bluuebunny/crossref_metadata_2025_split huggingface dataset:
Offspring of first-generation hatchery steelhead trout (Oncorhynchus mykiss) grow faster in the hatchery than offspring of wild fish, but survive worse in the wild: possible mechanisms for inadvertent domestication and fitness loss in hatchery salmon
Authors: Blouin Michael S , Wrey Madeleine C , Bollmann Stephanie R. , Skaar James C. , Twibell Ronald , Fuentes Claudio 
Published: September 2021

AbstractSalmonid fish raised in hatcheries often have lower fitness (number of returning adult offspring) than wild fish when both spawn in the wild. Body size at release from hatcheries is positively correlated with survival at sea. So one explanation for reduced fitness is that hatcheries inadvertently select for trait values that enhance growth rate under the unnatural environment of a hatchery, but that are maladaptive in the wild environment. A simple prediction of this hypothesis is that juveniles of hatchery origin should grow more quickly than fish of wild origin under hatchery conditions, but should have lower survival under wild conditions. We tested that hypothesis using multiple full sibling families of steelhead (Oncorhynchus mykiss) that were spawned using either two wild parents (WxW) or two first-generation hatchery (HxH) parents. Offspring from all the families were grown together under hatchery conditions and under semi-natural conditions in artificial streams. HxH families grew significantly faster in the hatchery, but had significantly lower survival in the streams. That we see this tradeoff after only a single generation of selection suggests that the traits involved are under very strong selection. We also considered one possible alteration to the hatchery environment that might reduce the intensity of selection among families in size at release. Here we tested whether reducing the fat content of hatchery feed would reduce the variance among families in body size. Although fish raised under a low-fat diet were slightly smaller, the variation among families in final size was unchanged. Thus, there is no evidence that reducing the fat content of hatchery feed would reduce the opportunity for selection among families on size at release.
Systems analysis shows a role of cytophilic antibodies in shaping innate tolerance to malaria
Authors: Lautenbach Maximilian Julius , Yman Victor , Kadri Nadir , Plaza David Fernando , Angenendt Sina , Sondén Klara , Färnert Anna , Sundling Christopher 
Published: September 2021

AbstractThe mechanism of acquisition and maintenance of natural immunity against Plasmodium falciparum malaria remains unclear. Although, clinical immunity develops over time with repeated malaria episodes, disease tolerance is more rapidly acquired compared to protective immunity. It remains unclear, how pre-existing immune responses impacts the mechanism responsible for disease tolerance. Here, we investigated a cohort of returning travelers treated for acute symptomatic P. falciparum malaria, either infected for the first time, or with a previous history of malaria. Through repeated sampling over one year in a malaria free setting, we were able to study the acute and longitudinal effects of the infection. We combined comprehensive immune cell and plasma protein profiling with integrated and data driven analysis, describing the immune landscape from acute disease to one year after infection. We identified a strong association between pro-inflammatory signatures and γδ T cell expansion. The association was significantly impacted by previous exposure to malaria, resulting in a dampened pro-inflammatory response, which translated to reduced Vδ2+ γδ T cell expansion compared to primary infected individuals. The dampened inflammatory signal was associated with early expansion of FcγRIII+ monocytes and parasite-specific antibodies of IgG1 and IgG3 isotypes.Our data suggest that the interplay of FcγRIII+ monocytes and a cytophilic parasite-specific IgG during the early blood stage infection lead to lower parasitemia and a dampened pro-inflammatory response with reduced γδ T cell expansion. This enhanced control and reduced inflammation points to a potential mechanism on how tolerance is established following repeated malaria exposure.One Sentence SummaryA systems immunology analysis on natural malaria sheds light on disease tolerance mechanism associated with gamma delta T cell expansion
A resource for improved predictions ofTrypanosomaandLeishmaniaprotein three-dimensional structure
Authors: Wheeler Richard John 
Published: September 2021

AbstractAlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily availableviathe AlphaFold database of predicted structures and AlphaFold/RoseTTAfold Colaboratory notebooks for custom predictions. However, predictions for some species tend to be lower confidence than model organisms. This includesTrypanosoma cruziandLeishmania infantum: important unicellular eukaryotic human parasites in an early-branching eukaryotic lineage. The cause appears to be due to poor sampling of this branch of life in the protein sequences databases used for the AlphaFold database and ColabFold. Here, by comprehensively gathering openly available protein sequence data for species from this lineage, significant improvements to AlphaFold2 protein structure prediction over the AlphaFold database and ColabFold are demonstrated. This is made available as an easy-to-use tool for the parasitology community in the form of Colaboratory notebooks for generating multiple sequence alignments and AlphaFold2 predictions of protein structure forTrypanosoma,Leishmaniaand related species.
Distal-lessandspaltare distal organisers of pierid wing patterns
Authors: Qi Wee Jocelyn Liang , Banerjee Tirtha Das , Prakash Anupama , Seah Kwi Shan , Monteiro Antónia 
Published: September 2021

AbstractTwo genes,Distal-less (Dll)andspalt (sal), are known to be involved in establishing nymphalid butterfly wing patterns. They function in several ways: in the differentiation of the eyespot’s central signaling cells, or foci; in the differentiation of the surrounding black disc; in overall scale melanisation (Dll); and in elaborating marginal patterns, such as parafocal elements. However, little is known about the functions of these genes in the development of wing patterns in other butterfly families. Here, we study the expression and function ofDllandsalin the development of spots and other melanic wing patterns of the Indian cabbage white,Pieris canidia, a pierid butterfly. InP. canidia, both Dll and Sal proteins are expressed in the scale-building cells at the wing tips, in chevron patterns along the pupal wing margins, and in areas of future scale melanisation. Additionally,Sal alone is expressed in the future black spots. CRISPR knockouts ofDllandsalshowed that each gene is required for the development of melanic wing pattern elements, and repressing pteridine granule formation, in the areas where they are expressed. We conclude that both genes likely play ancestral roles in organising distal butterfly wing patterns, across pierid and nymphalid butterflies, but are unlikely to be differentiating signalling centers in pierids black spots. The genetic and developmental mechanisms that set up the location of spots and eyespots are likely distinct in each lineage.
What do we know about survival of Common cranes? An elementary introduction with Euring databank
Authors: Bautista Luis M. , Alonso Juan C. 
Published: September 2021

AbstractThe increase of the western populations of Common cranes (Grus grus) in the last five decades highlights the need to estimate survival rates. According to Euring databank (EDB), the oldest Common crane ever known was 27 years old in year 2017. This lifespan was obtained by means of 24,900 recoveries of 2,124 ringed cranes collected between years 1936 and 2017. Nearly all cranes were ringed and observed in the last 30 years, and therefore the elapsed time was not enough to reach the maximum longevity reported for the species in captivity (43 years, Mitchell 1911). Life expectancy was five years on average after the ring was attached. Here we provide some elementary analyses to calculate the annualapparentsurvival rate (ϕ = 0.85) and the annual encounter probability (p= 0.45) of Common cranes, as a first step to advance in the knowledge of the species’ population dynamics. The great increase of breeding and wintering crane populations in western Europe in the last decades remains largely unexplained.
Transendothelial migration induces differential migration dynamics of leukocytes in tissue matrix
Authors: van Steen Abraham C.I. , Kempers Lanette , Schoppmeyer Rouven , Blokker Max , Beebe David J. , Nolte Martijn A. , van Buul Jaap D. 
Published: September 2021

AbstractLeukocyte extravasation into inflamed tissue is a complex process that is difficult to capture as a whole in vitro. We employed a blood-vessel-on-a-chip model in which endothelial cells were cultured in a tube-like lumen in a collagen-1 matrix. The vessels are leak-tight, creating a barrier for molecules and leukocytes. Addition of inflammatory cytokine TNF-α caused vasoconstriction, actin remodelling and upregulation of ICAM-1. Introducing leukocytes into the vessels allowed real-time visualisation of all different steps of the leukocyte transmigration cascade including migration into the extracellular matrix. Individual cell tracking over time distinguished striking differences in migratory behaviour between T-cells and neutrophils. Neutrophils cross the endothelial layer more efficiently than T-cells, but upon entering the matrix, neutrophils display high speed but low persistence, whereas T-cells migrate with low speed and rather linear migration. In conclusion, 3D imaging in real-time of leukocyte extravasation in a vessel-on-a-chip enables detailed qualitative and quantitative analysis of different stages of the full leukocyte extravasation process in a single assay.SummaryA functional hydrogel-based blood-vessel-on-a-chip model is used to study the complete leukocyte transendothelial migration process in real time. T-lymphocytes and neutrophils exhibit distinct migration dynamics in the extravascular matrix after transendothelial migration, which can be altered using a chemotactic gradient.
Nutrient availability shifts the biosynthetic potential of soil-derived microbial communities
Authors: Chevrette Marc G , Himes Bradley , Carlos-Shanley Camila 
Published: September 2021

AbstractSecondary metabolites produced by microorganisms are the main source of antimicrobials other pharmaceutical drugs. Soil microbes have been the primary discovery source for these secondary metabolites, often producing complex organic compounds with specific biological activities. Research suggests that secondary metabolism broadly shapes microbial ecological interactions, but little is known about the factors that shape the abundance, distribution, and diversity of biosynthetic gene clusters in the context of microbial communities. In this study, we investigate the role of nutrient availability on the abundance of biosynthetic gene clusters in soil-derived microbial consortia. We found that soil microbial consortia enriched in medium with 150 mg/L of glucose and 200 mg/L of trehalose (here defined as high sugar) had more biosynthetic gene cluster and higher inhibitory activity than soil microbial consortia enriched in medium with 15 mg/L of glucose + 20 mg/L of trehalose (here defined as low sugar). Our results demonstrate that laboratory microbial communities are a promising tool to study ecology of specialized metabolites.
Defective Desmosomal Adhesion Causes Arrhythmogenic Cardiomyopathy by involving an Integrin-αVβ6/TGF-β Signaling Cascade
Authors: Schinner Camilla , Franz Henriette , Zimmermann Aude , Wanuske Marie-Therès , Geier Florian , Pelczar Pawel , Lorenz Vera , Xu Lifen , Stüdle Chiara , Maly Piotr I , Kauferstein Silke , Beckmann Britt Maria , Kuster Gabriela M , Spindler Volker 
Published: September 2021

AbstractBackgroundArrhythmogenic Cardiomyopathy (ACM) is characterized by progressive loss of cardiomyocytes with fibrofatty replacement, systolic dysfunction and life-threatening arrhythmias. A substantial proportion of ACM is caused by mutations in genes of the desmosomal cell-cell adhesion complex, but the underlying mechanisms are not well understood. So far, treatment options are only symptomatic. Here, we investigate the relevance of defective desmosomal adhesion for ACM development and progression.MethodsWe mutated the binding site of desmoglein-2 (DSG2), a crucial desmosomal adhesion molecule in cardiomyocytes. This DSG2-W2A mutation abrogates the tryptophan swap, a central interaction mechanism of DSG2 based on structural data. Impaired adhesive function of DSG2-W2A was confirmed by cell-cell dissociation assays and force spectroscopy measurements by atomic force microscopy. We next generated a DSG2-W2A knock-in mouse model, which was analyzed by echocardiography and histological and bio-molecular techniques including RNA sequencing, transmission electron and super-resolution microscopy. The results were compared to ACM patient samples and their relevance was confirmed in cardiac slice cultures.ResultsThe DSG2-W2A mutation induced impaired binding and desmosomal adhesion dysfunction on cellular and molecular level. Mice bearing this mutation develop a severe cardiac phenotype recalling the characteristics of ACM, including cardiac fibrosis, impaired systolic function and arrhythmia. A comparison of the transcriptome of mutant mice with ACM patient data suggested deregulated integrin-αVβ6 and subsequent TGF-β signaling as driver of cardiac fibrosis. Accordingly, blocking antibodies targeting integrin-αVβ6 or inhibition of TGF-β receptor signaling both led to reduced expression of pro-fibrotic markers in cardiac slice cultures.ConclusionsHere, we show that disruption of desmosomal adhesion is sufficient to induce ACM, which confirms the dysfunctional adhesion hypothesis. Mechanistically, deregulation of integrin-αVβ6 signaling was identified as a central step towards fibrosis. This highlights the value of this model to discern mechanisms of cardiac fibrosis and to identify and test novel treatment options for ACM.
Genetic and genomic architecture in eight strains of the laboratory opossumMonodelphis domestica
Authors: Xiong Xiao , Samollow Paul B. , Cao Wenqi , Metz Richard , Zhang Chao , Leandro Ana C. , VandeBerg John L. , Wang Xu 
Published: September 2021

AbstractThe gray short-tailed opossum is an established laboratory-bred marsupial model for biomedical research. It serves as a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs. ancestral states of genomic/epigenomic characteristics for all eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction-site associated DNA sequencing (ddRAD-seq) and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 < F < 0.99), each derived from a different ancestral background. These strains are suitable for various experimental protocols requiring controlled genetic backgrounds and for intercrosses and backcrosses that can generate offspring with informative SNPs for studying a variety of genetic and epigenetic processes. Together with recent advances in reproductive manipulation and CRISPR/Cas9 techniques forM. domestica, the existence of distinctive inbred strains will enable genome editing on different genetic backgrounds, greatly expanding the utility of this marsupial model for biomedical research.
A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Authors: Zhang Runxuan , Kuo Richard , Coulter Max , Calixto Cristiane P. G. , Entizne Juan Carlos , Guo Wenbin , Marquez Yamile , Milne Linda , Riegler Stefan , Matsui Akihiro , Tanaka Maho , Harvey Sarah , Gao Yubang , Wießner-Kroh Theresa , Crespi Martin , Denby Katherine , Hur Asa ben , Huq Enamul , Jantsch Michael , Jarmolowski Artur , Koester Tino , Laubinger Sascha , Li Qingshun Quinn , Gu Lianfeng , Seki Motoaki , Staiger Dorothee , Sunkar Ramanjulu , Szweykowska-Kulinska Zofia , Tu Shih-Long , Wachter Andreas , Waugh Robbie , Xiong Liming , Zhang Xiao-Ning , Reddy Anireddy S.N. , Barta Andrea , Kalyna Maria , Brown John WS 
Published: September 2021

AbstractBackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis.ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage.ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.
Wildlife in Cameroon harbor diverse coronaviruses including many isolates closely related to human coronavirus 229E
Authors: Ntumvi Nkom F. , Ndze Valantine Ngum , Gillis Amethyst , Doux Diffo Joseph Le , Tamoufe Ubald , Takuo Jean-Michel , Mouiche Moctar M. M. , Nwobegahay Julius , LeBreton Matthew , Rimoin Anne W. , Schneider Bradley S. , Monagin Corina , McIver David J. , Roy Sanjit , Ayukekbong James A. , Saylors Karen , Joly Damien O. , Wolfe Nathan D. , Rubin Edward M. , Lange Christian E. 
Published: September 2021

AbstractZoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. SARS-CoV-2 highlights the global impact emergence events can have. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations.We sampled and tested wildlife in the central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection.Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n=8) and beta (n=9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human derived HCoV-229E isolates closest to those from camels in terms of the S and N genes, but closest to isolates from bats for the E, M, and RdRp genes. The CoV RNA positivity rate in bats varied significantly (p<0.001) between the wet (8.2%) and dry season (4.5%). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found.Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
“It needs to be the right blend”: a qualitative exploration of remote e-workers’ experience and well-being at work
Authors: Charalampous Maria , Grant Christine Anne , Tramontano Carlo 
Published: September 2021

PurposeThis present qualitative study explores the impact of the remote e-working experience on employees’ well-being.Design/methodology/approachForty (23 male) remote e-workers working for a British IT company were interviewed about their work-related well-being. Semi-structured interviews were framed within an existing theoretical of work-related well-being; hence, questions targeted five distinct dimensions of affective, professional, social, cognitive and psychosomatic well-being. However, data collection was not constrained by this model, allowing the exploration of other aspects interviewees considered relevant to their work-related well-being. Interview data were analysed using thematic analysis, where key themes emerged.FindingsFindings support the relevance of a multidimensional approach to understanding remote e-workers’ well-being as it provides an in-depth understanding of the inter-connectedness between relevant dimensions. Further insight into the overlooked issues of detachment from work and health-related behaviours when e-working remotely is also provided.Practical implicationsThis study proposes practical implications related to the organisational, managerial and individual level; providing individuals tailored guidance on how to remote e-work effectively and raising the importance of cultural change to support remote e-workers to be open about their working preferences.Originality/valueAn original contribution to the field of remote e-working is provided, by adopting a holistic approach to explore well-being, disentangling the interconnections between different well-being dimensions and discussing pivotal contributing factors that seemed to be understudied within extant remote e-working literature.