bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of disinfectant in barn cleaning alters microbial composition and increases carriage of Campylobacter jejuni in broiler chickens
Authors: Fan Yi , Forgie Andrew J. , Ju Tingting , Marcolla Camila , Inglis Tom , McMullen Lynn M. , Willing Benjamin P. , Korver Douglas R. 
Published: November 2021

AbstractTo maintain food safety and flock health in broiler chicken production, biosecurity approaches to keep chicken barns free of pathogens are important. Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection; FD) and may wash with water (water-wash; WW) throughout the year. However, many producers use FD after each flock, assuming a greater efficacy of more stringent cleaning protocols, although little information is known regarding how these two cleaning practices affect pathogen population and gut microbiota. In the current study, a cross-over experiment over four production cycles was conducted in seven commercial chicken barns to compare WW and FD. We evaluated the effects of barn cleaning method on the commercial broiler performance, cecal microbiota composition, pathogen occurrence and abundance, as well as short-chain fatty acid concentrations in the month-old broiler gut. The 30-day body weight and mortality rate were not affected by the barn cleaning methods. The WW resulted in a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis p = 0.05, and unweighted-UniFrac; adonis p = 0.01), with notable reductions in Campylobacter jejuni occurrence and abundance. In addition, the WW group had increased cecal acetate, butyrate and total short-chain fatty acid concentrations, which were negatively correlated with C. jejuni abundance. Our results support the use of WW over FD to enhance the activity of the gut microbiota and potentially reduce zoonotic transmission of C. jejuni in broiler production without previous disease challenges.
Impact of protein identity on tumor-associated antigen uptake into infiltrating immune cells: A comparison of different fluorescent proteins as model antigens
Authors: Yi Rulan , Chen Emily , Roberts Edward W , Krummel Matthew F , Serwas Nina K 
Published: November 2021

AbstractEffective immune responses depend on efficient antigen uptake in the periphery, transport of those antigens to, and presentation in draining lymph nodes (LNs). These processes have been studied intensively using stable fluorescent proteins (FPs) as model antigens. To date, ZsGreen is the only FP that can be tracked efficiently towards LNs, hence, it is difficult to compare studies using alternated tracking proteins.Here, we systematically compared six different FPs. We included ZsGreen, ZsYellow, DsRed, AsRed, mCherry, and mRFP based on sequence homology and/or origin species, and generated FP-expressing tumor cell lines. Stability of fluorescent signal was assessed in vitro over time, across different pH environments, and in vivo through FP antigen uptake and transfer to immune cells isolated from tumors and tumor-draining LNs.ZsGreen could be detected in high percentages of all analyzed tumor-infiltrating immune cells, with highest amounts in tumor-associated macrophages (TAMs) and type 2 conventional dendritic cells (cDC2s). ZsYellow, AsRed, and DsRed followed a similar pattern, but percentages of FP-containing immune cells in the tumor were lower than for ZsGreen. Strikingly, mRFP and mCherry demonstrated a ‘non-canonical’ antigen uptake pattern where percentages of FP-positive tumor-infiltrating immune cells were highest for cDC1s not TAMs and cDC2s despite comparable stabilities and localization of all FPs. Analysis of antigen-containing cells in the LN was hindered by intracellular degradation of FPs. Only ZsGreen could be efficiently tracked to the LN, though some signal was measurable for ZsYellow and DsRed.In summary, we find that detection of antigen uptake and distribution is subject to variabilities related to fluorophore nature. Future experiments need to consider that these processes might be impacted by protein expression, stability, or other unknown factors. Thus, our data sheds light on potential under-appreciated mechanisms regulating antigen transfer and highlights potential uses and necessary caveats to interpretation based on FP use.
Vitamin A and vitamin E metabolites comodulate amyloid-β aggregation
Authors: Joshi Priyanka , Chia Sean , Yang Xiaoting , Perni Michele , Habchi Johnny , Vendruscolo Michele 
Published: November 2021

AbstractAlzheimer’s disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-β peptide (Aβ). Since many vitamins are dysregulated in this disease, we explored whether these molecules participate in protein homeostasis by modulating Aβ aggregation. By screening 18 fat-soluble and water-soluble vitamins, we found that retinoic acid and α-tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect Aβ aggregation both in vitro and in a C. elegans model of Alzheimer’s disease. We also show that effects of these two vitamin metabolites in combination can cancel each other out, suggesting that the complex composition of the cellular environment could have a protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins and their metabolites may be added to the list of components of the quality control system that regulate protein aggregation.
Evolution of reduced mate harming tendency of males inDrosophila melanogasterpopulations selected for faster life history
Authors: Verma Tanya , Mohapatra Anuska , Senapati Harish Kumar , Muni Rakesh Kumar , Dasgupta Purbasha , Nandy Bodhisatta 
Published: November 2021

AbstractDetrimental effect of males on female, often termed mate harm, is a hallmark of sexual conflict. Allowed to evolve unchecked, mate harming traits are predicted to bring down average fitness of a population, unless mitigated by the evolution of resistance in females. In addition, life history may also modulate sexual conflict, but the mechanism is not clearly understood. Here we investigated the evolution of mate harm in a set of experimentally evolved laboratory populations ofDrosophila melanogasterwherein a faster aging has evolved in response to >1000 generations of selection for faster development and early reproduction. We quantified mortality and fecundity of Oregon R females held with evolved (ACO) and ancestral males (CO) to show that the evolved males are significantly less detrimental to their mates. We compared our results from the ACO males with that from a phenocopied version of the ancestral regime (CCO) to show that only part of the observed difference in mate harm can be attributed to the evolved difference in body size. We further show that the reduction in mate harming ability evolved despite an increase in courtship activity, especially early in life. We discuss the causative role of an evolved reproductive schedule and altered breeding ecology.Significance statementSexually antagonistic male effects can significantly bring down female fitness. Along with female counter evolution of resistance traits, life history has been conjectured to impose constrains on the evolution of such harming ability in males. Here, we report the evolution of mate harming ability in males of a set of five replicateDrosophila melanogasterpopulations that evolved smaller size and faster aging as a result of >1000 generations of experimental evolution for faster development and early reproduction. We show that in spite of ample scope of sexual selection, the faster aging males have evolved reduced mate harming ability despite being more active in courting their mates. To the best of our knowledge, this is one of the first clear evidences demonstrating the causal relationship between evolution of life history and reduction in sexual antagonism in a population.
Transcriptional evaluation of the ductus arteriosus at the single-cell level uncovers a requirement for vimentin for complete closure
Authors: Salvador Jocelynda , Hernandez Gloria E. , Ma Feiyang , Abrahamson Cyrus W. , Pellegrini Matteo , Goldman Robert , Ridge Karen M. , Iruela-Arispe M. Luisa 
Published: November 2021

ABSTRACTOBJECTIVEFailure to close the ductus arteriosus immediately post-birth, patent ductus arteriosus (PDA), accounts for up to 10% of all congenital heart defects. Despite significant advances in PDA management options, including pharmacological treatment targeting the prostaglandin pathway, a proportion of patients fail to respond and must undergo surgical intervention. Thus, further refinement of the cellular and molecular mechanisms that govern vascular remodeling of this vessel is required.APPROACH AND RESULTSAs anticipated, single-cell RNA sequencing on the ductus arteriosus in mouse embryos at E18.5, P0.5, and P5, revealed broad transcriptional alterations in the endothelial, smooth muscle, and fibroblast cell compartments. Making use of these data sets, vimentin emerged as an interesting candidate for further investigation. Subsequent studies demonstrated that, in fact, mice with genetic deletion of vimentin fail to complete vascular remodeling of the ductus arteriosus, as per presence of a functional lumen.CONCLUSIONSThrough single-cell RNA-sequencing and by tracking closure of the ductus arteriosus postnatally in mice, we uncovered the unexpected contribution of vimentin in driving complete closure of the ductus arteriosus potentially through regulation of the Notch signaling pathway.HIGHLIGHTSSingle-cell RNA-sequencing on the ductus arteriosus at E18.5, P0.5, and P5 reveals how the ductus arteriosus undergoes drastic transcriptional changes at the single-cell level.Endothelial cells increase levels of Vimentin, Notch1 and Jag1 transcripts soon after birth (P0.5), concurrent with ductus arteriosus closure.Loss of vimentin, the major intermediate filament protein of endothelial cells, prevents proper permanent closure of the ductus arteriosus.
OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Authors: Steenwyk Jacob L. , Goltz Dayna C. , Buida Thomas J. , Li Yuanning , Shen Xing-Xing , Rokas Antonis 
Published: November 2021

AbstractMolecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in one or more species—a phenomenon observed among several important families of genes such as transporters and transcription factors—are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across seven eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.
An Immunogold Single Extracellular Vesicular RNA and Protein (AuSERP) Biochip to Predict Responses to Immunotherapy in Non-Small Cell Lung Cancer Patients
Authors: Nguyen Luong T. H. , Wang Xinyu , Kwak Kwang Joo , Zhang Jingjing , Okimoto Tamio , Amann Joseph , Rima Xilal Y. , Yoon Min Jin , Shukuya Takehito , Walters Nicole , Ma Yifan , Belcher Donald , Li Hong , Palmer Andre F. , Carbone David P. , Lee L. James , Reátegui Eduardo 
Published: November 2021

AbstractConventional PD-L1 immunohistochemical tissue biopsies only predict 20~40% of non-small cell lung cancer (NSCLC) patients that will respond positively to anti-PD-1/PD-L1 immunotherapy. Herein, we present an immunogold biochip to quantify single extracellular vesicular RNA and protein (AuSERP) as a non-invasive alternative. With only 3 μL of serum, PD-1/PD-L1 proteins on the surface of extracellular vesicles (EVs) and EV PD-1/PD-L1 messenger RNA (mRNA) cargo were detected at a single-vesicle resolution and exceeded the sensitivities of ELISA and qRT-PCR by 1000 times. By testing a cohort of 27 non-responding and 27 responding NSCLC patients, AuSERP indicated that the single-EV mRNA biomarkers surpass the single-EV protein biomarkers at predicting patient responses to immunotherapy. Dual single-EV PD-1/PD-L1 mRNA detection differentiated responders from non-responders with an accuracy of 72.2% and achieved an NSCLC diagnosis accuracy of 93.2%, suggesting the potential for AuSERP to provide enhanced immunotherapy predictions and cancer diagnoses within the clinical setting.
Directional selection at gene expression level contributes to the speciation of Asian rice cultivars
Authors: Xie Lihong , Yu Kehan , Chen Dongjing 
Published: November 2021

AbstractDifferences in expression levels play important roles in phenotypic variation across species, especially those closely related species with limited genomic differences. Therefore, studying gene evolution at expression level is important for illustrating phenotypic differentiation between species, such as the two Asian rice cultivars, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. In this study, we evaluated the gene expression variation at inter-subspecies and intra-subspecies level using transcriptome data from seedlings of three indica and japonica rice and defined four groups of genes under different natural selections. We found a substantial of genes (about 79%) that are under stabilizing selection at the expression level in both subspecies, while about 16% of genes are under directional selection. Genes under directional selection have higher expression level and lower expression variation than those under stabilizing selection, which suggest a potential explanation to subspecies adaptation to different environments and interspecific phenotypic differences. Subsequent functional enrichment analysis of genes under directional selection shows that indica rice have experienced the adaptation to environmental stresses, and also show differences in biosynthesis and metabolism pathways. Our study provide an avenue of investigating indica-japonica differentiation through gene expression variation, which may guide to rice breeding and yield improvement.
A versatile mitochondria isolation- and analysis-pipeline generates 3D nano-topographies and mechano-physical surface maps of single organelles
Authors: Joshi Saurabh , Hater Friederike , Eirich Jürgen , Palovaara Joakim , Ellinghaus Henrik , Heinkow Paulina , Callenius Hannah , Peter Annette , Schweser Ole , Kubitschke Martin , Madduri Murali Krishna , Mathew Amal John , Ciacchi Lucio Colombi , Kirstein Janine , Maedler Kathrin , Masseck Olivia Andrea , Finkemeier Iris , Radmacher Manfred , Groß-Hardt Rita 
Published: November 2021

AbstractLiving eukaryotic cells typically contain large quantities of highly dynamic mitochondria, which sustain the cells’ energy and redox homeostasis. Growing evidence suggests that mitochondria can functionally differ among but also within cells. The extent and biological significance of mitochondrial diversity is still largely unexplored, due to technical limitations that hamper profiling of individual organelles. Previous measurements of the cell’s interior have shown that membrane-bound compartments respond to metabolic manipulation by changes in their surface stiffness, suggesting that mechano-physical properties are a valuable readout of mitochondrial function. We here present the establishment of a robust multi-step analysis pipeline that allows one to profile mechano-physical properties of single mitochondria at the nanoscale using Atomic Force Microscopy (AFM). Firstly, we developed a rapid cell-type specific isolation protocol (mRACE), which selectively functionalizes mitochondria with biotin, facilitating isolation by streptavidin decorated microbeads. We established the technique for human and rat cell cultures, the invertebrate Caenorhabditis elegans, and the model plant Arabidopsis thaliana. Based on this versatile tool, we detected diversity of mitochondrially associated proteins among different tissues, reflecting the trophic condition of the source material. Secondly, a rapid filtration-based mitochondria isolation protocol was established, which was combined with mRACE. Lastly, we established an AFM analysis platform, which generates 3D maps of the nano-topography and mechano-physical properties of individual mitochondria. The comparison of mitochondria with each other revealed an unprecedented diversity in their mechano-physical properties and suggests that shape is not the sole determining parameter for outer membrane stiffness. We expect our results to not only introduce a new dimension for basic mitochondrial research, but in addition to open the door for the exploitation of individual mitochondria for diagnostic characterization.
Optimized immunoglobulin knock-ins using Cas9 reveal peritoneal B cell lineage relationships in vivo
Authors: Erickson Steven A. , Zapata-Bultman Eliot , Degenstein Linda , Bendelac Albert 
Published: November 2021

ABSTRACTImmunoglobulin (Ig) knock-in mice are valuable tools in basic and translational immunological research. Here we present “Speed-Ig,” a rapid Cas9-based method for generating Ig knock-in mouse lines with high on-target integration rates at both heavy and light chain alleles. With standardized target sites and promoter regions, Speed-Ig mice can be used for comparative studies of B cell biology and vaccine optimization in vivo. We used Speed-Ig to create panels of mice with Ig pairs derived from B-1a, B-1b, and B-2 cells. Surprisingly, B-1b and B-2 Ig pairs drove both B-1b and B-2 phenotypes, suggesting a previously unknown lineage relationship between these subsets. We then confirmed the B-1:B-2 relationship with transcription factor reporter lines and through adoptive cell transfer experiments. In summary, our Ig knock-in approach facilitated the discovery of previously unappreciated aspect of innate-like B cell biology.
Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer
Authors: Kuchipudi Suresh V. , Surendran-Nair Meera , Ruden Rachel M. , Yon Michelle , Nissly Ruth H. , Nelli Rahul K. , Li Lingling , Jayarao Bhushan M. , Vandegrift Kurt J. , Maranas Costas D. , Levine Nicole , Willgert Katriina , Conlan Andrew J. K. , Olsen Randall J. , Davis James J. , Musser James M. , Hudson Peter J. , Kapur Vivek 
Published: November 2021

AbstractMany animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive “One Health” approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.One-Sentence SummarySARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.
Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes
Authors: Tandon Kshitij , Chiou Yu-Jing , Yu Sheng-Ping , Hsieh Hernyi Justin , Lu Chih-Ying , Hsu Ming-Tsung , Chiang Pei-Wen , Chen Hsing-Ju , Wada Naohisa , Tang Sen-Lin 
Published: November 2021

AbstractBacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.