bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host genomic variation shapes gut microbiome diversity in threespine stickleback fish
Authors: Small Clayton M. , Beck Emily A. , Currey Mark C. , Tavalire Hannah F. , Bassham Susan , Cresko William A. 
Published: November 2022

ABSTRACTVariation among host-associated microbiomes is well documented across species, populations, and individuals. However, the relative importance of host genetic differences for microbiome variation has been difficult to study. While research in humans has shown that genetic variation influences microbiome differences, confounding environmental effects have been very difficult to control. Isogenic laboratory models help isolate host genetic variants to test for influences of the environment or large-effect mutations on the microbiome, but such studies seldom incorporate natural genetic variation. Thus, although many important factors potentially impacting the microbiome have been identified, most studies have failed to test for the direct influence of natural host-genetic variation on microbiome differences within a controlled environment. Understanding the relationship between host-genetic and microbial variation also has biomedical implications, such as understanding why some humans are more susceptible to chronic inflammatory disorders like Crohn’s Disease and Ulcerative Colitis. To directly assess the relationship between host-genetic variation and microbiome variation, we performed a common garden experiment using laboratory lines of genetically divergent populations of threespine stickleback fish – a species that is an outbred model organism commonly used for determining the genetic basis of complex traits in the context of natural genetic variation. Using germ-free derivation and the powerful common garden design with these divergent lines, as well as hybrids between them, we detected clear associations between stickleback genetic dissimilarity and microbiome dissimilarity. Using genome-wide RAD-seq data we also identified regions of the genome underlying differences in microbiome composition. Importantly, we highlight that heritable morphological traits such as body size that are correlated with microbiome dissimilarity also need consideration in future microbiome studies.
Application of a Latent Trait Modeling Method for Missing Data Across Datasets: Guidance on Appropriate Factor Structure
Authors: Bartlett Christopher W. , Gorham Tyler J. , Knapp Emily A. , Kress Amii M. , Klamer Brett G. , Buyske Steven , Lau Bryan , Petrill Stephen A. 
Published: November 2022

AbstractLatent trait space can be leveraged to harmonize small data into big data when the constituent datasets measure the same underlying (latent) domains using a set of partially overlapping measurement instruments in each domain. The latent trait space then acts as a common metric space for each dataset, thus ensuring the same scale for the latent traits across datasets, despite the use of non-identical sets of measurement instruments within datasets. This approach, as originally published, only applied to a narrow set of circumstances, namely, that each measurement instrument occurred in more than one dataset. Here, we extend the latent trait approach to drop this requirement by using matrix completion methods. Using a simulation study, we evaluate the reliability of this extension and offer guidance on circumstances when the latent trait approach to missing data is robust and practical on real datasets.
CREATE’ing improvements in first-year students’ science efficacy that are independent of instructor rank and experience in a large, multi-section online introductory course
Authors: Garzke Jessica , Steinwand Blaire J. 
Published: November 2022

AbstractWith a primary objective to engage students in the process of science online, we transformed a long-standing laboratory course for first-year science students into a more accessible, immersive experience of current biological research using a narrow and focused set of primary literature and the CREATE pedagogy. The efficacy of the CREATE approach has been demonstrated in a diversity of higher education settings and courses. It is, however, not yet known if CREATE can be successfully implemented online with a large, diverse team of faculty untrained in the CREATE pedagogy. Here, we present the transformation of a large-enrollment, multi-section, multi-instructor course for first-year students in which instructors follow different biological research questions but work together to reach shared goals and outcomes. We assessed students’: (1) science self-efficacy and (2) epistemological beliefs about science throughout an academic year of instruction fully administered online as a result of ongoing threats posed by COVID-19. Our findings demonstrate that novice CREATE instructors with varying levels of teaching experience and ranks can achieve comparable outcomes and improvements in students’ science efficacy in the virtual classroom as a teaching team. This study extends the use of the CREATE strategy to large, team-taught, multi-section courses and shows its utility in the online teaching and learning environment.
Exome sequencing identifies variants associated with semen quality in Holstein Friesian and Hallikar bulls
Authors: Kunnath Sarin K. , Ramesha K.P. , Kataktalware Mukund A. , Kumaresan A. , Jeyakumar S. , Das D.N. , Manimaran A. , Devadasan M. Joel , Ashwitha A. , Mall Shweta , Keshava Prasad T.S. 
Published: November 2022

AbstractEffective fertility of bulls is dependent on semen quality, often determined based on standard semen evaluation tests. Here we report Whole Exome Sequencing (WES) of 12 bulls from two breeds Holstien Friesian and Hallikar selected based on Ejaculate Rejection Rate (ERR). We explored the possibility of identifying genetic variants from the conserved protein coding regions of genome. A total of 10,510 SNPs and 10.236 INDELs were identified post alignment against reference genome (ARS-UCD 1.2) and were annotated using SnpEff. The number of variants with high and modifier functional impact detected were 145 and 19,122, respectively. Genetic variants common to both high and low ERR group bulls among Holstein Friesian were 08 and in Hallikarthe common variants were 51. Prominentgenesviz.UCP2, PANK2, GPD2, PTPRG, LARP7, EZH1, DENND1BandTDRD9with a role in determining the semen quality were observed to be carriers of the genetic variant.
An attempt at restoring original radiocarbon ages in collagen from bioapatite
Authors: Trindade Dantas Mário André , Cherkinsky Alexander 
Published: November 2022

AbstractIn the literature there is a consensus that radiocarbon dating performed in bioapatite presents younger datings than those performed in collagen, thus, we propose a general regression that could be used to convert the radiocarbon dating performed in bioapatite to the original ones in collagen in fossil samples all of the world. This general regression presents several good indexes of quality, high correlation (R2= 0.98), lower values of percent predicted error (%PE = 0.01), and the standard error of the estimate (%SEE = 25), showing that is a good tool, as the predicted values are similar to those observed. Using this regression we converted the radiocarbon datings in bioapatite to collagen made for several taxa from the Brazilian Intertropical Region, and suggest that these datings could be 1-7 Cal BP kyr older than previously thought.
The City Nature Challenge – A global citizen science phenomenon contributing to biodiversity knowledge and informing local government practices
Authors: Palma Estibaliz , Mata Luis , Cohen Kylie , Evans Doug , Gandy Bernard , Gaskell Nadine , Hatchman Hiliary , Mezzetti Anna , Neumann Deborah , O’Keefe Jessica , Shaw Amy , Wells Millie , Williams Laurence , Hahs Amy K. 
Published: November 2022

AbstractThe bioblitz phenomenon has recently branched into cities, presenting exciting opportunities for local governments to channel participants’ efforts toward local issues. The City Nature Challenge (CNC) is one such initiative that has been quickly uptaken by hundreds of municipalities worldwide. Despite high participation, we still lack a framework for evaluating how the CNC contributes to local biodiversity knowledge and to inform local government practices. Here, we develop such a tool and present a case study that illustrates its applicability. We demonstrate that the collected records contributed to a better understanding of contemporary, local biodiversity patterns and provided a more realistic representation of understudied groups such as insects and fungi. Importantly, we show that the CNC presented local governments with a cost-effective tool to make informed, evidence-based management and policy decisions, improve education and engagement programs, foster cross-council collaborations, and support a stronger sense of environmental stewardship within the local community.
When and why grid cells appear or not in trained path integrators
Authors: Sorscher Ben , Mel Gabriel C. , Nayebi Aran , Giocomo Lisa , Yamins Daniel , Ganguli Surya 
Published: November 2022

AbstractRecent work has claimed that the emergence of grid cells from trained path-integrator circuits is a more fragile phenomenon than previously reported. In this note we critically assess the main analysis and simulation results underlying this claim, within the proper context of previously published theoretical work. Our assessment reveals that the emergence of grid cells is entirely consistent with this prior theory: hexagonal grid cells robustly emerge precisely when prior theory predicts they should, and don’t when prior theory predicts they should not.
A Peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms
Authors: Cao Min , Day Alison M , Galler Martin , Latimer Heather , Byrne Dominic P , Dwyer Emilia , Bennett Elise , Eyers Patrick A , Veal Elizabeth A 
Published: November 2022

SummaryPeroxiredoxins (Prdx) utilize reversibly oxidized cysteine residues to reduce peroxides but also to promote H2O2signal transduction, including H2O2-induced activation of P38 MAPK. Prdx form H2O2-induced disulfide complexes with many proteins, including multiple kinases involved in P38 MAPK signaling. Here we show that a genetically-encoded fusion between Prdx and the P38 MAPK is sufficient to hyperactivate the kinase in yeast and human cells by a mechanism that does not require the H2O2-sensing cysteine of the Prdx. In yeast, we demonstrate that a P38-Prdx fusion protein compensates for the loss of a scaffold protein and upstream MAP3K kinase activity, driving entry into mitosis. Based on our findings, we propose that the H2O2-induced formation of Prdx-MAPK disulfide complexes provides a scaffold and signaling platform for MAPKK-MAPK signaling. The demonstration that formation of a complex with a Prdx can be sufficient to modify the activity of a kinase has broad implications for peroxide-based signal transduction in eukaryotes.HighlightsP38-Prdx complexes increase P38 (Sty1/MAPK14) phosphorylation in yeast and human cellsTheS. pombePrdx promotes transient thioredoxin-mediated oxidation of a MAPK tyrosine phosphataseP38-Prdx complexes increase P38(Sty1) activity by phosphatase and MAP3K-independent mechanismsP38-Prdx complexes increase the stability and phosphorylation of theS. pombeP38 MAPKK (Wis1)Non-canonical, H2O2-induced autophosphorylation contributes to activation of the Wis1 MAPKK
A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists
Authors: Loos Daniel , Pereira da Costa Filho Ailton , Dutilh Bas E. , Barber Amelia E. , Panagiotou Gianni 
Published: November 2022

AbstractEnvironmental change coupled with alteration in human lifestyles are profoundly impact-ing the microbial communities that play critical roles in the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat changes respectively, we retrieved paired 16S and ITS rRNA amplicon sequence data from 1,580 host, soil, and aquatic samples and explored the ecological patterns of the thousands of detected bacterial and fungal genera. Through this large-scale analysis, we identified 48 bacterial and 4 fungal genera that were prevalent and abundant across the three biomes, demonstrating their fitness in diverse environmental conditions. The presence of generalists significantly contributed to the alpha diversity of their respective kingdom. Their distri-bution across samples explained a large percentage of the variation in the cross-kingdom community structure. We also found that the genomes of these generalists were larger and encoded more secondary metabolism and antimicrobial resistance genes, illuminating how they can dominate diverse microbial communities. Conversely, 30 bacterial and 19 fungal genera were only found in a single habitat, suggesting they cannot readily adapt to different and changing environments. These findings can contribute to our understanding of microbial niche breadth and its consequences for global diversity loss.
UNSUPERVISED HARMONIZATION OF BRAIN MRI USING 3D CYCLE GANS AND ITS EFFECT ON BRAIN AGE PREDICTION
Authors: Komandur Dheeraj , Gupta Umang , Chattopadhyay Tamoghna , Dhinagar Nikhil J. , Thomopoulos Sophia I. , Chen Jiu-Chiuan , Beavers Dan , Steeg Greg ver , Thompson Paul M. ,   the Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: November 2022

ABSTRACTDeep learning methods trained on brain MRI data from one scanner or imaging protocol can fail catastrophically when tested on data from other sites or protocols - a problem known asdomain shift. To address this, here we propose adomain adaptationmethod that trains a 3D CycleGAN (cycle-consistent generative adversarial network) to harmonize brain MRI data from 5 diverse sources (ADNI, WHIMS, OASIS, AIBL, and UK Biobank; total N=4,941 MRIs, age range: 46-96 years). The approach uses 2 generators and 2 discriminators to generate an image harmonized to a specific target dataset given an image from the source domain distribution andvice versa. We train the CycleGAN to jointly optimize an adversarial loss and cyclic consistency. We use a patch-based discriminator and impose identity loss to further regularize model training. To test the benefit of the harmonization, we show that brain age estimation - a common benchmarking task - is more accurate in GAN-harmonized versus raw data.t-SNE maps show the improved distributional overlap of the harmonized data in the latent space.
Peptidyl tRNA hydrolase is required for robust prolyl-tRNA turnover inMycobacterium tuberculosis
Authors: Tomasi Francesca G. , Schweber Jessica T. P. , Kimura Satoshi , Zhu Junhao , Cleghorn Laura A. T. , Davis Susan H. , Green Simon R. , Waldor Matthew K. , Rubin Eric J. 
Published: November 2022

AbstractEnzymes involved in rescuing stalled ribosomes and recycling translation machinery are ubiquitous in bacteria and required for growth. Peptidyl tRNA drop-off is a type of abortive translation that results in the release of a truncated peptide that is still bound to tRNA (peptidyl tRNA) into the cytoplasm. Peptidyl tRNA hydrolase (Pth) recycles the released tRNA by cleaving off the unfinished peptide and is essential in most bacterial species. We developed a sequencing-based strategy called Cu-tRNAseq to study the physiological role of Pth inMycobacterium tuberculosis(Mtb). While most peptidyl tRNA species accumulated in a strain with impaired Pth expression, peptidyl prolyl-tRNA was particularly enriched, suggesting that Pth is required for robust peptidyl prolyl-tRNA turnover. Reducing Pth levels increasedMtb’s susceptibility to tRNA synthetase inhibitors that are in development to treat tuberculosis (TB) and rendered this pathogen highly susceptible to macrolides, drugs that are ordinarily ineffective againstMtb. Collectively, our findings reveal the potency of Cu-tRNAseq for profiling peptidyl tRNAs and suggest that targeting Pth would open new therapeutic approaches for TB.
Evolutionarily diverse caveolins share a common structural framework built around amphipathic discs
Authors: Han Bing , Connolly Sarah , Wilson Louis F. L. , Schultz Darrin T. , Gulsevin Alican , Meiler Jens , Karakas Erkan , Ohi Melanie D. , Kenworthy Anne K. 
Published: November 2022

AbstractCaveolins are a unique family of membrane-remodeling proteins present broadly across animals (Metazoa), and in vertebrates form flask-shaped invaginations known as caveolae. While human caveolin-1 assembles into an amphipathic disc composed of 11 spirally packed protomers, the structural basis underlying caveolin function across animals remains elusive. Here, we predicted structures for 73 caveolins spanning animal diversity, as well as a newly identified choanoflagellate caveolin fromSalpingoeca rosetta,a unicellular relative to animals. This analysis revealed seven conserved structural elements and a propensity to assemble into amphipathic discs. Despite extreme sequence variability, new cryo-EM structures of caveolins from the choanoflagellate and the purple sea urchinStrongylocentrotus purpuratusexhibit striking structural similarities to human caveolin-1, validating the structural predictions. Lastly, tracing the chromosomal evolutionary history of caveolins revealed evolutionary branches where caveolins translocated and expanded, including a parahoxozoan ancestral chromosome as the origin of most caveolin diversity. These results show that caveolins possess an ancient structural framework predating Metazoa and provide a new structural paradigm to explore the molecular basis of caveolin function across diverse evolutionary lineages.
The effects of fasting on ischemic infarcts in the rat
Authors: Schneider Anna M , Buchan Alastair M , Couch Yvonne 
Published: November 2022

AbstractBackgroundInflammation has been found to be largely detrimental early in the acute phase of stroke but beneficial at more chronic stages. Fasting has been shown to reduce inflammation acutely. We aimed to determine whether post-ischemic fasting improves stroke outcomes through attenuated inflammation.MethodsAfter an endothelin-1 lesion was created in the striatum, animals were subjected to either normal feeding or water-only fasting for 24 hours.ResultsIt was found that at 24 hours, fasting reduced infarct volume and BBB breakdown and lowered both circulating and brain neutrophils.ConclusionsThese findings suggest that fasting is a potentially beneficial non-pharmacological additive therapeutic option for cerebral ischemia, which might act by reducing inflammation in the acute disease stage.
MiR-138-5p upregulation during neuronal maturation parallels with an increase in neuronal survival
Authors: Barreda-Manso M. Asunción , Soto Altea , Muñoz-Galdeano Teresa , Reigada David , Nieto-Díaz Manuel , Maza Rodrigo M. 
Published: November 2022

AbstractNeuronal maturation is a process that plays a key role in the development and regeneration of the central nervous system. Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal neuronal maturation are less understood. Among the mechanisms influencing such neuronal maturation process, apoptosis plays a key role. Several regulators have been described to modulate apoptosis, including post-transcriptional regulation by microRNAs. This study aimed to assess whether the strikingly induced miR-138-5p during neuronal maturation contributes to avoiding the neuronal death induced by apoptosis. Our results point out that the observed opposite expression of miR-138-5p and its target Caspase3 might modulate apoptosis favouring neuronal survival at distinct maturation stages. The unchanged expression of miR-138-5p in mature neurons contrasts with the significant downregulation in immature neurons upon apoptotic stimulation. Similarly, immunoblot and individual cellular assays confirmed that during maturation, not only the expression but processing of CASP-3 and caspase activity is reduced after apoptotic stimulation which resulted in a reduction of neuronal death. For all this data, we suggest that the upregulation of miR-138-5p during neuronal maturation is crucial in neuronal survival in pathological or traumatic conditions. Further studies would be needed to determine a more detailed role of miR-138-5p in apoptosis during neuronal maturation and the synergistic action of several microRNAs acting cooperatively on Caspase3 or other apoptotic targets.Graphical abstractHighligthsNeuronal maturation promotes cell survival.Neuronal maturation reduces the processing of CASP-3 and caspase activity after apoptotic stimulation.The expression changes of miR-138-5p and Caspase 3 are opposite during hippocampal neuron maturation.The increase of miR-138-5p expression throughout maturation is not influenced by apoptotic stimulation.MiR-138-5p is suggested as an essential factor concerning neuronal maturation, regulating Caspase 3 and favouring survival.
Modular gene interactions drive modular pan-genome evolution in bacteria
Authors: Castro Juan C. , Brown Sam P. 
Published: November 2022

AbstractDepending on the scale of observation, bacterial genomes are both organized and fluid. While individual bacterial genomes show signatures of organization (e.g., operons), pan-genomes reveal genome fluidity, both in terms of gene content and order (synteny). Here we ask how mutational forces (including recombination and horizontal gene transfer) combine with selection and gene interactions to shape genome organization and variation both within and across strains. We first build an evolutionary simulation model to assess the impact of gene interactions on pan-genome structure. A neutral evolutionary model can produce transient co-segregation of initially linked genes but is vulnerable on longer time-scales to perturbing mutational events. In contrast, incorporation of modular gene fitness interactions can produce sustainable clusters of linked and co-segregating genes, with the network of co-segregation recapitulating the defined simulation ‘ground-truth’ network of gene interactions. To test our model predictions, we exploit the increasing number of closed genomes in model species to define gene co-segregation networks in the pan-genomes ofEscherichia coliandPseudomonas aeruginosa. Using these highly curated pan-genomes, we identify modular clusters of physically linked and co-segregating genes and show that the resulting co-segregation networks map onto underlying gene-regulatory and metabolic gene interaction networks. The results imply that co-segregation networks can contribute to accessory genome annotation, and more generally that gene interactions are the primary force shaping genome structure and operon evolution.