Elaine M. Murtagh, Marie H. Murphy, Niamh M. Murphy, Catherine Woods, Alan M. Nevill, Aoife Lane The public health challenges associated with rapid population ageing are likely to be exacerbated by poor physical activity levels. The purpose of this study was to identify correlates of physical inactivity in a population-representative sample of older adults in Ireland. This paper reports a secondary analysis of data from 4892 adults aged 60+ from the Irish Longitudinal Study on Ageing (TILDA). TILDA includes an assessment of the mental and physical health, and social and financial circumstances of participants assessed in a home interview and self-completion questionnaire. Chi squared statistics and forced entry logistic regression were used to identify factors associated with physical inactivity. Females were over twice as likely to be inactive as their male counterparts (Odds Ratio 2.2). Increasing old age was associated with inactivity among males and females. Those who reported above secondary level education, no reported falls in the last year and no fear of falling were less likely to be physically inactive. While older adults who noted poor/fair self-reported health, that they did not look after grandchildren, did not own a car or did not attend a course were also more likely to be inactive than those who reported positively for these items. Gender displayed a strong but often contrasting influence on factors that affect physical activity among older adults. Among females, living alone or in a rural area, retirement, fair/poor emotional health and activity being limited by illness were all significantly associated with inactivity. While cohabiting, being employed and residing in an urban area were related to low levels of activity in males. Our findings identify specific groups of the older Irish population who may be at particular risk of physical inactivity and thereby the associated physiological and psychological hazards. These results can support the development of tailored interventions to promote healthy ageing.
    Electronic ISSN: 1932-6203
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  • 27
    Publication Date: 2015-02-14
    Description: by Zhimin Wang, Weng Lang Yang, Asha Jacob, Monowar Aziz, Ping Wang Widespread use of ionizing radiation has led to the realization of the danger associated with radiation exposure. Although studies in radiation countermeasures were initiated a half century ago, an effective therapy for a radiomitigator has not been identified. Ghrelin is a gastrointestinal hormone, and administration of ghrelin is protective in animal models of injuries including radiation combined injury. To test whether ghrelin can be protective in whole body irradiaton (WBI) alone, male Sprague Dawley (SD) rats were treated with human ghrelin (20 nmol/rat) daily for 6 days starting at either 24 h or 48 h after 10 Gray (Gy) WBI and survival outcome was examined. The 10 Gy WBI produced a LD 70/30 model in SD rats (30% survival in 30 days). The survival rate in rats treated with ghrelin starting at 24 h was significantly improved to 63% and when treatment was initiated at 48 h, the survival remained at 61%. At 7 days post WBI, plasma ghrelin was significantly reduced from the control value. Ghrelin treatment starting at 24 h after WBI daily for 6 days improved histological appearance of the intestine, reduced gut permeability, serum endotoxin levels and bacterial translocation to the liver by 38%, 42% and 61%, respectively at day 7 post WBI. Serum glucose and albumin were restored to near control levels with treatment. Ghrelin treatment also attenuated WBI-induced intestinal apoptosis by 62% as evidenced by TUNEL staining. The expression of anti-apoptotic cell regulator Bcl-xl was decreased by 38% in the vehicle and restored to 75% of the control with ghrelin treatment. Increased expression of intestinal CD73 and pAkt were observed with ghrelin treatment, indicating protection of the intestinal epithelium after WBI. These results indicate that human ghrelin attenuates intestinal injury and mortality after WBI. Thus, human ghrelin can be developed as a novel mitigator for radiation injury.
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  • 28
    Publication Date: 2015-02-14
    Description: by The PLOS ONE Staff
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  • 29
    Publication Date: 2015-02-14
    Description: by The PLOS ONE Staff
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  • 30
    Publication Date: 2015-02-14
    Description: by Rowan Haigh, Debby Ianson, Carrie A. Holt, Holly E. Neate, Andrew M. Edwards As the oceans absorb anthropogenic CO 2 they become more acidic, a problem termed ocean acidification (OA). Since this increase in CO 2 is occurring rapidly, OA may have profound implications for marine ecosystems. In the temperate northeast Pacific, fisheries play key economic and cultural roles and provide significant employment, especially in rural areas. In British Columbia (BC), sport (recreational) fishing generates more income than commercial fishing (including the expanding aquaculture industry). Salmon (fished recreationally and farmed) and Pacific Halibut are responsible for the majority of fishery-related income. This region naturally has relatively acidic (low pH) waters due to ocean circulation, and so may be particularly vulnerable to OA. We have analyzed available data to provide a current description of the marine ecosystem, focusing on vertical distributions of commercially harvested groups in BC in the context of local carbon and pH conditions. We then evaluated the potential impact of OA on this temperate marine system using currently available studies. Our results highlight significant knowledge gaps. Above trophic levels 2–3 (where most local fishery-income is generated), little is known about the direct impact of OA, and more importantly about the combined impact of multi-stressors, like temperature, that are also changing as our climate changes. There is evidence that OA may have indirect negative impacts on finfish through changes at lower trophic levels and in habitats. In particular, OA may lead to increased fish-killing algal blooms that can affect the lucrative salmon aquaculture industry. On the other hand, some species of locally farmed shellfish have been well-studied and exhibit significant negative direct impacts associated with OA, especially at the larval stage. We summarize the direct and indirect impacts of OA on all groups of marine organisms in this region and provide conclusions, ordered by immediacy and certainty.
    Electronic ISSN: 1932-6203
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  • 31
    Publication Date: 2015-02-17
    Description: by Jun Feng, Shusheng Li, Huawen Chen Background The high incidence of pesticide ingestion as a means to commit suicide is a critical public health problem. An important predictor of suicidal behavior is suicide ideation, which is related to stress. However, studies on how to defend against stress-induced suicidal thoughts are limited. Objective This study explores the impact of stress on suicidal ideation by investigating the mediating effect of self-efficacy and dispositional optimism. Methods Direct and indirect (via self-efficacy and dispositional optimism) effects of stress on suicidal ideation were investigated among 296 patients with acute pesticide poisoning from four general hospitals. For this purpose, structural equation modeling (SEM) and bootstrap method were used. Results Results obtained using SEM and bootstrap method show that stress has a direct effect on suicide ideation. Furthermore, self-efficacy and dispositional optimism partially weakened the relationship between stress and suicidal ideation. Conclusion The final model shows a significant relationship between stress and suicidal ideation through self-efficacy or dispositional optimism. The findings extended prior studies and provide enlightenment on how self-efficacy and optimism prevents stress-induced suicidal thoughts.
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  • 32
    Publication Date: 2015-02-17
    Description: by Jing Zhao, Jing Wang, Jinfeng Du, Hongli Xu, Wei Zhang, Quan-Xing Ni, Herbert Yu, Harvey A. Risch, Yu-Tang Gao, Ying Gao Pancreatic cancer has been increasing in importance in Shanghai over the last four decades. The etiology of the disease is still unclear. Evidence suggests that the COX-2 pathway, an important component of inflammation, may be involved in the disease. We aimed to evaluate the association between urinary prostaglandin E 2 metabolite (PGE-M) level and risk of pancreatic cancer. From a recent population-based case-control study in Shanghai, 200 pancreatic ductal adenocarcinoma cases and 200 gender- and age- frequency matched controls were selected for the present analysis. Urinary PGE-M was measured with a liquid chromatography/mass spectrometric assay. Adjusted unconditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). A positive association was observed between PGE-M leve and pancreatic cancer risk: OR = 1.63 (95% CI 1.01–2.63) for the third tertile compared to the first. Though the interactions were not statistically significant, the associations tended to be stronger among subjects with diabetes history (OR = 3.32; 95% CI 1.20–9.19) and higher meat intake (OR = 2.12; 95% CI 1.10–4.06). The result suggests that higher urinary PGE-M level may be associated with increased risk of pancreatic ductal adenocarcinoma.
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  • 33
    Publication Date: 2015-02-17
    Description: by Junhee Seok Murine models are an essential tool to study human immune responses and related diseases. However, the use of traditional murine models has been challenged by recent systemic surveys that show discordance between human and model immune responses in their gene expression. This is a significant problem in translational biomedical research for human immunity. Here, we describe evidence-based translation (EBT) to improve the analysis of genomic responses of murine models in the translation to human immune responses. Based on evidences from prior experiments, EBT introduces pseudo variances, penalizes gene expression changes in a model experiment, and finally detects false positive translations of model genomic responses that poorly correlate with human responses. Demonstrated over multiple data sets, EBT significantly improves the agreement of overall responses (up to 56%), experiment-specific responses (up to 143%), and enriched biological contexts (up to 100%) between human and model systems. In addition, we provide the category of genes specifically benefiting from EBT and the factors affecting the performance of EBT. The overall result indicates the usefulness of the proposed computational translation in biomedical research for human immunity using murine models.
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  • 34
    Publication Date: 2015-02-17
    Description: by Renyuan Wu, Zhencai Zhu, Guohua Cao The behavior of rope-guided conveyances is so complicated that the rope-guided hoisting system hasn’t been understood thoroughly so far. In this paper, with user-defined functions loaded, ANSYS FLUENT 14.5 was employed to simulate lateral motion of rope-guided conveyances in two typical kinds of shaft layouts. With rope-guided mine elevator and mine cages taken into account, results show that the lateral aerodynamic buffeting force is much larger than the Coriolis force, and the side aerodynamic force have the same order of magnitude as the Coriolis force. The lateral aerodynamic buffeting forces should also be considered especially when the conveyance moves along the ventilation air direction. The simulation shows that the closer size of the conveyances can weaken the transverse aerodynamic buffeting effect.
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  • 35
    Publication Date: 2015-02-17
    Description: by Xiya Yu, Shupeng Liu, Jinbao Li, Xiaohua Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng Post-operative cognitive dysfunction (POCD) is a commonly-seen postoperative complication in elderly patients. However, the underlying mechanisms of POCD remain unclear. miRNAs, which are reported to be involved in the pathogenesis of the nervous system diseases, may also affect POCD. In this study, miRNA microarray technology was used to analyze the circulating miRNA expression profile of POCD patients. Among the altered miRNAs, miR-572 had the greatest decrease, which was also verified in vivo in rat POCD model. Further analysis found that miR-572 could regulate the expression of NCAM1 in the hippocampal neurons and interfering miR-572 expression could facilitate the restoration of cognitive function in vivo. Moreover, clinical correlation analysis found that the miR-572 expression was associated with the incidence of POCD. Collectively, miR-572 is involved in the development and restoration of POCD and it may serve as a biological marker for early diagnosis of POCD.
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  • 36
    Publication Date: 2015-02-17
    Description: by Warren N. Fawley, C. W. Knetsch, Duncan R. MacCannell, Celine Harmanus, Tim Du, Michael R. Mulvey, Ashley Paulick, Lydia Anderson, E. J. Kuijper, Mark H. Wilcox PCR-ribotyping has been adopted in many laboratories as the method of choice for C. difficile typing and surveillance. However, issues with the conventional agarose gel-based technique, including inter-laboratory variation and interpretation of banding patterns have impeded progress. The method has recently been adapted to incorporate high-resolution capillary gel-based electrophoresis (CE-ribotyping), so improving discrimination, accuracy and reproducibility. However, reports to date have all represented single-centre studies and inter-laboratory variability has not been formally measured or assessed. Here, we achieved in a multi-centre setting a high level of reproducibility, accuracy and portability associated with a consensus CE-ribotyping protocol. Local databases were built at four participating laboratories using a distributed set of 70 known PCR-ribotypes. A panel of 50 isolates and 60 electronic profiles (blinded and randomized) were distributed to each testing centre for PCR-ribotype identification based on local databases generated using the standard set of 70 PCR-ribotypes, and the performance of the consensus protocol assessed. A maximum standard deviation of only ±3.8bp was recorded in individual fragment sizes, and PCR-ribotypes from 98.2% of anonymised strains were successfully discriminated across four ribotyping centres spanning Europe and North America (98.8% after analysing discrepancies). Consensus CE-ribotyping increases comparability of typing data between centres and thereby facilitates the rapid and accurate transfer of standardized typing data to support future national and international C. difficile surveillance programs.
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  • 37
    Publication Date: 2015-02-17
    Description: by Stephen W. Waldo, Daniel A. Brenner, James M. McCabe, Mark Dela Cruz, Brian Long, Venkata A. Narla, Joseph Park, Ameya Kulkarni, Elizabeth Sinclair, Stephen Y. Chan, Suzaynn F. Schick, Namita Malik, Peter Ganz, Priscilla Y. Hsue Objective The endothelium is a key mediator of vascular homeostasis and cardiovascular health. Molecular research on the human endothelium may provide insight into the mechanisms underlying cardiovascular disease. Prior methodology used to isolate human endothelial cells has suffered from poor yields and contamination with other cell types. We thus sought to develop a minimally invasive technique to obtain endothelial cells derived from human subjects with higher yields and purity. Methods Nine healthy volunteers underwent endothelial cell harvesting from antecubital veins using guidewires. Fluorescence-activated cell sorting (FACS) was subsequently used to purify endothelial cells from contaminating cells using endothelial surface markers (CD34 / CD105 / CD146) with the concomitant absence of leukocyte and platelet specific markers (CD11b / CD45). Endothelial lineage in the purified cell population was confirmed by expression of endothelial specific genes and microRNA using quantitative polymerase chain reaction (PCR). Results A median of 4,212 (IQR: 2161 – 6583) endothelial cells were isolated from each subject. Quantitative PCR demonstrated higher expression of von Willebrand Factor (vWF, P
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  • 38
    Publication Date: 2015-02-17
    Description: by Chawalit Siriboon, Yu-Hsuan Lin, Michel Kere, Chun-Da Chen, Lih-Ren Chen, Chien-Hong Chen, Ching-Fu Tu, Neng-Wen Lo, Jyh-Cherng Ju We attempted to isolate ES cell lines using inner cell masses from high-quality cloned porcine blastocysts. After being seeded onto feeders, embryos had better ( P 〈 0.05) attachment, outgrowth formation and primary colonization in both 2× and 3× aggregated cloned embryos (62.8, 42.6 and12.8% vs . 76.2, 55.2 and 26.2%, respectively) compared to the non-aggregated group (41.6, 23.4 and 3.9%). Effects of feeder types (STO vs . MEF) and serum sources (FBS vs . KSR) on extraction of cloned embryo-derived porcine ES cells were examined. More (17.1%) ntES cell lines over Passage 3 were generated in the MEF/KSR group. However, ntES cells cultured in KSR-supplemented medium had a low proliferation rate with defective morphology, and eventually underwent differentiation or apoptosis subsequently. Approximately 26.1, 22.7 and 35.7% of primary colonies were formed after plating embryos in DMEM, DMEM/F12 and α-MEM media, respectively. Survival rates of ntES cells cultured in α-MEM, DMEM and DMEM/F12 were 16.7, 4.3 and 6.8%, respectively ( P 〉 0.05). We further examined the beneficial effect of TSA treatment of 3× aggregated cloned embryos on establishment of ntES cell lines. Primary colony numbers and survival rates of ntES cells beyond passage 3 were higher ( P 〈 0.05) in those derived from TSA-treated 3× blastocysts (36.7 and 26.7%) than from the non-treated aggregated group (23.1 and 11.5%). These cells, remaining undifferentiated over 25 passages, had alkaline phosphatase activity and expressed ES specific markers Oct4, Nanog, Sox2, and Rex01. Moreover, these ntES cells successfully differentiated into embryoid bodies (EBs) that expressed specific genes of all three germ layers after being cultured in LIF-free medium. In conclusion, we have successfully derived putative porcine ntES cells with high efficiency from quality cloned embryos produced by embryo aggregation, and optimized the ES cell culture system suitable for establishing and maintaining ntES cell lines in undifferentiated state.
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  • 39
    Publication Date: 2015-02-17
    Description: by Elena Arriero, Inge Müller, Risto Juvaste, Francisco Javier Martínez, Albert Bertolero The ability to control infections is a key trait for migrants that must be balanced against other costly features of the migratory life. In this study we explored the links between migration and disease ecology by examining natural variation in parasite exposure and immunity in several populations of Lesser Black-backed Gulls ( Larus fuscus ) with different migratory strategies. We found higher activity of natural antibodies in long distance migrants from the nominate subspecies L . f.fuscus . Circulating levels of IgY showed large variation at the population level, while immune parameters associated with antimicrobial activity showed extensive variation at the individual level irrespective of population or migratory strategy. Pathogen prevalence showed large geographical variation. However, the seroprevalence of one of the gull-specific subtypes of avian influenza (H16) was associated to the migratory strategy, with lower prevalence among the long-distance migrants, suggesting that migration may play a role in disease dynamics of certain pathogens at the population level.
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  • 40
    Publication Date: 2015-02-17
    Description: by Marije aan het Rot, D. S. Moskowitz, Peter J. de Jong Facial blushing may usually be undesirable but may have an ameliorative function for some individuals under some circumstances. Researchers have studied the blush in laboratory settings, but not in daily life. In the present research, conducted with young adults, we employed for the first time an event-contingent recording method for assessing facial blushing during every-day social encounters. Blushing was associated with feeling embarrassed, ashamed, and exposed. These findings, though based on correlational analyses, are consistent with the idea that blushing is often unpleasant and can be maladaptive, and may contribute to the common belief that blushing is an undesirable response. Frequent blushers generally reported lower levels of dominant behavior, higher levels of submissive behavior, and perceived their social interaction partners as more powerful and less affiliative. This was independent of whether they blushed or not, suggesting that altered social behaviors and perceptions are associated with blushing-associated traits rather than with the blushing state. The experience of the blush varied as a function of the frequency with which a person blushed. Blushing was associated with higher levels of shame in frequent blushers than in infrequent blushers. In infrequent blushers, blushing was associated with higher levels of pleasant affect, suggesting that for infrequent blushers the blush may occur in positive social encounters.
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  • 41
    Publication Date: 2015-02-17
    Description: by Yi Rang Na, Yi Na Yoon, Dain Son, Daun Jung, Gyo Jeong Gu, Seung Hyeok Seok Macrophages play important roles in defense against infection, as well as in homeostasis maintenance. Thus alterations of macrophage function can have unexpected pathological results. Cyclooxygenase (COX) inhibitors are widely used to relieve pain, but the effects of long-term usage on macrophage function remain to be elucidated. Using bone marrow-derived macrophage culture and long-term COX inhibitor treatments in BALB/c mice and zebrafish, we showed that chronic COX inhibition drives macrophages into an inflammatory state. Macrophages differentiated in the presence of SC-560 (COX-1 inhibitor), NS-398 (COX-2 inhibitor) or indomethacin (COX-1/2 inhibitor) for 7 days produced more TNFα or IL-12p70 with enhanced p65/IκB phosphoylation. YmI and IRF4 expression was reduced significantly, indicative of a more inflammatory phenotype. We further observed that indomethacin or NS-398 delivery accelerated zebrafish death rates during LPS induced sepsis. When COX inhibitors were released over 30 days from an osmotic pump implant in mice, macrophages from peritoneal cavities and adipose tissue produced more TNFα in both the basal state and under LPS stimulation. Consequently, indomethacin-exposed mice showed accelerated systemic inflammation after LPS injection. Our findings suggest that macrophages exhibit a more inflammatory phenotype when COX activities are chronically inhibited.
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  • 42
    Publication Date: 2015-02-17
    Description: by Hongxia Wang, Julio C. Ayala, Jorge A. Benitez, Anisia J. Silva The histone-like nucleoid structuring protein (H-NS) functions as a transcriptional silencer by binding to AT-rich sequences at bacterial promoters. However, H-NS repression can be counteracted by other transcription factors in response to environmental changes. The identification of potential toxic factors, the expression of which is prevented by H-NS could facilitate the discovery of new regulatory proteins that may contribute to the emergence of new pathogenic variants by anti-silencing. Vibrio cholerae hns mutants of the El Tor biotype exhibit altered virulence, motility and environmental stress response phenotypes compared to wild type. We used an RNA-seq analysis approach to determine the basis of the above hns phenotypes and identify new targets of H-NS transcriptional silencing. H-NS affected the expression of 18% of all predicted genes in a growth phase-dependent manner. Loss of H-NS resulted in diminished expression of numerous genes encoding methyl-accepting chemotaxis proteins as well as chemotaxis toward the attractants glycine and serine. Deletion of hns also induced an endogenous envelope stress response resulting in elevated expression of rpoE encoding the extracytoplamic sigma factor E (σ E ). The RNA-seq analysis identified new genes directly repressed by H-NS that can affect virulence and biofilm development in the El Tor biotype cholera bacterium. We show that H-NS and the quorum sensing regulator HapR silence the transcription of the vieSAB three-component regulatory system in El Tor biotype V. cholerae . We also demonstrate that H-NS directly represses the transcription of hlyA (hemolysin), rtxCA (the repeat in toxin or RTX), rtxBDE (RTX transport) and the biosynthesis of indole. Of these genes, H-NS occupancy at the hlyA promoter was diminished by overexpression of the transcription activator HlyU. We discuss the role of H-NS transcriptional silencing in phenotypic differences exhibited by V. cholerae biotypes.
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  • 43
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    Publication Date: 2015-02-17
    Description: by Catherine E. Morris, Emil A. Prikryl, Béla Joós K-selective voltage-gated channels (Kv) are multi-conformation bilayer-embedded proteins whose mechanosensitive (MS) Popen (V) implies that at least one conformational transition requires the restructuring of the channel-bilayer interface. Unlike Morris and colleagues, who attributed MS-Kv responses to a cooperative V-dependent closed-closed expansion↔compaction transition near the open state, Mackinnon and colleagues invoke expansion during a V-independent closed↔open transition. With increasing membrane tension, they suggest, the closed↔open equilibrium constant, L , can increase 〉100-fold, thereby taking steady-state Popen from 0→1; “exquisite sensitivity to small…mechanical perturbations”, they state, makes a Kv “as much a mechanosensitive…as…a voltage-dependent channel”. Devised to explain successive g K (V) curves in excised patches where tension spontaneously increased until lysis, their L -based model falters in part because of an overlooked IK feature; with recovery from slow inactivation factored in, their g(V) datasets are fully explained by the earlier model (a MS V-dependent closed-closed transition, invariant L≥4 ). An L -based MS-Kv predicts neither known Kv time courses nor the distinctive MS responses of Kv-ILT. It predicts Kv densities (hence gating charge per V -sensor) several-fold different from established values. If opening depended on elevated tension ( L -based model), standard g K (V) operation would be compromised by animal cells’ membrane flaccidity. A MS V-dependent transition is, by contrast, unproblematic on all counts. Since these issues bear directly on recent findings that mechanically-modulated Kv channels subtly tune pain-related excitability in peripheral mechanoreceptor neurons we undertook excitability modeling (evoked action potentials). Kvs with MS V-dependent closed-closed transitions produce nuanced mechanically-modulated excitability whereas an L -based MS-Kv yields extreme, possibly excessive (physiologically-speaking) inhibition.
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  • 44
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-17
    Description: by Nelson H. Koshoji, Sandra K. Bussadori, Carolina C. Bortoletto, Renato A. Prates, Marcelo T. Oliveira, Alessandro M. Deana Erosion is a highly prevalent condition known as a non-carious lesion that causes progressive tooth wear due to chemical processes that do not involve the action of bacteria. Speckle images proved sensitive to even minimal mineral loss from the enamel. The aim of the present study was to investigate the use of laser speckle imaging analysis in the spatial domain to quantify shifts in the microstructure of the tooth surface in an erosion model. 32 fragments of the vestibular surface of bovine incisors were divided in for groups (10 min, 20 min. 30 min and 40 min of acid etching) immersed in a cola-based beverage (pH approximately 2.5) twice a day during 7 days to create an artificial erosion. By analyzing the laser speckle contrast map (LASCA) in the eroded region compared to the sound it was observed that the LASCA map shifts, proportionally to the acid each duration, by: 18%; 23%; 39% and 44% for the 10 min; 20 min; 30 min and 40 min groups, respectively. To the best of our knowledge, this is the first study to demonstrate the correlation between speckle patterns and erosion progression.
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  • 45
    Publication Date: 2015-02-17
    Description: by Patricia V. L. Moreira, Larissa Galastri Baraldi, Jean-Claude Moubarac, Carlos Augusto Monteiro, Alex Newton, Simon Capewell, Martin O’Flaherty Background The global burden of non-communicable diseases partly reflects growing exposure to ultra-processed food products (UPPs). These heavily marketed UPPs are cheap and convenient for consumers and profitable for manufacturers, but contain high levels of salt, fat and sugars. This study aimed to explore the potential mortality reduction associated with future policies for substantially reducing ultra-processed food intake in the UK. Methods and Findings We obtained data from the UK Living Cost and Food Survey and from the National Diet and Nutrition Survey. By the NOVA food typology, all food items were categorized into three groups according to the extent of food processing: Group 1 describes unprocessed/minimally processed foods. Group 2 comprises processed culinary ingredients. Group 3 includes all processed or ultra-processed products. Using UK nutrient conversion tables, we estimated the energy and nutrient profile of each food group. We then used the IMPACT Food Policy model to estimate reductions in cardiovascular mortality from improved nutrient intakes reflecting shifts from processed or ultra-processed to unprocessed/minimally processed foods. We then conducted probabilistic sensitivity analyses using Monte Carlo simulation. Results Approximately 175,000 cardiovascular disease (CVD) deaths might be expected in 2030 if current mortality patterns persist. However, halving the intake of Group 3 (processed) foods could result in approximately 22,055 fewer CVD related deaths in 2030 ( minimum estimate 10,705, maximum estimate 34,625 ). An ideal scenario in which salt and fat intakes are reduced to the low levels observed in Group 1 and 2 could lead to approximately 14,235 ( minimum estimate 6,680, maximum estimate 22,525 ) fewer coronary deaths and approximately 7,820 ( minimum estimate 4,025, maximum estimate 12,100 ) fewer stroke deaths, comprising almost 13% mortality reduction. Conclusions This study shows a substantial potential for reducing the cardiovascular disease burden through a healthier food system. It highlights the crucial importance of implementing healthier UK food policies.
    Electronic ISSN: 1932-6203
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  • 46
    Publication Date: 2015-02-17
    Description: by Yoni Vortman, Rebecca J. Safran, Tali Reiner Brodetzki, Roi Dor, Arnon Lotem The level of expression of sexually selected traits is generally determined by genes, environment and their interaction. In species that use multiple sexual signals which may be costly to produce, investing in the expression of one sexual signal may limit the expression of the other, favoring the evolution of a strategy for resource allocation among signals. As a result, even when the expression of sexual signals is condition dependent, the relative level of expression of each signal may be heritable. We tested this hypothesis in the East-Mediterranean barn swallow ( Hirundo rustica transitiva ), in which males have been shown to express two uncorrelated sexual signals: red-brown ventral coloration, and long tail streamers. We show that variation in both signals may partially be explained by age, as well as by paternal origin (genetic father-son regressions), but that the strongest similarity between fathers and sons is the relative allocation towards one trait or the other (relative expression index), rather than the expression of the traits themselves. These results suggest that the expression of one signal is not independent of the other, and that genetic strategies for resource allocation among sexual signals may be selected for during the evolution of multiple sexual signals.
    Electronic ISSN: 1932-6203
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  • 47
    Publication Date: 2015-02-17
    Description: by Debora B. Lima, José Wagner S. Melo, Nelsa Maria P. Guedes, Lessando M. Gontijo, Raul Narciso C. Guedes, Manoel Guedes C. Gondim Synthetic pesticide use has been the dominant form of pest control since the 1940s. However, biopesticides are emerging as sustainable pest control alternatives, with prevailing use in organic agricultural production systems. Foremost among botanical biopesticides is the limonoid azadirachtin, whose perceived environmental safety has come under debate and scrutiny in recent years. Coconut production, particularly organic coconut production, is one of the agricultural systems in which azadirachtin is used as a primary method of pest control for the management of the invasive coconut mite, Aceria guerreronis Keifer (Acari: Eriophyidae). The management of this mite species also greatly benefits from predation by Neoseiulus baraki (Athias-Henriot) (Acari: Phytoseiidae). Here, we assessed the potential behavioral impacts of azadirachtin on the coconut mite predator, N. baraki . We explored the effects of this biopesticide on overall predator activity, female searching time, and mating behavior and fecundity. Azadirachtin impairs the overall activity of the predator, reducing it to nearly half; however, female searching was not affected. In contrast, mating behavior was compromised by azadirachtin exposure particularly when male predators were exposed to the biopesticide. Consequently, predator fecundity was also compromised by azadirachtin, furthering doubts about its environmental safety and selectivity towards biological control agents.
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  • 48
    Publication Date: 2015-02-17
    Description: by Kohta Suzuki, Miri Sato, Wei Zheng, Ryoji Shinohara, Hiroshi Yokomichi, Zentaro Yamagata Pregestational weight status and maternal smoking during pregnancy are significantly associated with fetal and childhood growth. However, few studies have examined associations between childhood growth and combinations of these factors using multilevel analysis. This study aimed to describe differences in childhood growth trajectories according to these combinations, using data from a prospective cohort study in Japan. The study participants were 1,973 women and their singletons, who were born between April 1, 1991 and March 31, 2003. Children were categorized according to whether they were born to normal-weight, nonsmoking mothers (NN); normal-weight, smoking mothers (NS); underweight, nonsmoking mothers (UN); underweight, smoking mothers (US); overweight, nonsmoking mothers (ON); or overweight, smoking mothers (OS). Birth weight and anthropometric data were collected from 1,965 children at birth (99.6%), 1,655 aged 3 (83.9%), 1,527 aged 5 (77.4%), 1,497 aged 7–8 (75.9%), and 1,501 aged 9–10 (76.1%). Multilevel analysis examining both individual and age as different level variables according to sex was used to describe the trajectories of body mass index z scores for statistical analyses. Although children of the OS group were the leanest at birth, their body mass indices had increased rapidly by 3 years of age. Moreover, body mass index was also likely to increase in boys in the NS and ON groups. A different trend was observed in girls. Body mass index decreased from 5 years of age in girls in the US group. There were no remarkable differences in body mass index trajectories between children in the other groups. In conclusion, childhood growth trajectories differed according to combinations of pregestational weight status and maternal smoking during pregnancy. Further, there were sex-related differences in the associations between childhood growth and factor combinations.
    Electronic ISSN: 1932-6203
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  • 49
    Publication Date: 2015-02-17
    Description: by Débora M. Trombetta, Simone C. Cardoso, Victor G. L. Alves, Alessandro Facure, Delano V. S. Batista, Ademir X. da Silva The combination of radiotherapy treatments and breast reconstruction, using temporary tissue expanders, generates several concerns due to the presence of a magnetic valve inside the radiation field. The objective of this work is to evaluate a radiotherapy treatment planning for a patient using a tissue expander. Isodose curve maps, obtained using radiochromic films, were compared to the ones calculated with two different dose calculation algorithms of the Eclipse radiotherapy Treatment Planning System (TPS), considering the presence or absence of the heterogeneity. The TPS calculation considering the presence of the heterogeneity shows changes around 5% in the isodose curves when they were compared with the calculation without heterogeneity correction. This calculation did not take in account the real density value of the heterogeneity. This limitation was quantified to be around 10% in comparison with the TPS calculation and experimental measurements using the radiochromic film. These results show that the magnetic valve should be taken in account in dose calculations of the TPS. With respect to the AAA and Pencil Beam Convolution algorithms, when the calculation is compared with the real distribution, AAA presents a distribution more similar to experimental dose distribution.
    Electronic ISSN: 1932-6203
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  • 50
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    Publication Date: 2015-02-17
    Description: by Zhiwen Yu, Jiming Liu, Xianjun Zhu Researchers have recently paid attention to social contact patterns among individuals due to their useful applications in such areas as epidemic evaluation and control, public health decisions, chronic disease research and social network research. Although some studies have estimated social contact patterns from social networks and surveys, few have considered how to infer the hierarchical structure of social contacts directly from census data. In this paper, we focus on inferring an individual’s social contact patterns from detailed census data, and generate various types of social contact patterns such as hierarchical-district-structure-based, cross-district and age-district-based patterns. We evaluate newly generated contact patterns derived from detailed 2011 Hong Kong census data by incorporating them into a model and simulation of the 2009 Hong Kong H1N1 epidemic. We then compare the newly generated social contact patterns with the mixing patterns that are often used in the literature, and draw the following conclusions. First, the generation of social contact patterns based on a hierarchical district structure allows for simulations at different district levels. Second, the newly generated social contact patterns reflect individuals social contacts. Third, the newly generated social contact patterns improve the accuracy of the SEIR-based epidemic model.
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  • 51
    Publication Date: 2015-02-17
    Description: by The PLOS ONE Staff
    Electronic ISSN: 1932-6203
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  • 52
    Publication Date: 2015-02-17
    Description: by Robin Cristofari, Emiliano Trucchi, Jason D. Whittington, Stéphanie Vigetta, Hélène Gachot-Neveu, Nils Christian Stenseth, Yvon Le Maho, Céline Le Bohec How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus , return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.
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  • 53
    Publication Date: 2015-02-17
    Description: by Matthew D. Johnson, Yesenia L. De León Understanding how invasive plants may alter predator avoidance behaviors is important for granivorous rodents because their foraging can trigger ripple effects in trophic webs. Previous research has shown that European beach grass Ammophila arenaria , an invasive species in coastal California, affects the predation of other seeds by the rodents Microtus californicus , Peromyscus maniculatus , and Reithrodontomys megalotis . This may be due to lower perceived predation risk by rodents foraging in close proximity to the cover provided by Ammophila , but this mechanism has not yet been tested. We examined the perceived predation risk of rodents by measuring the ‘giving up density’ of food left behind in experimental patches of food in areas with and without abundant cover from Ammophila and under varying amount of moonlight. We found strong evidence that giving up density was lower in the thick uniform vegetation on Ammophila -dominated habitat than it was in the more sparsely and diversely vegetated restored habitat. There was also evidence that moonlight affected giving up density and that it mediated the effects of habitat, although with our design we were unable to distinguish the effects of lunar illumination and moon phase. Our findings illustrate that foraging rodents, well known to be risk-averse during moonlit nights, are also affected by the presence of an invasive plant. This result has implications for granivory and perhaps plant demography in invaded and restored coastal habitats. Future research in this system should work to unravel the complex trophic links formed by a non-native invasive plant (i.e., Ammophila ) providing cover favored by native rodents, which likely forage on and potentially limit the recruitment of native and non-native plants, some of which have ecosystem consequences of their own.
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  • 54
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Philip Lieberman
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 55
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Johan J. Bolhuis, Ian Tattersall, Noam Chomsky, Robert C. Berwick
    Print ISSN: 1544-9173
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    Topics: Biology
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  • 56
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Janelle Weaver
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  • 57
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    Publication Date: 2015-02-18
    Description: by Mark L. Siegal No organism lives in a constant environment. Based on classical studies in molecular biology, many have viewed microbes as following strict rules for shifting their metabolic activities when prevailing conditions change. For example, students learn that the bacterium Escherichia coli makes proteins for digesting lactose only when lactose is available and glucose, a better sugar, is not. However, recent studies, including three PLOS Biology papers examining sugar utilization in the budding yeast Saccharomyces cerevisiae , show that considerable heterogeneity in response to complex environments exists within and between populations. These results join similar recent results in other organisms that suggest that microbial populations anticipate predictable environmental changes and hedge their bets against unpredictable ones. The classical view therefore represents but one special case in a range of evolutionary adaptations to environmental changes that all organisms face.
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  • 58
    Publication Date: 2015-02-18
    Description: by Elsie Premereur, Ilse C. Van Dromme, Maria C. Romero, Wim Vanduffel, Peter Janssen Extrastriate cortical areas are frequently composed of subpopulations of neurons encoding specific features or stimuli, such as color, disparity, or faces, and patches of neurons encoding similar stimulus properties are typically embedded in interconnected networks, such as the attention or face-processing network. The goal of the current study was to examine the effective connectivity of subsectors of neurons in the same cortical area with highly similar neuronal response properties. We first recorded single- and multi-unit activity to identify two neuronal patches in the anterior part of the macaque intraparietal sulcus (IPS) showing the same depth structure selectivity and then employed electrical microstimulation during functional magnetic resonance imaging in these patches to determine the effective connectivity of these patches. The two IPS subsectors we identified—with the same neuronal response properties and in some cases separated by only 3 mm—were effectively connected to remarkably distinct cortical networks in both dorsal and ventral stream in three macaques. Conversely, the differences in effective connectivity could account for the known visual-to-motor gradient within the anterior IPS. These results clarify the role of the anterior IPS as a pivotal brain region where dorsal and ventral visual stream interact during object analysis. Thus, in addition to the anatomical connectivity of cortical areas and the properties of individual neurons in these areas, the effective connectivity provides novel key insights into the widespread functional networks that support behavior.
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  • 59
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Veronica Rodilla, Alessandro Dasti, Mathilde Huyghe, Daniel Lafkas, Cécile Laurent, Fabien Reyal, Silvia Fre The hierarchical relationships between stem cells and progenitors that guide mammary gland morphogenesis are still poorly defined. While multipotent basal stem cells have been found within the myoepithelial compartment, the in vivo lineage potential of luminal progenitors is unclear. Here we used the expression of the Notch1 receptor, previously implicated in mammary gland development and tumorigenesis, to elucidate the hierarchical organization of mammary stem/progenitor cells by lineage tracing. We found that Notch1 expression identifies multipotent stem cells in the embryonic mammary bud, which progressively restrict their lineage potential during mammary ductal morphogenesis to exclusively generate an ERα neg luminal lineage postnatally. Importantly, our results show that Notch1-labelled cells represent the alveolar progenitors that expand during pregnancy and survive multiple successive involutions. This study reveals that postnatal luminal epithelial cells derive from distinct self-sustained lineages that may represent the cells of origin of different breast cancer subtypes.
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  • 60
    Publication Date: 2015-02-18
    Description: by Laura R. González-Ramírez, Omar J. Ahmed, Sydney S. Cash, C. Eugene Wayne, Mark A. Kramer Epilepsy—the condition of recurrent, unprovoked seizures—manifests in brain voltage activity with characteristic spatiotemporal patterns. These patterns include stereotyped semi-rhythmic activity produced by aggregate neuronal populations, and organized spatiotemporal phenomena, including waves. To assess these spatiotemporal patterns, we develop a mathematical model consistent with the observed neuronal population activity and determine analytically the parameter configurations that support traveling wave solutions. We then utilize high-density local field potential data recorded in vivo from human cortex preceding seizure termination from three patients to constrain the model parameters, and propose basic mechanisms that contribute to the observed traveling waves. We conclude that a relatively simple and abstract mathematical model consisting of localized interactions between excitatory cells with slow adaptation captures the quantitative features of wave propagation observed in the human local field potential preceding seizure termination.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 61
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    Publication Date: 2015-02-18
    Description: by Xufeng Fei, Jiaping Wu, Zhe Kong, George Christakos Breast cancer is one of the most commonly diagnosed cancers worldwide. The primary aim of this work is the study of breast cancer disparity among Chinese women in urban vs. rural regions and its associations with socioeconomic factors. Data on breast cancer incidence were obtained from the Chinese cancer registry annual report (2005–2009). The ten socioeconomic factors considered in this study were obtained from the national population 2000 census and the Chinese city/county statistical yearbooks. Student’s T test was used to assess disparities of female breast cancer and socioeconomic factors in urban vs. rural regions. Pearson correlation and ordinary least squares (OLS) models were employed to analyze the relationships between socioeconomic factors and cancer incidence. It was found that the breast cancer incidence was significantly higher in urban than in rural regions. Moreover, in urban regions, breast cancer incidence remained relatively stable, whereas in rural regions it displayed an annual percentage change (APC) of 8.55. Among the various socioeconomic factors considered, breast cancer incidence exhibited higher positive correlations with population density, percentage of non-agriculture population, and second industry output. On the other hand, the incidence was negatively correlated with the percentage of population employed in primary industry. Overall, it was observed that higher socioeconomic status would lead to a higher breast cancer incidence in China. When studying breast cancer etiology, special attention should be paid to environmental pollutants, especially endocrine disruptors produced during industrial activities. Lastly, the present work’s findings strongly recommend giving high priority to the development of a systematic nationwide breast cancer screening program for women in China; with sufficient participation, mammography screening can considerably reduce mortality among women.
    Electronic ISSN: 1932-6203
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  • 62
    Publication Date: 2015-02-18
    Description: by Luying Liu, Xuefang Xu, Lili Jing, Gengyin Zhou, Zhang Cao, Yanchun Han, Rouli Zhou Objective The purpose of this work was to analyze the relationships between the expression status of Lysosomal-associated protein transmembrane-4 beta 35 (LAPTM4B-35) in cancerous tissues and clinicopathological characteristics and prognosis of the patients with gastric carcinoma (GC). Methods The GC samples from 157 patients in a discovery cohort and 148 patients in a testing cohort with follow-up data were used to validate the feasibility of expression of LAPTM4B-35 protein in predicting GC prognosis. Immunohistochemical staining was used to determine the expression of LAPTM4B-35 protein in precancerous gastric lesions and gastric carcinomas. The correlation between the expression of LAPTM4B-35 and clinicopathologic characteristics of patients with gastric carcinoma was analyzed using chi-square test. Univariate and multivariate analyses were performed to determine the association between LAPTM4B-35 expression and prognosis. Results LAPTM4B-35 expression was increased steadily in sequential stages of precancerous gastric lesions. Positive LAPTM4B-35 expression was more frequently detected in patients with distant metastasis ( P = 0.023) and III+IV TNM stages ( P = 0.042) in the discovery cohort. Kaplan-Meier survival curves and univariate analysis showed that expression of LAPTM4B-35 had a significant impact on overall survival of patients with gastric carcinoma in discovery cohort ( P
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  • 63
    Publication Date: 2015-02-18
    Description: by Nabanita Majumder, Faujdar Ram Objectives We examined the overall contributions of the poor and non-poor in fertility decline across the Asian countries. Further, we analyzed the direct and indirect factors that determine the reproductive behaviour of two distinct population sub-groups. Design Data from several new rounds of DHS surveys are available over the past few years. The DHS provides cross-nationally comparable and useful data on fertility, family planning, maternal and child health along with the other information. Six selected Asian countries namely: Bangladesh, India, Indonesia, Nepal, Philippines, and Vietnam are considered for the purpose of the study. Three rounds of DHS surveys for each country (except Vietnam) are considered in the present study. Methods Economic status is measured by computing a “wealth index”, i.e. a composite indicator constructed by aggregating data on asset ownership and housing characteristics using principal components analysis (PCA). Computed household wealth index has been broken into three equal parts (33.3 percent each) and the lowest and the highest 33.3 percent is considered as poor and non-poor respectively. The Bongaarts model was employed to quantify the contribution of each of the proximate determinants of fertility among poor and non-poor women. Results Fertility reduction across all population subgroups is now an established fact despite the diversity in the level of socio-economic development in Asian countries. It is clear from the analysis that fertility has declined irrespective of economic status at varying degrees within and across the countries which can be attributed to the increasing level of contraceptive use especially among poor women. Over the period of time changing marriage pattern and induced abortion are playing an important role in reducing fertility among poor women. Conclusions Fertility decline among majority of the poor women across the Asian countries is accompanied by high prevalence of contraceptive use followed by changing marriage pattern and induced abortion.
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  • 64
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    Publication Date: 2015-02-18
    Description: by Laura Avanzino, Marco Bove, Elisa Pelosin, Carla Ogliastro, Giovanna Lagravinese, Davide Martino It is increasingly clear that we extract patterns of temporal regularity between events to optimize information processing. The ability to extract temporal patterns and regularity of events is referred as temporal expectation. Temporal expectation activates the same cerebral network usually engaged in action selection, comprising cerebellum. However, it is unclear whether the cerebellum is directly involved in temporal expectation, when timing information is processed to make predictions on the outcome of a motor act. Healthy volunteers received one session of either active (inhibitory, 1Hz) or sham repetitive transcranial magnetic stimulation covering the right lateral cerebellum prior the execution of a temporal expectation task. Subjects were asked to predict the end of a visually perceived human body motion (right hand handwriting) and of an inanimate object motion (a moving circle reaching a target). Videos representing movements were shown in full; the actual tasks consisted of watching the same videos, but interrupted after a variable interval from its onset by a dark interval of variable duration. During the ‘dark’ interval, subjects were asked to indicate when the movement represented in the video reached its end by clicking on the spacebar of the keyboard. Performance on the timing task was analyzed measuring the absolute value of timing error, the coefficient of variability and the percentage of anticipation responses. The active group exhibited greater absolute timing error compared with the sham group only in the human body motion task. Our findings suggest that the cerebellum is engaged in cognitive and perceptual domains that are strictly connected to motor control.
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  • 65
    Publication Date: 2015-02-18
    Description: by Jin-Ju Jeong, Kyung-Ah Kim, Se-Eun Jang, Jae-Yeon Woo, Myung Joo Han, Dong-Hyun Kim To evaluate the anti-inflammaging effect of lactic acid bacteria (LAB) on age-dependent inflammation, we first screened and selected a tumor necrosis factor (TNF)-α and reactive oxygen species (ROS)-inhibitory LAB, Lactobacillus pentosus var. plantarum C29, among the LABs isolated from fermented vegetables using LPS-stimulated mouse peritoneal macrophages. Oral administration of C29 (2 × 10 9 CFU/rat) for 8 weeks in aged Fischer 344 rats (age, 16 months) inhibited the expression of the inflammatory markers myeloperoxidase, inducible nitric oxide (NO) synthase, cyclooxygenase-2, pro-inflammatory cytokines tumor necrosis factor (TNF)-α and IL-6 and the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), activator protein 1 (AP1), and mitogen-activated protein kinases (MAPKs). Treatment with C29 induced the expression of tight junction proteins ZO-1, occludin, and claudin-1, and reduced intestinal microbial LPS and plasmatic LPS levels and ROS, as well as the Firmicutes to Bacteroidetes ratio, which is significantly higher in aged rats than in young rats. C29 treatment also reduced plasmatic reactive oxygen species, malondialdehyde, C-reactive protein, and TNF-α, and suppressed expression of senescence markers p16 and p53 in the colon of the aged rats, but increased SIRT 1 expression. Based on these findings, we concluded that C29 treatment may suppress aging-dependent colitis by inhibiting NF-κB, AP1, and MAPK activation via the inhibition of gut microbiota LPS production and the induction of tight junction protein expression.
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  • 66
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    Publication Date: 2015-02-18
    Description: by Jon P. Costanzo, Alice M. Reynolds, M. Clara F. do Amaral, Andrew J. Rosendale, Richard E. Lee Wood frogs ( Rana sylvatica ) exhibit marked geographic variation in freeze tolerance, with subarctic populations tolerating experimental freezing to temperatures at least 10-13 degrees Celsius below the lethal limits for conspecifics from more temperate locales. We determined how seasonal responses enhance the cryoprotectant system in these northern frogs, and also investigated their physiological responses to somatic freezing at extreme temperatures. Alaskan frogs collected in late summer had plasma urea levels near 10 μmol ml -1 , but this level rose during preparation for winter to 85.5 ± 2.9 μmol ml -1 (mean ± SEM) in frogs that remained fully hydrated, and to 186.9 ± 12.4 μmol ml -1 in frogs held under a restricted moisture regime. An osmolality gap indicated that the plasma of winter-conditioned frogs contained an as yet unidentified osmolyte(s) that contributed about 75 mOsmol kg -1 to total osmotic pressure. Experimental freezing to –8°C, either directly or following three cycles of freezing/thawing between –4 and 0°C, or –16°C increased the liver’s synthesis of glucose and, to a lesser extent, urea. Concomitantly, organs shed up to one-half (skeletal muscle) or two-thirds (liver) of their water, with cryoprotectant in the remaining fluid reaching concentrations as high as 0.2 and 2.1 M, respectively. Freeze/thaw cycling, which was readily survived by winter-conditioned frogs, greatly increased hepatic glycogenolysis and delivery of glucose (but not urea) to skeletal muscle. We conclude that cryoprotectant accrual in anticipation of and in response to freezing have been greatly enhanced and contribute to extreme freeze tolerance in northern R. sylvatica .
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Shunyao Wu, Fengjing Shao, Jun Ji, Rencheng Sun, Rizhuang Dong, Yuanke Zhou, Shaojie Xu, Yi Sui, Jianlong Hu Based on the hypothesis that the neighbors of disease genes trend to cause similar diseases, network-based methods for disease prediction have received increasing attention. Taking full advantage of network structure, the performance of global distance measurements is generally superior to local distance measurements. However, some problems exist in the global distance measurements. For example, global distance measurements may mistake non-disease hub proteins that have dense interactions with known disease proteins for potential disease proteins. To find a new method to avoid the aforementioned problem, we analyzed the differences between disease proteins and other proteins by using essential proteins (proteins encoded by essential genes) as references. We find that disease proteins are not well connected with essential proteins in the protein interaction networks. Based on this new finding, we proposed a novel strategy for gene prioritization based on protein interaction networks. We allocated positive flow to disease genes and negative flow to essential genes, and adopted network propagation for gene prioritization. Experimental results on 110 diseases verified the effectiveness and potential of the proposed method.
    Electronic ISSN: 1932-6203
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    Publication Date: 2015-02-18
    Description: by Qiudong Su, Yao Yi, Feng Qiu, Xuexin Lu, Junying Ding, Zhiyuan Jia, Ruiguang Tian, Yan Gao, Shengli Bi Background Hepatitis B vaccine that contains an aluminum hydroxide adjuvant induces apoptotic death of Hepa 1–6 cells. Difficult-to-degrade chemical additives in vaccines effectively enhance vaccine immunogenicity, but also affect the host tissue. Identification of bio-molecules that are readily degraded and compatible in vivo as an adjuvant is important for vaccine research. The hapten–carrier effect suggests that stimulation of helper T (Th) cells by carrier adjuvants is feasible. Protein D (PD) of non-typeable Haemophilus influenzae covalently conjugated to some polysaccharide vaccines has been confirmed to convert T-cell independent (TI) antigens into T-cell dependent (TD) antigens, and elicit strong T-cell responses ultimately. Herein, we would substitube PD for aluminum hydroxide adjuvant in Hepatitis B vaccine. Methods and results Truncated PD (amino acids 20–364) was expressed in Escherichia coli and purified by (NH 4 ) 2 SO 4 precipitation and DEAE chromatography. After evaluation of antigenicity by western blotting, PD was covalently conjugated to yeast-derived recombinant HBsAg by cross-linking with glutaraldehyde. Intramuscular immunization with the conjugate induced higher level of HBsAg-specific antibody than did HBsAg alone ( p 〈 0.05), and was comparable to commercial Hepatitis B vaccine. During the surveillance period (days 35–105), anti-HBs titers were hold high. Moreover, the conjugated vaccine enhanced Th1 immune responses, while Th2 responses were also activated and induced an antibody response, as determined by IFN-γ ELISPOT and IgG1/IgG2a ratio assays. Conclusions Recombinant truncated PD covalently conjugated to HBsAg antigen enhanced the immunogenicity of the antigen in mice simultaneously by humoral and cellular immune response, which would facilitate therapeutic hepatitis B vaccines.
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    Publication Date: 2015-02-18
    Description: by Yu-Yen Chen, Dachen Chu, Pesus Chou Purpose To distinguish the frequently misdiagnosed plateau iris eyes from pupillary block group and normal group, we compared the ocular biometrical parameters of them by A-scan ultrasongraphy. Methods In total, we retrospectively reviewed general characteristics and ocular findings including ocular biometric measurements of 71 normal, 39 plateau iris, and 83 pupillary block eyes. Results The normal controls, plateau iris group and pupillary block group were significantly different in age, but not in gender. The anterior chamber depth tended to decrease and the lens thickness tended to increase from normal to plateau iris to pupillary block eyes. Compared to those of plateau iris group, the pupillary block group had significantly shallower anterior chamber depth (2.90mm vs. 2.33mm; p
    Electronic ISSN: 1932-6203
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    Publication Date: 2015-02-18
    Description: by Fernanda de Oliveira Demitto, Renata Claro Ribeiro do Amaral, Flaviane Granero Maltempe, Vera Lúcia Dias Siqueira, Regiane Bertin de Lima Scodro, Mariana Aparecida Lopes, Katiany R. Caleffi-Ferracioli, Pedro Henrique Canezin, Rosilene Fressatti Cardoso The aim of the present study was to evaluate the effect of the combination of rifampicin (RIF) and verapamil (VP) against the Mycobacterium tuberculosis H 37 Rv reference strain and six multidrug-resistant (MDR) M. tuberculosis clinical isolates by determining Time-Kill Curves and the ability to efflux drug by fluorometry. The RIF+VP combination showed synergism in one MDR clinical isolate. For the other five MDR clinical isolates, the drug combination showed no interaction. The MDR clinical isolate had lower ethidium bromide (EtBr) accumulation when exposed to the RIF+VP combination, compared with RIF and VP exposure alone. The other MDR clinical isolates showed no significant difference in EtBr accumulation. These results suggest greater efflux action in one of the MDR clinical isolates compared with the M. tuberculosis H 37 Rv reference strain. The other five MDR isolates may have additional mechanisms of drug resistance to RIF. The use of the RIF+VP combination made one MDR bacillus more susceptible to RIF probably by inhibiting efflux pumps, and this combination therapy, in some cases, may contribute to a reduction of resistance to RIF in M. tuberculosis .
    Electronic ISSN: 1932-6203
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by He Cheng, Han Zheng, Jia Xin Wu, Wei Xu, Lihan Zhou, Kam Chew Leong, Eugene Fitzgerald, Raj Rajagopalan, Heng Phon Too, Wee Kiong Choi We demonstrated the surface functionalization of a highly three-dimensional, superhydrophilic wicking substrate using light to immobilize functional biomolecules for sensor or microarray applications. We showed here that the three-dimensional substrate was compatible with photo-attachment and the performance of functionalization was greatly improved due to both increased surface capacity and reduced substrate reflectivity. In addition, photo-attachment circumvents the problems induced by wicking effect that was typically encountered on superhydrophilic three-dimensional substrates, thus reducing the difficulty of producing miniaturized sites on such substrate. We have investigated various aspects of photo-attachment process on the nanowire substrate, including the role of different buffers, the effect of wavelength as well as how changing probe structure may affect the functionalization process. We demonstrated that substrate fabrication and functionalization can be achieved with processes compatible with microelectronics processes, hence reducing the cost of array fabrication. Such functionalization method coupled with the high capacity surface makes the substrate an ideal candidate for sensor or microarray for sensitive detection of target analytes.
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Li Li, Nabeel Hamzeh, May Gillespie, Jill Elliott, Jieru Wang, Eva Brigitte Gottschall, Peggy M. Mroz, Lisa A. Maier CD14 dim CD16+ and CD14 bright CD16+ cells, which compose a minor population of monocytes in human peripheral blood mononuclear cells (PBMC), have been implicated in several inflammatory diseases. The aim of this study was to investigate whether this phenotype was present as a subset of lung infiltrative alveolar macrophages (AMs) in the granulomatous lung disease, chronic beryllium disease (CBD). The monocytes subsets was determined from PBMC cells and bronchoalveolar lavage (BAL) cells from CBD, beryllium sensitized Non-smoker (BeS-NS) and healthy subjects (HS) using flow cytometry. The impact of smoking on the AMs cell phenotype was determined by using BAL cells from BeS smokers (BeS-S). In comparison with the other monocyte subpopulations, CD14 dim CD16+ cells were at decreased frequency in PBMCs of both BeS-NS and CBD and showed higher HLA-DR expression, compared to HS. The AMs from CBD and BeS-NS demonstrated a CD14 dim CD16+phenotype, while CD14 bright CD16+ cells were found at increased frequency in AMs of BeS, compared to HS. Fresh AMs from BeS-NS and CBD demonstrated significantly greater CD16, CD40, CD86 and HLA-DR than HS and BeS-S. The expression of CD16 on AMs from both CBD and BeS-NS was downregulated significantly after 10μM BeSO 4 stimulation. The phagocytic activity of AMs decreased after 10μM BeSO 4 treatment in both BeS-NS and CBD, although was altered or reduced in HS and BeS-S. These results suggest that Be increases the CD14 dim CD16+ subsets in the lung of CBD subjects. We speculate that Be-stimulates the compartmentalization of a more mature CD16+ macrophage phenotype and that in turn these macrophages are a source of Th1 cytokines and chemokines that perpetuate the Be immune response in CBD. The protective effect of cigarette smoking in BeS-S may be due to the low expression of co-stimulatory markers on AMs from smokers as well as the decreased phagocytic function.
    Electronic ISSN: 1932-6203
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Matthew R. McCann, Priya Patel, Agya Frimpong, Yizhi Xiao, Walter L. Siqueira, Cheryle A. Séguin Low back pain is the most common musculoskeletal problem and the single most common cause of disability, often attributed to degeneration of the intervertebral disc. Lack of effective treatment is directly related to our limited understanding of the pathways responsible for maintaining disc health. While transcriptional analysis has permitted initial insights into the biology of the intervertebral disc, complete proteomic characterization is required. We therefore employed liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) protein/peptide separation and mass spectrometric analyses to characterize the protein content of intervertebral discs from skeletally mature wild-type mice. A total of 1360 proteins were identified and categorized using PANTHER. Identified proteins were primarily intracellular/plasma membrane (35%), organelle (30%), macromolecular complex (10%), extracellular region (9%). Molecular function categorization resulted in three distinct categories: catalytic activity (33%), binding (molecule interactions) (29%), and structural activity (13%). To validate our list, we confirmed the presence of 14 of 20 previously identified IVD-associated markers, including matrix proteins, transcriptional regulators, and secreted proteins. Immunohistochemical analysis confirmed distinct localization patterns of select protein with the intervertebral disc. Characterization of the protein composition of healthy intervertebral disc tissue is an important first step in identifying cellular processes and pathways disrupted during aging or disease progression.
    Electronic ISSN: 1932-6203
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  • 74
    Publication Date: 2015-02-18
    Description: by Cheol Woong Jeong, Guen Tae Park, Hyein Yun, Tzung-Fu Hsieh, Yang Do Choi, Yeonhee Choi, Jong Seob Lee Genomic imprinting, an epigenetic process in mammals and flowering plants, refers to the differential expression of alleles of the same genes in a parent-of-origin-specific manner. In Arabidopsis , imprinting occurs primarily in the endosperm, which nourishes the developing embryo. Recent high-throughput sequencing analyses revealed that more than 200 loci are imprinted in Arabidopsis ; however, only a few of these imprinted genes and their imprinting mechanisms have been examined in detail. Whereas most imprinted loci characterized to date are maternally expressed imprinted genes (MEGs), PHERES1 ( PHE1 ) and ADMETOS ( ADM ) are paternally expressed imprinted genes (PEGs). Here, we report that UPWARD CURLY LEAF1 ( UCL1 ), a gene encoding an E3 ligase that degrades the CURLY LEAF (CLF) polycomb protein, is a PEG. After fertilization, paternally inherited UCL1 is expressed in the endosperm, but not in the embryo. The expression pattern of a β-glucuronidase ( GUS ) reporter gene driven by the UCL1 promoter suggests that the imprinting control region (ICR) of UCL1 is adjacent to a transposable element in the UCL1 5′-upstream region. Polycomb Repressive Complex 2 (PRC2) silences the maternal UCL1 allele in the central cell prior to fertilization and in the endosperm after fertilization. The UCL1 imprinting pattern was not affected in paternal PRC2 mutants. We found unexpectedly that the maternal UCL1 allele is reactivated in the endosperm of Arabidopsis lines with mutations in cytosine DNA METHYLTRANSFERASE 1 ( MET1 ) or the DNA glycosylase DEMETER ( DME ), which antagonistically regulate CpG methylation of DNA. By contrast, maternal UCL1 silencing was not altered in mutants with defects in non-CpG methylation. Thus, silencing of the maternal UCL1 allele is regulated by both MET1 and DME as well as by PRC2, suggesting that divergent mechanisms for the regulation of PEGs evolved in Arabidopsis .
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    Publication Date: 2015-02-18
    Description: by Saharnaz Bigdeli, Roger O. Dettloff, Curtis W. Frank, Ronald W. Davis, Laurel D. Crosby Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA) or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides . This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated cells in common bulk reactions, although further work must be done to improve the amplification coverage of single genomes.
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    Public Library of Science (PLoS)
    Publication Date: 2015-02-18
    Description: by Maïtena R. N. Jean, Silvina Gonzalez-Rizzo, Pauline Gauffre-Autelin, Sabine K. Lengger, Stefan Schouten, Olivier Gros Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperate waters, as well as hydrothermal vents, where they form dense mats on the floor. However, they have never been described in tropical marine mangroves. Here, we describe two new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangrove roots. We combined phylogenetic and lipid analysis with electron microscopy in order to describe these organisms. Furthermore, oxygen and sulphide measurements in and ex situ were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as Candidatus Maribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves.
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    Publication Date: 2015-02-18
    Description: by Francesca Prandi, Marco Piola, Monica Soncini, Claudia Colussi, Yuri D’Alessandra, Eleonora Penza, Marco Agrifoglio, Maria Cristina Vinci, Gianluca Polvani, Carlo Gaetano, Gianfranco Beniamino Fiore, Maurizio Pesce Saphenous vein graft disease is a timely problem in coronary artery bypass grafting. Indeed, after exposure of the vein to arterial blood flow, a progressive modification in the wall begins, due to proliferation of smooth muscle cells in the intima. As a consequence, the graft progressively occludes and this leads to recurrent ischemia. In the present study we employed a novel ex vivo culture system to assess the biological effects of arterial-like pressure on the human saphenous vein structure and physiology, and to compare the results to those achieved in the presence of a constant low pressure and flow mimicking the physiologic vein perfusion. While under both conditions we found an activation of Matrix Metallo-Proteases 2/9 and of microRNAs-21/146a/221, a specific effect of the arterial-like pressure was observed. This consisted in a marked geometrical remodeling, in the suppression of Tissue Inhibitor of Metallo-Protease-1, in the enhanced expression of TGF-β1 and BMP-2 mRNAs and, finally, in the upregulation of microRNAs-138/200b/200c. In addition, the veins exposed to arterial-like pressure showed an increase in the density of the adventitial vasa vasorum and of cells co-expressing NG2, CD44 and SM22α markers in the adventitia. Cells with nuclear expression of Sox-10, a transcription factor characterizing multipotent vascular stem cells, were finally found in adventitial vessels. Our findings suggest, for the first time, a role of arterial-like wall strain in the activation of pro -pathologic pathways resulting in adventitial vessels growth, activation of vasa vasorum cells, and upregulation of specific gene products associated to vascular remodeling and inflammation.
    Electronic ISSN: 1932-6203
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    Publication Date: 2015-02-18
    Description: by Xinxing Lu, Qiuling Fan, Li Xu, Lin Li, Yuan Yue, Yanyan Xu, Yan Su, Dongcheng Zhang, Lining Wang Objective To investigate the effect of ursolic acid on autophagy mediated through the miRNA-21-targeted phosphoinositide 3 kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) pathway in rat mesangial cells cultured under high glucose (HG) conditions. Methods Rat glomerular mesangial cells were cultured under normal glucose, HG, HG with the PI3K inhibitor LY294002 or HG with ursolic acid conditions. Cell proliferation and hypertrophy were assayed using an MTT assay and the ratio of total protein to cell number, respectively. The miRNA-21 expression was detected using RT-qPCR. The expression of phosphatase and tensin homolog (PTEN)/AKT/mTOR signaling signatures, autophagy-associated protein and collagen I was detected by western blotting and RT-qPCR. Autophagosomes were observed using electron microscopy. Results Compared with mesangial cells cultured under normal glucose conditions, the cells exposed to HG showed up-regulated miRNA-21 expression, down-regulated PTEN protein and mRNA expression, up-regulated p85PI3K, pAkt, pmTOR, p62/SQSTMI, and collagen I expression and down-regulated LC3II expression. Ursolic acid and LY294002 inhibited HG-induced mesangial cell hypertrophy and proliferation, down-regulated p85PI3K, pAkt, pmTOR, p62/SQSTMI, and collagen I expression and up-regulated LC3II expression. However, LY294002 did not affect the expression of miRNA-21 and PTEN. Ursolic acid down-regulated miRNA-21 expression and up-regulated PTEN protein and mRNA expression. Conclusions Ursolic acid inhibits the glucose-induced up-regulation of mesangial cell miRNA-21 expression, up-regulates PTEN expression, inhibits the activation of PI3K/Akt/mTOR signaling pathway, and enhances autophagy to reduce the accumulation of the extracellular matrix and ameliorate cell hypertrophy and proliferation.
    Electronic ISSN: 1932-6203
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    Publication Date: 2015-02-18
    Description: by Julia Fiona-Maree Gilmartin, Saku Väätäinen, Soili Törmälehto, J. Simon Bell, Eija Lönnroos, Lotta Salo, Ilona Hallikainen, Janne Martikainen, Anne M. Koivisto, the ALSOVA Study Group Neuropsychiatric symptoms of Alzheimer’s disease (AD) such as depression may be associated with pain, which according to the literature may be inadequately recognized and managed in this population. This study aimed to identify the factors associated with analgesic use in persons with AD; in particular, how AD severity, functional status, neuropsychiatric symptoms of AD, co-morbidities and somatic symptoms are associated with analgesic use. 236 community-dwelling persons with very mild or mild AD at baseline, and their caregivers, were interviewed over five years as part of the prospective ALSOVA study. Generalized Estimating Equations (GEEs) were used to estimate unadjusted and adjusted odds ratios (ORs) for the factors associated with analgesic use over a five year follow-up. The proportion of persons with AD using any analgesic was low (13.6%) at baseline and remained relatively constant during the follow-up (15.3% at Year 5). Over time, the most prevalent analgesic changed from non-steroidal anti-inflammatories (8.1% of persons with AD at Year 1) to acetaminophen (11.1% at Year 5). Depressive symptoms (measured by the Beck Depression Inventory, BDI) were independently associated with analgesic use, after effects of age, gender, education, AD severity, comorbidities and somatic symptoms were taken into account. For every one unit increase in BDI, the odds of analgesic use increased by 4% (OR = 1.04, 95% confidence interval CI = 1.02-1.07). Caregiver depressive symptoms were not statistically significantly associated with analgesic use of the person with AD. Depressive symptoms were significantly associated with analgesic use during the five year follow-up period. Possible explanations warranting investigation are that persons with AD may express depressive symptoms as painful somatic complaints, or untreated pain may cause depressive symptoms. Greater awareness of the association between depressive symptoms and analgesic use may lead to safer and more effective prescribing for these conditions.
    Electronic ISSN: 1932-6203
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    Publication Date: 2015-02-18
    Description: by Lin Hu, Yu-hong Xiao, Ming Fang, Yu Gao, Li Huang, An-qi Jia, Ji-hua Chen Objective This study was designed to evaluate the effects of type I collagen degradation on the durability of three adhesive systems in the early phase of dentin bonding. Methods Bonded dentin specimens were prepared using three different types of adhesive systems. Micro-tensile bond strength and degradation of collagen were tested before, and after 1 month or 4 months of aging in artificial saliva. The relationship between micro-tensile bond strength and collagen degradation was analyzed by calculating their Pearson’s correlation coefficient. Results Aging induced time-dependent reduction in micro-tensile bond strengths for all the tested adhesive systems, although such reduction for the single-step self-etching adhesive G-Bond (GB) was not statistically significant. The bond strength of the two-step self-etching primer adhesive system Clearfil SE Bond (SEB) was similar to that of the two-step etch-and-rinse self-priming adhesive system Single Bond 2 (SB), and they were both significantly reduced after one or four months of aging. A negative correlation was found between the degree of collagen degradation and magnitude of micro-tensile bond strength ( r = - 0.65, p = 0.003). The Pearson’s correlation coefficient was 0.426, indicating that 42.6% of the aging-induced reduction in bond strength can be explained by the degradation of collagen. Conclusions In the early phase of dentin bonding, there was a negative correlation between the degree of collagen degradation and the magnitude of micro-tensile bond strength. The reduction of bond strength was accompanied by the degradation of collagen. These results provide evidence for the causative relationship between the degradation of collagen and the deterioration of dentin-adhesive interface.
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