bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations
Authors: Gustafson Kyle D. , Gagne Roderick B. , Buchalski Michael R. , Vickers T. Winston , Riley Seth P.D. , Sikich Jeff , Rudd Jaime L. , Dellinger Justin A. , LaCava Melanie E.F. , Ernest Holly B. 
Published: October 2021

ABSTRACTUrbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California’s central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.
Cetylpyridinium chloride (CPC) reduces zebrafish mortality from influenza infection: Super-resolution microscopy reveals CPC interference with multiple protein interactions with phosphatidylinositol 4,5-bisphosphate in immune function
Authors: Raut Prakash , Weller Sasha R. , Obeng Bright , Soos Brandy L. , West Bailey E. , Potts Christian M. , Sangroula Suraj , Kinney Marissa S. , Burnell John E. , King Benjamin L. , Gosse Julie A. , Hess Samuel T. 
Published: October 2021

AbstractThe COVID-19 pandemic raises significance for a potential influenza therapeutic compound, cetylpyridinium chloride (CPC), which has been extensively used in personal care products as a positively-charged quaternary ammonium antibacterial agent. CPC is currently in clinical trials to assess its effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) morbidity. Two published studies have provided mouse and human data indicating that CPC may alleviate influenza infection, and here we show that CPC (0.1 μM, 1 hour) reduces zebrafish mortality and viral load following influenza infection. However, CPC mechanisms of action upon viral-host cell interaction are currently unknown. We have utilized super-resolution fluorescence photoactivation localization microscopy to probe the mode of CPC action. Reduction in density of influenza viral protein hemagglutinin (HA) clusters is known to reduce influenza infectivity: here, we show that CPC (at non-cytotoxic doses, 5-10 µM) reduces HA density and number of HA molecules per cluster within the plasma membrane of NIH-3T3 mouse fibroblasts. HA is known to colocalize with the negatively-charged mammalian lipid phosphatidylinositol 4,5-bisphosphate (PIP2); here, we show that nanoscale co-localization of HA with the PIP2-binding Pleckstrin homology (PH) reporter in the plasma membrane is diminished by CPC. CPC also dramatically displaces the PIP2-binding protein myristoylated alanine-rich C-kinase substrate (MARCKS) from the plasma membrane of rat RBL-2H3 mast cells; this disruption of PIP2is correlated with inhibition of mast cell degranulation. Together, these findings offer a PIP2-focused mechanism underlying CPC disruption of influenza and suggest potential pharmacological use of this drug as an influenza therapeutic to reduce global deaths from viral disease.
Self-grooming promotes social attraction in mice via chemosensory communication
Authors: Zhang Yun-Feng , Janke Emma , Bhattarai Janardhan P. , Wesson Daniel W. , Ma Minghong 
Published: October 2021

AbstractSelf-grooming is a stereotyped behavior displayed by nearly all animals. Among other established functions, self-grooming is implicated in social communication in some animals. However, whether self-grooming specifically influences behaviors of nearby individuals has not been directly tested, partly due to the technical challenge of inducing self-grooming in a reliable and temporally controllable manner. We recently found that optogenetic activation of dopamine D3 receptor expressing neurons in the ventral striatal islands of Calleja robustly induces orofacial grooming in mice. Using this optogenetic manipulation, here we demonstrate that observer mice exhibit social preference for mice that groom more regardless of biological sex. Moreover, grooming-induced social attraction depends on volatile chemosensory cues broadcasted from grooming mice. Collectively, our study establishes self-grooming as a means of promoting social attraction among mice via volatile cues, suggesting an additional benefit for animals to allocate a significant amount of time to this behavior.
Islet transplantation tolerance in animals with defined histocompatibility and diabetes
Authors: Bhagchandani Preksha , Chang Charles A. , Zhao Weichen , Ghila Luiza , Herrera Pedro L. , Chera Simona , Kim Seung K. 
Published: October 2021

SummaryAdvances in organ transplantation benefit from development of genetically inbred animal strains with defined histocompatibility and cell-specific markers to distinguish donor and host cell subsets. For studies of pancreatic islet transplantation tolerance in diabetes, an invariant method to ablate host β cells and induce diabetes would provide an immense additional advantage. Here we detail development and use ofB6 RIP-DTRmice, an immunocompetent line permitting diabetes induction with 100% penetrance. This inbred line is homozygous for the C57BL/6J major histocompatibility complex (MHC) haplotype and expresses the mutantCD45.1allele in the hematopoietic lineage. β cell-specific expression of a high-affinity receptor for diphtheria toxin (DT) permits experimental β cell ablation and diabetes induction after DT administration. Diabetes reversal for over one year was achieved after transplantation with congenic C57BL/6J islets, but not with MHC-mismatched BALB/c islets, which were rapidly rejected. In summary, the generation of a C57BL/6J congenic line harboring theCD45.1allele andIns2-HBEGFtransgene should advance studies of islet transplantation tolerance and mechanisms to improve islet engraftment and function, thereby optimizing development of cell replacement strategies for diabetes mellitus.
Wind and route choice affect performance of bees flying above versus within a cluttered obstacle field
Authors: Burnett Nicholas P. , Badger Marc A. , Combes Stacey A. 
Published: October 2021

ABSTRACTBees flying through natural landscapes encounter physical challenges, such as wind and cluttered vegetation. The influence of these factors on the flight performance of bees remains unknown. We analyzed 548 videos of wild-caught honeybees (Apis mellifera) flying through an enclosure containing a field of vertical obstacles that bees could fly within (through open corridors, without maneuvering) or above. We examined how obstacle field height, wind presence and direction (headwinds or tailwinds) affected altitude, ground speed, and side-to-side casting (lateral excursions) of bees. When obstacle fields were short, bees flew at altitudes near the midpoint between the tunnel floor and ceiling. When obstacle fields approached or exceeded this midpoint, bees typically, but not always, increased their altitudes to fly over the obstacles. Bees that flew above the obstacle fields exhibited 40% faster ground speeds and 36% larger lateral excursions than bees that flew within the obstacle fields, likely due to the visual feedback from obstacles and narrow space available within the obstacle field. Wind had a strong effect on ground speed and lateral excursions, but not altitude. Bees flew 12-19% faster in tailwinds than in the other wind conditions, but their lateral excursions were 19% larger in any wind, regardless of its direction, than in still air. Our results show that bees flying through complex environments display flexible flight behaviors (e.g., flying above versus within obstacles), which affect flight performance. Similar choices in natural landscapes could have broad implications for foraging efficiency, pollination, and mortality in wild bees.
Inferring the mode and strength of ongoing selection
Authors: Barroso Gustavo V. , Lohmueller Kirk E. 
Published: October 2021

ABSTRACTGenome sequence data is no longer scarce. The UK Biobank alone comprises 200,000 individual genomes, with more on the way, leading the field of human genetics towards sequencing entire populations. Within the next decades, other model organisms will follow suit, especially domesticated species such as crops and livestock. Having sequences from most individuals in a population will present new challenges for using these data to improve health and agriculture in the pursuit of a sustainable future. Existing population genetic methods are designed to model hundreds of randomly sampled sequences, but are not optimized for extracting the information contained in the larger and richer datasets that are beginning to emerge, with thousands of closely related individuals. Here we develop a new method called TIDES (Trio-based Inference of Dominance and Selection) that uses data from tens of thousands of family trios to make inferences about natural selection acting in a single generation. TIDES further improves on the state-of-the-art by making no assumptions regarding demography, linkage or dominance. We discuss how our method paves the way for studying natural selection from new angles.
An intein-mediated split–nCas9 system for base editing in plants
Authors: Yuan Guoliang , Lu Haiwei , Hassan Md Mahmudul , Liu Yang , Li Yi , Abraham Paul E. , Tuskan Gerald A. , Yang Xiaohan 
Published: October 2021

AbstractVirus-assisted delivery of the clustered regularly interspaced short palindromic (CRISPR)/CRISPR-associated (Cas) system represents a promising approach for editing plant genomes. However, the relatively large size of the CRISPR/Cas9 system is challenging to package into viral vectors with confined packaging capacity. To address this technical challenge, we developed a strategy that splits the required CRISPR-Cas9 components across a dual-vector system in which CRISPR-Cas reassembles into an active form following co-infection to achieve targeted genome editing in plant cells. An intein-mediated split system was adapted and optimized in plant cells by successfully demonstrating split-eYGFPuv expression. Using a plant-based biosensor, we demonstrated for the first time that the split-SpnCas9 is capable of inducing efficient base editing in plant cells and identified several valid split sites for future biodesign strategies. Overall, this strategy provides new opportunities to bridge different CRISPR/Cas9 tools including base editor, prime editor, and CRISPR activation with virus-mediated gene editing.
Cheating the cheater: Suppressing false positive enrichment during biosensor-guided biocatalyst engineering
Authors: Trivedi Vikas D. , Mohan Karishma , Chappell Todd C. , Mays Zachary J. S. , Nair Nikhil U. 
Published: October 2021

ABSTRACTTranscription factor (TF)-based biosensors are very desirable reagents for high-throughput enzyme and strain engineering campaigns. Despite their potential, they are often difficult to deploy effectively as the small molecules being detected can leak out of high-producer cells, into low-producer cells, and activate the biosensor therein. This crosstalk leads to the overrepresentation of false positive/cheater cells in the enriched population. While the host cell can be engineered to minimize crosstalk (e.g., by deleting responsible transporters), this is not easily applicable to all molecules of interest, particularly those that can diffuse passively. One such biosensor recently reported for trans-cinnamic acid (tCA) suffers from crosstalk when used for phenylalanine ammonia-lyase (PAL) enzyme engineering by directed evolution. We report that desensitizing the biosensor (i.e., increasing the limit of detection, LOD) suppresses cheater population enrichment. Further we show that, if we couple the biosensor-based screen with an orthogonal pre-screen that eliminates a large fraction of true negatives, we can successfully reduce the cheater population during the fluorescence-activated cell sorting (FACS). Using the approach developed here, we were successfully able to isolate PAL variants with ~70% high kcat after a single sort. These mutants have tremendous potential in Phenylketonuria (PKU) treatment and flavonoid production.
In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris
Authors: Rybak Jeffrey M. , Barker Katherine S. , Muñoz José F. , Parker Josie E. , Ahmad Suhail , Mokaddas Eiman , Abdullah Aneesa , Elhagracy Rehab S. , Kelly Steve L. , Cuomo Christina A. , Rogers P. David 
Published: October 2021

ABSTRACTCandida auris has emerged as a healthcare-associated and multidrug-resistant fungal pathogen of great clinical concern. While as much as 50% of C. auris clinical isolates are reported to be resistant to amphotericin B, to date, no mechanisms contributing to this resistance have been identified. We report here mutations in the C. auris sterol-methyltransferase gene, ERG6, as the first identified mechanism of amphotericin B resistance in this emerging pathogen and describe the clinical case in which this high-level amphotericin B resistance was acquired in vivo during therapy. Whole genome sequencing revealed the four C. auris isolates obtained from this single patient case to be genetically related and identified a mutation in ERG6 as being associated with amphotericin B resistance. Cas9-mediated genetic manipulations confirmed this mutation alone to confer a >32-fold increase in amphotericin B resistance, and comprehensive sterol profiling revealed an abrogation of ergosterol biosynthesis and a corresponding accumulation of cholesta-type sterols in isolates and strains harboring the clinically derived ERG6 mutation. Together these findings represent the first significant step forward in the understanding of clinical amphotericin B resistance in C. auris.
Mutagenesis-Visualization: Analysis of Site-Saturation Mutagenesis Datasets in Python
Authors: Hidalgo Frank , Templeton Sage , Gallegos Che Olavarria , Wang Joanne 
Published: October 2021

AbstractSummarySite-saturation mutagenesis experiments have been transformative in our study of protein function. Despite the rich data generated from such experiments, current tools for processing, analyzing, and visualizing the data offer only a limited set of static visualization tools that are difficult to customize. Furthermore, usage of the tools requires extensive experience and programming knowledge, slowing the research process for those in the biological field who are unfamiliar with programming. Here, we introducemutagenesis-visualization, a Python package for creating publication-quality figures for site-saturation mutagenesis datasets without the need for prior Python or statistics experience, where each of the graphs is generated with a one-line command. The plots can be rendered as nativeMatplotlibobjects (easy to stylize) orPlotlyobjects (interactive graphs). Additionally, the software offers the possibility to visualize the datasets onPymol.Availability and implementationThe software can be installed fromPyPIorGitHubusing thepippackage manager and is compatible with Python ≥ 3.8. Thedocumentationcan be found atreadthedocsand thesource codeonGitHub.
Identification of Iron-Sulfur (Fe-S) and Zn-binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome
Authors: Wehrspan Zachary J. , McDonnell Robert T. , Elcock Adrian H. 
Published: October 2021

AbstractDeepMind’s AlphaFold2 software has ushered in a revolution in high quality, 3D protein structure prediction. In very recent work by the DeepMind team, structure predictions have been made for entire proteomes of twenty-one organisms, with >360,000 structures made available for download. Here we show that thousands of novel binding sites for iron-sulfur (Fe-S) clusters and zinc ions can be identified within these predicted structures by exhaustive enumeration of all potential ligand-binding orientations. We demonstrate that AlphaFold2 routinely makes highly specific predictions of ligand binding sites: for example, binding sites that are comprised exclusively of four cysteine sidechains fall into three clusters, representing binding sites for 4Fe-4S clusters, 2Fe-2S clusters, or individual Zn ions. We show further: (a) that the majority of known Fe-S cluster and Zn-binding sites documented in UniProt are recovered by the AlphaFold2 structures, (b) that there are occasional disputes between AlphaFold2 and UniProt with AlphaFold2 predicting highly plausible alternative binding sites, (c) that the Fe-S cluster binding sites that we identify in E. coli agree well with previous bioinformatics predictions, (d) that cysteines predicted here to be part of Fe-S cluster or Zn-binding sites show little overlap with those shown via chemoproteomics techniques to be highly reactive, and (e) that AlphaFold2 occasionally appears to build erroneous disulfide bonds between cysteines that should instead coordinate a ligand. These results suggest that AlphaFold2 could be an important tool for the functional annotation of proteomes, and the methodology presented here is likely to be useful for predicting other ligand-binding sites.
Mistic: an open-source multiplexed image t-SNE viewer
Authors: Prabhakaran Sandhya , Gatenbee Chandler , Robertson-Tessi Mark , West Jeffrey , Beg Amer A. , Gray Jhanelle , Antonia Scott , Gatenby Robert A. , Anderson Alexander R. A. 
Published: October 2021

AbstractUnderstanding the complex ecology of a tumor tissue and the spatio-temporal relationships between its cellular and microenvironment components is becoming a key component of translational research, especially in immune-oncology. The generation and analysis of multiplexed images from patient samples is of paramount importance to facilitate this understanding. In this work, we present Mistic, an open-source multiplexed image t-SNE viewer that enables the simultaneous viewing of multiple 2D images rendered using multiple layout options to provide an overall visual preview of the entire dataset. In particular, the positions of the images can be taken from t-SNE or UMAP coordinates. This grouped view of all the images further aids an exploratory understanding of the specific expression pattern of a given biomarker or collection of biomarkers across all images, helps to identify images expressing a particular phenotype or to select images for subsequent downstream analysis. Currently there is no freely available tool to generate such image t-SNEs. Mistic is open-source and can be downloaded at:https://github.com/MathOnco/Mistic.
The duration of caffeine treatment plays an essential role in its effect on sleep and circadian rhythm
Authors: Segu Aishwarya , Kannan Nisha N 
Published: October 2021

AbstractSleep is regulated by the homeostatic system and the circadian clock. The circadian clock governs the timing of sleep-wake cycles and the homeostatic mechanisms modulate the amount and depth of sleep. Caffeine intake promotes wakefulness inDrosophila. In humans, caffeine is consumed on a daily basis and hence it is important to understand the effect of prolonged caffeine intake on both circadian and homeostatic regulation of sleep. Furthermore, sleep changes with age and the impact of caffeine on age dependent sleep fragmentation is yet to be understood. Hence in the present study, we examined the effect of short exposure to caffeine on homeostatic sleep and age dependent sleep fragmentation inDrosophila. We further assessed the effect of prolonged exposure to caffeine on homeostatic sleep and circadian clock inDrosophila. The results of our study showed that short exposure to caffeine reduces sleep in flies and enhances sleep fragmentation with increasing age. On the other hand, prolonged caffeine exposure did not exert any significant effect on duration of sleep in mature flies. Nevertheless, prolonged caffeine ingestion decreased the morning and evening anticipatory activity in these flies indicating that it affects the circadian rhythm. These flies also exhibited phase delay in the clock genetimelesstranscript oscillation and altered behavioral rhythm with either a longer free running period or arrhythmicity under constant darkness. In summary, the results of our studies showed that short exposure to caffeine increases the sleep fragmentation with age whereas prolonged caffeine exposure disrupts the circadian clock.Statement of SignificanceIn the present study, we assessed the effect of duration of caffeine intake on age dependent sleep fragmentation and circadian clock by usingDrosophilaas a model organism. We found that short exposure to caffeine reduced sleep and food intake in flies. It also increased the sleep fragmentation with age. On the other hand prolonged caffeine exposure did not affect the sleep and feeding indicating that these flies developed tolerance to caffeine. As in mammals, caffeine slows down the circadian clock in flies. Most importantly, prolonged caffeine treatment disrupted the circadian rhythm inDrosophila. Our studies provide new insights into the differential effect of duration of caffeine intake on circadian clock and sleep.