bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating behaviour and ecology into global biodiversity conservation strategies
Authors: Tobias Joseph A. , Pigot Alex L. 
Published: July 2019

Insights into animal behaviour play an increasingly central role in species-focused conservation practice. However, progress towards incorporating behaviour into regional or global conservation strategies has been more limited, not least because standardized datasets of behavioural traits are generally lacking at wider taxonomic or spatial scales. Here we make use of the recent expansion of global datasets for birds to assess the prospects for including behavioural traits in systematic conservation priority-setting and monitoring programmes. Using International Union for Conservation of Nature Red List classifications for more than 9500 bird species, we show that the incidence of threat can vary substantially across different behavioural categories, and that some types of behaviour—including particular foraging, mating and migration strategies—are significantly more threatened than others. The link between behavioural traits and extinction risk is partly driven by correlations with well-established geographical and ecological factors (e.g. range size, body mass, human population pressure), but our models also reveal that behaviour modifies the effect of these factors, helping to explain broad-scale patterns of extinction risk. Overall, these results suggest that a multi-species approach at the scale of communities, continents and ecosystems can be used to identify and monitor threatened behaviours, and to flag up cases of latent extinction risk, where threatened status may currently be underestimated. Our findings also highlight the importance of comprehensive standardized descriptive data for ecological and behavioural traits, and point the way towards deeper integration of behaviour into quantitative conservation assessments.
This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
A study of knowledge, experience and beliefs about hepatitis B virus (HBV) infection in south western Uganda
Authors: Mugisha Joseph , Mokaya Jolynne , Bukenya Dominic , Ssembajja Fatuma , Mayambala Denis , Newton Robert , Matthews Philippa C , Seeley Janet 
Published: July 2019

ABSTRACTIntroductionUnited Nations sustainable development goals aim for the elimination of viral hepatitis as a public health threat by 2030, leading to efforts to upscale the availability and accessibility of hepatitis B virus (HBV) vaccination, diagnosis and treatment globally. However, a variety of societal factors, including beliefs, traditions, and stigma, can be a major obstacle to all of these interventions. We therefore set out to investigate how HBV is understood and described in communities in Uganda, and whether there is evidence of potential stigma.MethodWe carried out a qualitative formative study in two sites in South Western Uganda: a village in Kalungu district (site A) and an area on the outskirts of Masaka town (site B). We undertook a rapid assessment to investigate how adults describe HBV infection and their perceptions about the infection. We collected data by conducting a transect walk, observations, community group discussions, and in-depth interviews, sampling a total of 131 individuals. We used inductive content analysis to extract key themes associated with HBV.ResultsThere is no specific word for HBV infection in local languages, and knowledge about this infection is varied. While some individuals were completely unfamiliar with HBV infection, some had heard of HBV. Radio was a common source of information. There was awareness of HBV as a cause of liver disease, limited knowledge regarding the cause, mode of transmission and treatment. Stigma in HBV may be rare in this community due to limited understanding and experience of HBV.ConclusionThere is an ongoing need to improve awareness and understanding of HBV in this community. Careful dissemination of accurate information is required to promote acceptance of interventions for prevention, diagnosis and treatment.
Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition inNeurospora crassa
Authors: Horta Maria Augusta Crivelente , Thieme Nils , Gao Yuqian , Burnum-Johnson Kristin E. , Nicora Carrie D. , Gritsenko Marina A. , Lipton Mary S. , Mohanraj Karthikeyan , de Assis Leandro José , Lin Liangcai , Tian Chaoguang , Braus Gerhard H. , Borkovich Katherine A. , Schmoll Monika , Larrondo Luis F. , Samal Areejit , Goldman Gustavo H. , Benz J. Philipp 
Published: July 2019

AbstractFungal plant cell wall degradation processes are governed by complex regulatory mechanisms, allowing the organisms to adapt their metabolic program with high specificity to the available substrates. While the uptake of representative plant cell wall mono- and disaccharides is known to induce specific transcriptional and translational responses, the processes related to early signal reception and transduction remain largely unkown. A fast and reversible way of signal transmission are post-translational protein modifications, such as phosphorylations, which could initiate rapid adaptations of the fungal metabolism to a new condition. To elucidate how changes in the initial substrate recognition phase ofNeurospora crassaaffect the global phosphorylation pattern, phospho-proteomics was performed after a short (2 minutes) induction period with several plant cell wall-related mono- and disaccharides. The MS/MS-based peptide analysis revealed large-scale substrate-specific protein phosphorylation and de-phosphorylations. Using the proteins identified by MS/MS, a protein-protein-interaction (PPI) network was constructed. The variance in phosphorylation of a large number of kinases, phosphatases and transcription factors indicate the participation of many known signaling pathways, including circadian responses, two-component regulatory systems, MAP kinases as well as the cAMP-dependent and heterotrimeric G-protein pathways. Adenylate cyclase, a key component of the cAMP pathway, was identified as a potential hub for carbon source-specific differential protein interactions. In addition, four phosphorylated F-Box proteins were identified, two of which, Fbx-19 and Fbx-22, were found to be involved in carbon catabolite repression responses. Overall, these results provide unprecedented and detailed insights into a so far less well known stage of the fungal response to environmental cues and allow to better elucidate the molecular mechanisms of sensory perception and signal transduction during plant cell wall degradation.
Targeted metagenomic sequencing enhances the identification of pathogens associated with acute infection
Authors: Goh Cyndi , Golubchik Tanya , Ansari M Azim , de Cesare Mariateresa , Trebes Amy , Elliott Ivo , Bonsall David , Piazza Paolo , Brown Anthony , Slawinski Hubert , Martin Natalie , Defres Sylviane , Griffiths Mike J , Bray James E , Maiden Martin C , Hutton Paula , Hinds Charles J , Solomon Tom , Barnes Ellie , Pollard Andrew J , Sadarangani Manish , Knight Julian C , Bowden Rory 
Published: July 2019

AbstractThe routine identification of pathogens during infection remains challenging because it relies on multiple modalities such as culture and nucleic acid amplification and tests that tend to be specific for very few of an enormous number of possible infectious agents. Metagenomics promises single-test identification, but shotgun sequencing remains unwieldy and expensive or in many cases insufficiently sensitive to detect the amount of pathogen material in a clinical sample. Here we present the validation and application of Castanet, a method for metagenomic sequencing with enrichment that exploits clinical knowledge to construct a broad panel of relevant organisms for detection at low cost with sensitivity comparable to PCR. Castanet targets both DNA and RNA, works with small sample volumes, and can be implemented in a high-throughput diagnostic setting. We used Castanet to analyse plasma samples from 573 patients from the GAinS sepsis cohort and CSF samples from 243 patients from the ChiMES meningitis cohort that had been evaluated using standard clinical microbiology methods, identifying relevant pathogens in many cases where no pathogen had previously been detected. Castanet is intended for use in defining the distribution of pathogens in samples, diseases and populations, for large-scale clinical studies and for verifying the performance of routine testing regimens. By providing sequence as output, Castanet combines pathogen identification directly with subtyping and phylo-epidemiology.
Ecological divergence in sympatry causes gene misregulation in hybrids
Authors: McGirr Joseph A. , Martin Christopher H. 
Published: July 2019

AbstractEcological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. However, it is unknown whether divergent ecological selection on gene regulation can directly cause reproductive isolation. Selection favoring regulatory divergence between species could result in gene misregulation in F1 hybrids and ultimately lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to test this hypothesis in a young, sympatric radiation ofCyprinodonpupfishes endemic to San Salvador Island, Bahamas, which consists of a dietary generalist and two novel trophic specialists – a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misregulated in their F1 hybrids. Consistent with divergent ecological selection causing misregulation, a subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle, and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length – the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can cause hybrid gene misregulation which may act as a primary reproductive barrier between nascent species.SignificanceIt is unknown whether the same genes that regulate ecological traits can simultaneously contribute to reproductive barriers between species. We measured gene expression in two trophic specialist species ofCyprinodonpupfishes that rapidly diverged from a generalist ancestor. We found genes differentially expressed between species that also showed extreme expression levels in their hybrid offspring. Many of these genes showed signs of selection and have putative effects on the development of traits that are important for ecological specialization. This suggests that genetic variants contributing to adaptive trait divergence between parental species negatively interact to cause hybrid gene misregulation, potentially producing unfit hybrids. Such loci may be important barriers to gene flow during the early stages of speciation, even in sympatry.
Increased sensorimotor activity during categorisation of ambiguous emotional expressions
Authors: Karakale Ozge , Moore Matthew R. , McNair Nicolas , Kirk Ian J. 
Published: July 2019

AbstractActions are rarely devoid of emotional content. Thus, a more complete picture of the neural mechanisms underlying mental simulation of observed actions requires more research using emotion information. The present study used electroencephalography (EEG) to investigate mental simulation associated with facial emotion categorisation. Mu rhythm modulation was measured to infer the degree of sensorimotor simulation. Categorising static images of neutral faces as happy or sad was associated with stronger mu suppression than categorising clearly happy or sad faces. Results suggest the sensitivity of the sensorimotor activity to emotional information rather than visual attentional engagement, because further control analyses revealed (1) no effect of emotion type on occipital alpha modulation, and (2) no difference in mu modulation between the conditions of a control task, which required categorising images with the head oriented right, left, or forward as right or left. This finding provides evidence for the role of the sensorimotor activity in a higher form of mental simulation. Consistent with a predictive coding account of action perception, stronger mu suppression during attempted emotion categorisation of neutral faces may involve minimising the mismatch between predicted kinematics of a happy/sad face and the observed stationarity of neutral faces.
Cellular dialogues that enable self-organization of dynamic spatial patterns
Authors: Dang Yiteng , Grundel Douwe , Youk Hyun 
Published: July 2019

SummaryCells form spatial patterns by coordinating their gene expressions. How a group of mesoscopic numbers (hundreds-to-thousands) of cells, without pre-defined morphogens and spatial organization, self-organizes spatial patterns remains incompletely understood. Of particular importance are dynamic spatial patterns - such as spiral waves that perpetually move and transmit information over macroscopic length-scales. We developed an open-source, expandable software that can simulate a field of cells communicating with any number of cell-secreted molecules in any manner. With it and a theory developed here, we identified all possible “cellular dialogues” - ways of communicating with two diffusing molecules - and core architectures underlying them that enable diverse, self-organized dynamic spatial patterns that we classified. The patterns form despite widely varying cellular response to the molecules, gene-expression noise, and spatial arrangement and motility of cells. Three-stage, “order-fluctuate-settle” process forms dynamic spatial patterns: cells form long-lived whirlpools of wavelets that, through chaos-like interactions, settle into a dynamic spatial pattern. These results provide a blueprint to help identify missing regulatory links for observed dynamic-pattern formations and in building synthetic tissues.
Assigning metabolic rate measurements to torpor and euthermy in heterothermic endotherms: “torpor”, a new package for R
Authors: Fasel Nicolas J. , Vullioud Colin , Genoud Michel 
Published: July 2019

AbstractTorpor is a state of controlled reduction of metabolic rate (M) in endotherms. Assigning measurements of M to torpor or euthermy can be challenging, especially when the difference between euthermic M and torpid M is small, in species defending a high minimal body temperature in torpor, in thermolabile species, and slightly below the thermoneutral zone (TNZ). Here, we propose a novel method for distinguishing torpor from euthermy. We use the variation in M measured during euthermic rest and torpor at varying ambient temperatures (Ta) to objectively estimate the lower critical temperature (Tlc) of the TNZ and to assign measurements to torpor, euthermic rest or rest within TNZ. In addition, this method allows the prediction of M during euthermic rest and torpor at varying Ta, including resting M within the TNZ. The present method has shown highly satisfactory results using 28 published sets of metabolic data obtained by respirometry on 26 species of mammals. Ultimately, this novel method aims to facilitate analysis of respirometry data in heterothermic endotherms. Finally, the development of the associated R-package (torpor) will enable widespread use of the method amongst biologists.Summary statementThe presented method and its associated R-package (torpor) enable the assignment of metabolic rate measurements to torpor or euthermy, ultimately improving the standardization of respirometry analyses in heterotherms.
Lymphocytes contribute to DUX4 target genes in FSHD muscle biopsies
Authors: Banerji Christopher R. S. , Panamarova Maryna , Zammit Peter S. 
Published: July 2019

SummaryFacioscapulohumeral muscular dystrophy (FSHD) is an incurable myopathy linked to overexpression of DUX4. However, DUX4 is difficult to detect in FSHD myoblasts and target gene expression is not a consistent FSHD muscle biopsy biomarker, displaying efficacy only on pathologically inflamed samples. Immune gene misregulation occurs in FSHD muscle biopsies with DUX4 targets enriched for inflammatory processes. However, assessment of the FSHD immune cell transcriptome, and the evaluation of DUX4 and target gene expression has not yet been performed. We show that FSHD lymphoblastoid cell lines (LCLs) display robust DUX4 expression, and express early and late DUX4 targets. Moreover, genes elevated on FSHD LCLs are elevated in FSHD muscle biopsies, correlating with DUX4 target activation and histological inflammation. These genes are importantly unaltered in FSHD myoblasts/myotubes, implying a non-muscle source in biopsies. Our results indicate an immune cell source of DUX4 and target gene expression in FSHD muscle biopsies.
Competition amongGardnerellasubgroups from the human vaginal microbiome
Authors: Khan Salahuddin , Voordouw Maarten J. , Hill Janet E. 
Published: July 2019

AbstractGardnerellaspp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome.Gardnerellahas four subgroups (A, B, C and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the fourGardnerellasubgroups were investigatedin vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of theGardnerellasubgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3 or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of additive interactions, most (69.3%) of the mixed communities exhibited competition (p < 0.0001). Competition reduced the growth rates of subgroups A, B and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups (p < 0.0001). All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition amongGardnerellasubgroups, which likely contributes to the observed distributions ofGardnerellaspp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.
Vps4 triggers sequential subunit exchange in ESCRT-III polymers that drives membrane constriction and fission
Authors: Pfitzner Anna-Katharina , Mercier Vincent , Roux Aurélien 
Published: July 2019

AbstractESCRT-III is a ubiquitous complex which catalyzes membrane fission from within membrane necks via an as yet unknown mechanism. Here, we reconstituted in vitro the ESCRT-III complex onto membranes. We show that based on variable affinities between ESCRT-III proteins and the ATPase Vps4, subunits are recruited to the membrane in a Vps4-driven sequence that starts with Snf7 and ends with Did2 and Ist1 which, together, form a fission-active subcomplex. Sequential recruitment of ESCRT-III subunits is coupled to membrane remodeling. Binding of Did2 promoted the formation of membrane protrusions which later constricted and underwent fission mediated by the recruitment of Ist1. Overall, our results provide a mechanism to explain how a sequence of ESCRT-III subunits drives membrane deformation and fission.
Epidemiological survey of serum titers from adults against various Gram-negative bacterial V-antigens
Authors: Kinoshita Mao , Shimizu Masaru , Akiyama Koichi , Kato Hideya , Moriyama Kiyoshi , Sawa Teiji 
Published: July 2019

AbstractThe V-antigen, a virulence-associated protein, was first identified inYersinia pestismore than half a century ago. Since then, other V-antigen homologs and orthologs have been discovered and are now considered vital molecules for the toxic effects mediated by the type III secretion system in infections caused by various pathogenic Gram-negative bacteria. After purifying recombinant V-antigen proteins including PcrV fromPseudomonas aeruginosa, LcrV fromYersinia, LssV fromPhotorhabdus luminescens, AcrV fromAeromonas salmonicida, and VcrV fromVibrio parahaemolyticus, we developed an enzyme-linked immunoabsorbent assay to measure titers against each V-antigen in the sera collected from 186 adult volunteers. Different titer-specific correlation levels were determined for the five V-antigens. The anti-LcrV and anti-AcrV titers shared the highest correlation with each other, with a correlation coefficient of 0.84. The next highest correlation coefficient was between anti-AcrV and anti-VcrV titers at 0.79, while the lowest correlation was found between anti-LcrV and anti-VcrV titers, which were still higher than 0.7 Sera from mice immunized with one of the five recombinant V-antigens displayed cross-antigenicity with some of the other four V-antigens, supporting the results from the human sera. Thus, the serum anti-V-antigen titer measurement system could potentially be used for epidemiological investigations on various pathogenic Gram-negative bacteria.
Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird
Authors: Murray Maureen H. , Lankau Emily W. , Kidd Anjelika D. , Welch Catharine N. , Ellison Taylor , Adams Henry C. , Lipp Erin K. , Hernandez Sonia M. 
Published: July 2019

AbstractMicrobial communities in the gastrointestinal tract influence many aspects of host health, including metabolism and susceptibility to pathogen colonization. These relationships and the environmental and individual factors that drive them are relatively unexplored for free-living wildlife. We quantified the relationships between urban habitat use, diet, and age with microbiome composition and diversity for 82 American white ibises (Eudocimus albus) captured along an urban gradient in south Florida and tested whether gut microbial diversity was associated withSalmonella entericaprevalence. Shifts in community composition were significantly associated with urban land cover and, to a lesser extent, diets higher in provisioned food. The diversity of genera was negatively associated with community composition associated with urban land cover, positively associated with age class, and negatively associated withSalmonellashedding. Our results suggest that shifts in both habitat use and diet for urban birds significantly alter gut microbial composition and diversity in ways that may influence health and pathogen susceptibility as species adapt to urban habitats.