bluuebunny/crossref_metadata_2025_split huggingface dataset:
High admixture between forest an cultivated chestnut (Castanea sativaMill.) in France
Authors: Bouffartigue Cathy , Debille Sandrine , Fabreguette Olivier , Ramos Cabrer Ana , Pereira-Lorenzo Santiago , Flutre Timothée , Harvengt Luc 
Published: October 2019

ABSTRACTContextRenewed interest in European chestnut in France is focused on finding locally adapted populations partially resistant to ink disease and identifying local landraces.AimsWe genotyped trees to assess (i) the genetic diversity of wild and cultivated chestnut across most of its range in France, (ii) their genetic structure, notably in relation with the sampled regions, and (iii) relations with its neighbors in Spain and Italy.MethodsA total of 693 trees in 16 sampling regions in France were genotyped at 24 SSRs, and 1,401 trees in 17 sampling regions at 13 SSRs.ResultsGenetic diversity was high in most sampling regions, with redundancy between them. No significant differentiation was found between wild and cultivated chestnut. A genetic structure analysis with noa prioriinformation found a low, yet significant structure, and identified two clusters. One cluster gathers trees from south-east France and Corsica (RPP1) and another cluster gathers trees from all other sampled regions (RPP2). A substructure was detected at 13 SSRs suggesting differentiation within both RPP1 and RPP2. RPP1 was split between south-east France and Corsica. RPP2 was split between north-west France, Aveyron, Pyrenees and a last cluster gathering individuals from several other regions.ConclusionThe genetic structure within and between our sampling regions is likely the result of natural events (recolonization after the last glaciation) and human activities (migration and exchanges). Notably, we provide evidence for a common origin of most French and Iberian chestnut trees, except those from south-east France that were associated with the Italian gene pool. This advances our knowledge of chestnut genetic diversity and structure, will benefit conservation and help our local partners’ valorization efforts.
Determinants of telomere length across human tissues
Authors: Demanelis Kathryn , Jasmine Farzana , Chen Lin S. , Chernoff Meytal , Tong Lin , Shinkle Justin , Sabarinathan Mekala , Lin Hannah , Ramirez Eduardo , Oliva Meritxell , Kim-Hellmuth Sarah , Stranger Barbara E. , Ardlie Kristin G. , Aguet François , Ahsan Habibul ,   GTEx Consortium, Doherty Jennifer , Kibriya Muhammad G. , Pierce Brandon L. 
Published: October 2019

ABSTRACTTelomere shortening is a hallmark of aging. Telomere length (TL) in blood cells has been studied extensively as a biomarker of human aging and disease; however, little is known regarding variability in TL in non-blood, disease-relevant tissue types. Here we characterize variability in TL measurements for 6,391 tissue samples, representing >20 tissue types and 952 individuals from the Genotype-Tissue Expression (GTEx) Project. We describe differences across tissue types, positive correlation among tissue types, and associations with age and ancestry. We show that genetic variation impacts TL in multiple tissue types, and that TL can mediate the effect of age on gene expression. Our results provide the foundational knowledge regarding TL in healthy tissues that is needed to interpret epidemiological studies of TL and human health.ONE SENTENCE SUMMARYTelomere length varies by tissue type but is generally correlated among tissue types (positively) and with age (negatively).
Physical fitness in community dwelling older adults is linked to dietary intake, gut microbiota and metabolomic signatures
Authors: Castro-Mejía Josué L. , Khakimov Bekzod , Krych Łukasz , Bülow Jacob , Bechshøft Rasmus L. , Højfeldt Grith , Mertz Kenneth H. , Garne Eva Stahl , Schacht Simon R. , Ahmad Hajar F. , Kot Witold , Hansen Lars H. , Perez-Cueto Federico J. A. , Lind Mads V. , Lassen Aske J. , Tetens Inge , Jensen Tenna , Reitelseder Søren , Jespersen Astrid P. , Holm Lars , Engelsen Søren B. , Nielsen Dennis S. 
Published: October 2019

AbstractWhen humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.
Representation of Task Structure in Human Hippocampus and Orbitofrontal Cortex
Authors: Mizrak Eda , Bouffard Nichole R. , Libby Laura A. , Boorman Erie , Ranganath Charan 
Published: October 2019

ABSTRACTThe hippocampus is thought to support episodic memory, or memory for specific events, but recent work also suggests that it may be involved in extracting structure from the world to guide future decisions and predictions. Recent evidence in rodents suggests that the hippocampus supports decision-making in cooperation with orbitofrontal cortex (OFC), possibly based on representation of task structure. Here, we used functional magnetic resonance imaging (fMRI) to test how the human hippocampus and OFC represents decision-relevant information extracted from previous experiences. Participants performed a task in which they learned values of different foods in grocery store contexts. The task was structured such that we could examine the degree to which neural representations could reflect generalized information about different task structures. Specifically, we manipulated whether a food’s desirability varied with store context or not. Some foods were desirable in some store contexts and not in others; some foods were always desirable or undesirable. Participants needed to extract these two task sub-structures (i.e., context-determined vs. context-invariant) from the task structure. We examined hippocampal and OFC activity patterns during a decision-making task after participants were trained with the task structure. Our results showed that both hippocampus and OFC carried task structure information that was relevant to the decision outcomes. Hippocampal and lateral OFC representations differentiated between context-determined (deterministic) and context-invariant (probabilistic) task structures. The degree of this differentiation, an index of task structure representation, was highly correlated between hippocampus and lateral OFC. These results add to a mounting evidence suggesting that the hippocampus and OFC support decision-making by representing task relevant information to the decision outcomes after the task structure is learned.
Venlafaxine stimulates an MMP-9-dependent increase in excitatory/inhibitory balance in a stress model of depression
Authors: Alaiyed Seham , McCann Mondona , Mahajan Gouri , Rajkowska Grazyna , Stockmeier Craig A. , Kellar Kenneth J. , Wu Jian Young , Conant Katherine 
Published: October 2019

AbstractEmerging evidence suggests that there is a reduction in overall cortical excitatory to inhibitory balance in major depressive disorder (MDD), which afflicts approximately 14-20% of individuals. Reduced pyramidal cell arborization occurs with stress and MDD, and may diminish excitatory neurotransmission. Enhanced deposition of perineuronal net (PNN) components also occurs with stress. Since parvalbumin-expressing interneurons are the predominant cell population that is enveloped by PNNs, which enhance their ability to release GABA, excess PNN deposition likely increases pyramidal cell inhibition. In the present study we investigate the potential for matrix metalloprotease-9 (MMP-9), an endopeptidase secreted in response to neuronal activity, to contribute to the antidepressant efficacy of venlafaxine, a serotonin/norepinephrine reuptake inhibitor. Chronic venlafaxine increases MMP-9 levels in murine cortex, and increases both pyramidal cell arborization and PSD-95 expression in the cortex of wild-type but not MMP-9 null mice. We have previously shown that venlafaxine reduces PNN deposition and increases the power ofex vivogamma oscillations in conventionally-housed mice. Gamma power is increased with pyramidal cell disinhibition and with remission from MDD. Herein we observe that PNN expression is increased in a corticosterone-induced stress model of disease and reduced by venlafaxine. As compared to mice that receive concurrent venlafaxine, corticosterone treated mice also display reducedex vivogamma power and impaired working memory. Autopsy-derived prefrontal cortex samples show elevated MMP-9 levels in anti-depressant treated MDD patients as compared to controls. These preclinical and postmortem findings highlight a link between extracellular matrix regulation and MDD.
Senescence and entrenchment in evolution of amino acid sites
Authors: Stolyarova A. V. , Nabieva E. , Ptushenko V. V. , Favorov A. V. , Popova A. V. , Neverov A. D. , Bazykin G. A. 
Published: October 2019

AbstractAmino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome; alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: its fitness tends to increase with the time since its origin due to epistasis (“entrenchment”), but to decrease due to random environmental fluctuations (“senescence”). We analyse the phylogenetic distribution of substitutions in nuclear genomes, and show that among the amino acids originating at negatively selected sites of vertebrates, nearly all experience strong entrenchment. By contrast, among the amino acids originating at positively selected sites, 18% experience senescence. A similar pattern is observed in phylogenies of insects. We propose that senescence of the current allele is a cause of adaptive evolution.
Orbitofrontal control of visual cortex gain promotes visual associative learning
Authors: Liu Dechen , Deng Juan , Zhang Zhewei , Zhang Zhi-Yu , Sun Yan-Gang , Yang Tianming , Yao Haishan 
Published: October 2019

AbstractThe orbitofrontal cortex (OFC) encodes expected outcomes and plays a critical role in flexible, outcome-guided behavior. The OFC projects to primary visual cortex (V1), yet the function of this top-down projection is unclear. We find that optogenetic activation of OFC projection to V1 reduces the amplitude of V1 visual responses via the recruitment of local somatostatin-expressing (SST) interneurons. Using mice performing a Go/No-Go visual task, we show that the OFC projection to V1 mediates the outcome-expectancy modulation of V1 responses to the reward-irrelevant No-Go stimulus. Furthermore, V1-projecting OFC neurons reduce firing during expectation of reward. In addition, chronic optogenetic inactivation of OFC projection to V1 impairs, whereas chronic activation of SST interneurons in V1 improves the learning of Go/No-Go visual task, without affecting the immediate performance. Thus, OFC top-down projection to V1 is crucial to drive visual associative learning by modulating the response gain of V1 neurons to non-relevant stimulus.
Introducing ExHiBITT – Exploring Host microbiome inTeractions in Twins-, a colon multiomic cohort study
Authors: Mora-Ortiz Marina , Ibraheim Hajir , Kottoor Sherine Hermangild , Bowyer Ruth C. E. , Metrustry Sarah , Sanderson Jeremy , Powell Nicholas , Spector Tim D. , Small Kerrin S. , Steves Claire J. 
Published: October 2019

AbstractThe colon is populated by approximately 1012 microorganisms, but the relationships between this microbiome and the host health status are still not completely understood. Participants from the TwinsUK cohort were recruited to study the interactions between the microbiome and host adaptive immunity. In total, 205 monozygotic twins were recruited from the wider TwinsUK cohort. They completed health questionnaires, and provided saliva, blood, colon biopsies from three different locations, caecal fluid, and two faecal-samples.Here, our objective is to present the cohort characteristics of ExHiBITT including i) biomedical phenotypes, ii) environmental factors and ii) colonoscopic findings. A significant proportion of this apparently normal cohort had colonic polyps (28%), which are of interest as potential precursors of colorectal cancer, and as expected, the number of polyps found was significantly correlated with BMI and age. Hitherto undiagnosed diverticulosis was also not infrequently found during colonoscopy (26%) and was associated in changes in Hybrid Th1-17 cells in the colon. Twin proband cooccurrence rate for diverticulosis (82%), was much higher than for polyps (42%). Familial factors affecting morphology or tolerance may contribute to the ease of endoscopy, as both the time to reach the caecum, and pain perceived were highly concordant (proband concordance: 85% and 56% respectively). We found the expected positive relationship between BMI and colonoscopic anomalies such as diverticular disease and polyps in the whole population, but within twin pairs this association was reversed. This suggests that familial factors confound these associations. Host and microbial Next Generation Sequencing and metabolomics of the samples collected are planned in this cohort.
GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations
Authors: Manchanda Nancy , Portwood John L. , Woodhouse Margaret R. , Seetharam Arun S. , Lawrence-Dill Carolyn J. , Andorf Carson M. , Hufford Matthew B. 
Published: October 2019

AbstractBackgroundGenome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.FindingsOur application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.ConclusionsThe GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license.All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
Architectural analyses of tree forking habit with single-image photogrammetry: a case study of post-mature temperate oaks
Authors: Kędra Kamil 
Published: October 2019

AbstractTree forking is both ecologically and economically relevant, but remains much understudied. Here, thirty post-mature temperate oaks (Quercus robur or Q. petraea) forking habit was both qualitatively and quantitatively analysed with the single-image photogrammetry (SIP), in a north-exposed mixed, deciduous forest remnant (near Krakow; Poland). A new classification of mature oak architectures was proposed, based on the original Hallé-Oldeman model, with modified locations of the main branches and presence or absence of bifurcation in the main stem. Two of the new classes were most clearly represented by the studied oaks. It was found that the trees tended to either keep branches at varying heights, with no forks, or to iterate forking, with no major (non-fork) branches below the first fork. The quantitative analysis confirmed the applicability of the branch to parent stem diameter ratio to define a fork. Branching ratio was positively correlated with both tree diameter and height of a branch above the ground, which is consistent with a previous study, based on much younger trees. It is concluded, that most probably the tree-level factors and phenomena, such as water supplies and posture control, played the key role in the studied oaks forking habit. The SIP method enabled valuable insights into the large oaks’ forking, both at the tree and branch levels, and may be further employed to study mature trees’ bifurcation patterns. Based on this study, some possible improvements to the methodology were discussed.
Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach
Authors: Hassan Ali Asma Ali , Abdalla Mohamed Sahar Abdeen , Omer Musa Marwa Abdulrahman , Bushra ELtahier Amani Faisal , Abdelrahman Ali Walaa Mohammed Alsamani , Ali Ibrahim Elaf Ahmed Mohammed , Hamdi Ahmed , Hassan Mohamed A. 
Published: October 2019

AbstractAichi virus, AiV is single stranded negative sense RNA genome belonging to the genusKobuviru, a family ofPicornaviridaethat causes severe gastroenteritis. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immunoinformatic approaches to analyze the viral Protein VP1 of AiV-1 strain, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 38 Aichi virus VP1 retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell was (PLPPDT, PPLPTP, and LPPLPTP). For T cell, two epitopes showed high affinity to MHC class I (FSIPYTSPL and TMVSFSIPY) and high coverage against the whole world population. Also, in MHC class II, three epitopes that interact with most frequent MHC class II alleles (FTYIAADLR and YMAEVPVSA) with high coverage in the whole world population. For both MHCI and MHCII the T-cell peptide with the strongest affinity to the worldwide population was FSIPYTSPL.Peptide vaccine against AiV is powerfully displace the normal produced vaccines based on the experimental biochemistry tools, as it designed to handle with a wide range of mutated strains, which will effectively minimize the frequent outbreaks and their massive economical wastage consequences.
Observations on the interactions of mammals and birds with badger (Meles meles) dung pits at a site used by a single social group in an urban area
Authors: Hughes Morgan , Brown Scott 
Published: October 2019

AbstractDuring a monitoring study of a single social group of badger (Meles meles) at an urban site, incidental observations were noted of mammalian and avian species feeding within and removing material fromM. melesdung pits. In response to these observations, infra-red cameras were deployed at dung pits for a 10-week period to document the nature, timing and frequency of these behaviours. Cameras were triggered a total of 954 times by a total of nine mammal and 12 bird species. Harvesting of material accounted for 28 % of latrine-associated behaviours. Results may have implications for disease transmission and the efficacy of badger surveys, particularly in areas where brown rats are prevalent.
Long-range interhemispheric projection neurons show biased response properties and fine-scale local subnetworks in mouse visual cortex
Authors: Hagihara Kenta M. , Ishikawa Ayako W. , Yoshimura Yumiko , Tagawa Yoshiaki , Ohki Kenichi 
Published: October 2019

SummaryIntegration of information processed separately in distributed brain regions is essential for brain functions. This integration is enabled by long-range projection neurons, and further, concerted interactions between long-range projections and local microcircuits are crucial. It is not well known, however, how this interaction is implemented in cortical circuits. Here, to decipher this logic, using callosal projection neurons (CPNs) as a model of long-range projections, we found that CPNs exhibited distinct response properties and fine-scale local connectivity patterns. In vivo 2-photon calcium imaging revealed that CPNs showed a higher ipsilateral eye (with respect to their somata) preference, and that CPN pairs showed stronger signal/noise correlation than random pairs. Slice recordings showed CPNs were preferentially connected to CPNs, demonstrating the existence of projection target-dependent fine-scale subnetworks. Collectively, our results suggest that long-range projection target predicts response properties and local connectivity of cortical projection neurons.
Mechanism of interaction of an endofungal bacterium Serratia marcescens D1 with its host and non-host fungi
Authors: Hazarika Dibya Jyoti , Gautom Trishnamoni , Parveen Assma , Goswami Gunajit , Barooah Madhumita , Modi Mahendra Kumar , Boro Robin Chandra 
Published: October 2019

AbstractAssociation of bacteria with fungi is a major area of research in infection biology, however, very few strains of bacteria have been reported that can invade and reside within fungal hyphae. Here, we report the characterization of an endofungal bacterium Serratia marcescens D1 from Mucor irregularis SS7 hyphae. Upon re-inoculation, colonization of the endobacterium S. marcescens D1 in the hyphae of Mucor irregularis SS7 was demonstrated using stereo microscopy. However, S. marcescens D1 failed to invade into the hyphae of the tested Ascomycetes (except Fusarium oxysporum) and Basidiomycetes. Remarkably, Serratia marcescens D1 could invade and spread over the culture of F. oxysporum that resulted in mycelial death. Prodigiosin, the red pigment produced by the Serratia marcescens D1, helps the bacterium to invade fungal hyphae as revealed by the increasing permeability in fungal cell membrane. On the other hand, genes encoding the type VI secretion system (T6SS) assembly protein TssJ and an outer membrane associated murein lipoprotein also showed significant up-regulation during the interaction process, suggesting the involvement of T6SS in the invasion process.