bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brain and blood single-cell transcriptomics in acute and subacute phases after experimental stroke
Authors: Garcia-Bonilla Lidia , Shahanoor Ziasmin , Sciortino Rose , Nazarzoda Omina , Racchumi Gianfranco , Iadecola Costantino , Anrather Josef 
Published: April 2023

SummaryCerebral ischemia triggers a powerful inflammatory reaction involving both peripheral leukocytes and brain resident cells. Recent evidence indicates that their differentiation into a variety of functional phenotypes contributes to both tissue injury and repair. However, the temporal dynamics and diversity of post-stroke immune cell subsets remain poorly understood. To address these limitations, we performed a longitudinal single-cell transcriptomic study of both brain and mouse blood to obtain a composite picture of brain-infiltrating leukocytes, circulating leukocytes, microglia and endothelium diversity over the ischemic/reperfusion time. Brain cells and blood leukocytes isolated from mice 2 or 14 days after transient middle cerebral artery occlusion or sham surgery were purified by FACS sorting and processed for droplet-based single-cell transcriptomics. The analysis revealed a strong divergence of post-ischemic microglia, macrophages, and neutrophils over time, while such diversity was less evident in dendritic cells, B, T and NK cells. Conversely, brain endothelial cells and brain associated-macrophages showed altered transcriptomic signatures at 2 days post-stroke, but low divergence from sham at day 14. Pseudotime trajectory inference predicted the in-situ longitudinal progression of monocyte-derived macrophages from their blood precursors into day 2 and day 14 phenotypes, while microglia phenotypes at these two time points were not connected. In contrast to monocyte-derived macrophages, neutrophils were predicted to be continuously de-novo recruited from the blood. Brain single-cell transcriptomics from both female and male aged mice did not show major changes in respect to young mice, but aged and young brains differed in their immune cell composition. Furthermore, blood leukocyte analysis also revealed altered transcriptomes after stroke. However, brain-infiltrating leukocytes displayed higher transcriptomic divergence than their circulating counterparts, indicating that phenotypic diversification into cellular subsets occurs within the brain in the early and the recovery phase of ischemic stroke. In addition, this resource report contains a searchable databasehttps://anratherlab.shinyapps.io/strokevis/to allow user-friendly access to our data. The StrokeVis tool constitutes a comprehensive gene expression atlas that can be interrogated at the gene and cell type level to explore the transcriptional changes of endothelial and immune cell subsets from mouse brain and blood after stroke.
Tunable photoinitiated hydrogel microspheres for direct quantification of cell-generated forces in complex three-dimensional environments
Authors: Garcia-Herreros Antoni , Yeh Yi-Ting , Tu Yunpeng , Kandasamy Adithan , del Alamo Juan C. , Criado-Hidalgo Ernesto 
Published: April 2023

AbstractWe present a high-throughput method using standard laboratory equipment and microfluidics to produce cellular force microscopy probes with controlled size and elastic modulus. Mechanical forces play crucial roles in cell biology but quantifying these forces in physiologically relevant systems remains challenging due to the complexity of the native cell environment. Polymerized hydrogel microspheres offer great promise for interrogating the mechanics of processes inaccessible to classic force microscopy methods. However, despite significant recent advances, their small size and large surface-to-volume ratio impede the high-yield production of probes with tunable, monodisperse distributions of size and mechanical properties.To overcome these limitations, we use a flow-focusing microfluidic device to generate large quantities of droplets with highly reproducible, adjustable radii. These droplets contain acrylamide gel precursor and the photoinitiator Lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) as a source of free radicals. LAP provides fine control over microsphere polymerization due to its high molar absorptivity at UV wavelengths and moderate water solubility. The polymerized microspheres can be functionalized with different conjugated extracellular matrix proteins and embedded with fluorescent nanobeads to promote cell attachment and track microsphere deformation.As proof of concept, we measure the mechanical forces generated by a monolayer of vascular endothelial cells engulfing functionalized microspheres. Individual nanobead motions are tracked in 3D and analyzed to determine the 3D traction forces within seconds and without the need for solving an ill-posed inverse problem. These results reveal that the cell monolayer collectively exerts strong radial compression and subtle lateral distortions on the encapsulated probe.
Seasonal variation in great tit (Parus major) energy requirements: reallocation versus increased demand
Authors: Pacioni Cesare , Sentís Marina , Hambly Catherine , Speakman John R , Kerimov Anvar , Bushuev Andrey , Lens Luc , Strubbe Diederik 
Published: April 2023

AbstractUnderstanding how birds annually allocate energy to cope with changing environmental conditions and physiological states is a fundamental question in avian ecology. The two main hypotheses to explain annual patterns in energy use are “reallocation” and “increased demand”. The reallocation hypothesis suggests equal energetic costs in winter and breeding seasons, while the increased demand suggests that energy demand should be highest during breeding. Under the standard aerobic capacity model of endothermy, birds are expected to adjust the mass and/or metabolic intensity of their bodies in ways that are consistent with expected cold- and/or activity-induced costs. Here, we look for metabolic signatures of reallocation versus increased demands in the energy requirements of a small, resident passerine of a temperate-zone (great tit,Parus major). To do so, we measured whole-body and mass-independent basal (BMR), summit (Msum), and field (FMR) metabolic rates during late winter and during the chick-rearing period (breeding). We also assessed whether, and to what extent, metabolic rates conform to the predictions of the aerobic capacity model of endothermy. We found that great tits showed no substantial differences in energy expenditure between winter and the breeding season, providing support for the reallocation hypothesis. Only mass-independent Msumshowed seasonal variation, with significantly higher values (∼4%) in winter compared to the breeding season. Our results also lend support to the predictions of the aerobic capacity model for the evolution of endothermy, as we found that whole-body BMR and Msumwere positively related. We argue that both energy reallocation and the limited increase in mass-independent Msumare consistent with the relatively mild winter temperatures recorded during our study period. Our results confirm that both BMR and Msumare flexible traits that vary in ways that are consistent with expected cold- and/or activity-induced costs.
A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison
Authors: Wehrenberg Gerrit , Tokarska Małgorzata , Cocchiararo Berardino , Nowak Carsten 
Published: April 2023

AbstractThe European bison was saved from the brink of extinction due to considerable conservation efforts since the early 20thcentury. The current global population of > 9,500 individuals is the result of successfulex situbreeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in furtherBosspecies with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world’s first studbook of a threatened species.
In silicopredictions of the hepatic metabolic clearance in humans for 10 drugs with highly variablein vitropharmacokinetics
Authors: Fagerholm Urban 
Published: April 2023

AbstractChallenges/problems forin vitromethodologies for prediction of human clinical pharmacokinetics include inter- and intra-laboratory variability, and common occurance of high limits of quantification, low recovery, low parameter validity and low reproducibility. In this study, 10 drugs with substantial differences in human hepatocyte intrinsic metabolic clearance (CLint) and fraction unbound in plasma (fu) between laboratories were selected. The average and maximum ratios between highest and lowest reported predictedin vivohepatic metabolic clearance (CLH) for the drugs were 529- and 2436-fold, respectively. Thein vivoCLHwas predicted usingin vitroCLintand fudata from the various highly sources and using ourin silicomethodology. The main aim was to compare the predictive accuracies for thein vitroandin silicomethodologies. Prediction errors forin vitromethodology ranged from 1.1-to 578-fold, with an average of 150-fold for lowest predicted estimates and 16-fold for highest predicted estimates. Thein vitrobased predictions produced 36-to 38-fold higher average and maximum prediction errors than thein silicomethodology, respectively. Mean and maximumin silicoprediction errors were 4.2- and 15-fold, respectively, which is consistent with earlier results. In contrast to thein vitromethodology thein silicomodels did not predict high hepatic extraction ratio for drugs with low CLH. Overall, thein silicomethod clearly outperformedin vitrodata for prediction of CLHin man for 10 drugs with large interlaboratory variability.
Conserved domains of meiosis-specific CHK2 protein in budding yeast contribute to its kinase activity
Authors: Padmarajan Jinsha , Edilyam Abhijna Krishnan , Subramanian Vijayalakshmi V. 
Published: April 2023

AbstractProgrammed double strand DNA breaks in meiosis can be repaired as inter-homologue crossovers and thereby aid the faithful segregation of homologous chromosomes. Biased repair mechanisms enforce repair with the homologue. Further, DNA breaks left unrepaired lead to checkpoint activation. Meiosis-specific Chk2 kinase in budding yeast mediates the biased repair of meiotic DSBs using homologue partner but also enforces the meiotic checkpoint. Here we investigate Mek1 kinase activity in budding yeast by analyzing novel point mutants derived from an EMS mutagenesis screen. The point mutants in different domains of Mek1 abolish its activity that cannot be rescued by complementation in transheterozygotes. Our findings lend insight on the mechanism of Mek1 function during meiosis.
A class of antibodies that overcome a steric barrier to cross-group neutralization of influenza viruses
Authors: Simmons Holly C. , Watanabe Akiko , Oguin Thomas H. , Sempowski Gregory D. , Kuraoka Masayuki , Kelsoe Garnett , McCarthy Kevin R. 
Published: April 2023

AbstractAntibody titers that inhibit the influenza virus hemagglutinin (HA) from engaging its receptor are the accepted correlate of protection from infection. Many potent antibodies with broad, intra-subtype specificity bind HA at the receptor binding site (RBS). One barrier to broad H1-H3 cross-subtype neutralization is an insertion (133a) between positions 133 and 134 on the rim of the H1 HA RBS. We describe here a class of antibodies that overcome this barrier. These genetically unrestricted antibodies are abundant in the human B-cell memory compartment. Analysis of the affinities of selected members of this class for historical H1 and H3 isolates suggest that they were elicited by H3 exposure and broadened or diverted by later exposure(s) to H1 HA. RBS mutations in egg-adapted vaccine strains cause the new H1 specificity of these antibodies to depend on the egg adaptation. The results suggest that suitable immunogens might elicit 133a-independent, H1-H3 cross neutralization by RBS-directed antibodies.
Disruption of a BTB-ZF transcription factor causes female sterility and melanization in the larval body of the silkworm,Bombyx mori
Authors: Tomihara Kenta , Kiuchi Takashi 
Published: April 2023

AbstractThedilute black(bd) of the silkwormBombyx moriis a recessive mutant that produces a grayish-black color in the larval integument, instead of the characteristic white color found in wild-type larvae. In addition, eggs produced bybdfemales are sterile due to a deficiency in the micropylar apparatus. We identified candidate genes responsible for thebdphenotype using publicly available RNA-seq data. One of these candidate genes was homologous to thematernal gene required for meiosis(mamo) ofDrosophila melanogaster, which encodes a broad-complex, tramtrack, and bric-à-brac-zinc finger (BTB-ZF) transcription factor essential for female fertility. In three independentbdstrains, the expression of theB. mori mamo(Bmmamo) was downregulated in the larval integument. Using a CRISPR/Cas9-mediated knockout strategy, we found thatBmmamoknockout mutants exhibit a grayish-black color in the larval integument and female infertility. Moreover, larvae obtained from the complementation cross betweenbd/+mutants and heterozygous knockouts for theBmmamoalso exhibited a grayish-black color, indicating thatBmmamois responsible for thebdphenotype. Gene expression analysis usingBmmamoknockout mutants suggested that the BmMamo protein suppresses the expression of melanin synthesis genes. Previous comparative genome analysis revealed that theBmmamowas selected during silkworm domestication, and we found thatBmmamoexpression in the larval integument is higher inB. morithan in the wild silkwormB. mandarina, suggesting that theBmmamois involved in domestication-associated pigmentation changes of the silkworm.Graphical Abstract
Advanced PCL-Chitosan Nanofibrous Wound Care Material for Enhanced Wound Healing
Authors: R Velikkakath G , Wilson Jijo J , Thomas L V 
Published: April 2023

AbstractWet electrospinning has many advantages over conventional electrospinning processes. However, the technique is not commonly used due to the limited availability of suitable materials and accessibility of the technique. In this study different ratios of PCL-chitosan blend was prepared and fabricated into a highly porous scaffold system by wet electrospinning. The keratinocytes and fibroblast cells were seeded on the top and bottom side of the scaffold respectively to develop a bilayer skin construct. We conducted tests to examine the biological properties of the material including their cell viability, in vitro wound healing efficiency, and gene expression of collagen-I, collagen-III, cytokeratin-14, and cytokeratin-5. The findings indicate that PCL-chitosan can serve as a highly effective wound dressing material, with remarkable wound healing properties.
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
Authors: Xiang Guanjue , He Xi , Giardine Belinda M. , Isaac Kathryn J. , Taylor Dylan J. , McCoy Rajiv C. , Jansen Camden , Keller Cheryl A. , Wixom Alexander Q. , Cockburn April , Miller Amber , Qi Qian , He Yanghua , Li Yichao , Lichtenberg Jens , Heuston Elisabeth F. , Anderson Stacie M. , Luan Jing , Vermunt Marit W. , Yue Feng , Sauria Michael E.G. , Schatz Michael C. , Taylor James , Göttgens Berthold , Hughes Jim R. , Higgs Douglas R. , Weiss Mitchell J. , Cheng Yong , Blobel Gerd A. , Bodine David M. , Zhang Yu , Li Qunhua , Mahony Shaun , Hardison Ross C. 
Published: April 2023

AbstractKnowledge of locations and activities ofcis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in ourValidatedSystematicIntegration(VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas
Authors: Spencer Noah , Łukasik Piotr , Meyer Mariah , Veloso Claudio , McCutcheon John P. 
Published: April 2023

AbstractBacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the same evolutionary processes that drive genome reduction and simplification may also sometimes cause genome expansion and complexification. A bacterial endosymbiont of cicadas,Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a singleHodgkinialineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each newHodgkinialineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages sum to the total found in the ancestral single genome. This splitting process creates genetically distinctHodgkiniacells that must function together to carry out basic cellular processes, but also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA ofHodgkiniafrom different cicada species with different amounts of splitting – along with those of its structurally stable, unsplit partner endosymbiontSulcia muelleri– we show thatHodgkiniadoes not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find evidence thatHodgkiniahas a reduced capacity for basic transcriptional control independent of the splitting process. Collectively, these findings reveal another layer of degeneration that further pushes the limits of canonical molecular and cell biology inHodgkinia, and may in part explain its propensity to go extinct through symbiont replacement.SignificanceMany cicadas host two bacterial endosymbionts,HodgkiniaandSulcia, which produce essential amino acids missing from the insect’s xylem sap diet. Following 100+ million years of strict host association, both bacteria have lost many genes and posses extremely tiny genomes. In some cicadas,Hodgkiniahas split into multiple cell lineages, distributing its genes, with little respect to their function, among separate lineages present at (sometimes wildly) different abundances. We find no transcriptional response to this inHodgkinia, resulting in similarly imbalanced mRNA abundances. We also find less control of transcription inHodgkiniacompared toSulcia.Hodgkinia’s transcriptome embodies an extreme, even relative to other highly-reduced endosymbionts, and raises questions about how cell biology in multi-lineageHodgkiniacan function at all.
Chromosomal instability can favor macrophage-mediated immune response and induce a broad, vaccination-like anti-tumor IgG response
Authors: Hayes Brandon H. , Wang Mai , Zhu Hui , Phan Steven H. , Dooling Lawrence J. , Andrechak Jason C. , Chang Alexander H. , Tobin Michael P. , Ontko Nicholas M. , Marchena Tristan , Discher Dennis E. 
Published: April 2023

AbstractChromosomal instability (CIN), a state in which cells undergo mitotic aberrations that generate chromosome copy number variations, generates aneuploidy and is thought to drive cancer evolution. Although associated with poor prognosis and reduced immune response, CIN generates aneuploidy-induced stresses that could be exploited for immunotherapies. In such contexts, macrophages and the CD47-SIRPα checkpoint are understudied. Here, CIN is induced pharmacologically induced in poorly immunogenic B16F10 mouse melanoma cells, generating persistent micronuclei and diverse aneuploidy while skewing macrophages towards an anti-cancer M1-like phenotype, based on RNA-sequencing profiling, surface marker expression and short-term antitumor studies. These results further translate toin vivoefficacy: Mice bearing CIN-afflicted tumors with wild-type CD47 levels survive only slightly longer relative to chromosomally stable controls, but long-term survival is maximized when combining macrophage-stimulating anti-tumor IgG opsonization and some form of disruption of the CD47-SIRPα checkpoint. Survivors make multi-epitope,de novoanti-cancer IgG that promote macrophage-mediated phagocytosis of CD47 knockout B16F10 cells and suppress tumoroidsin vitroand growth of tumorsin vivo. CIN does not greatly affect the level of the IgG response compared to previous studies but does significantly increase survival. These results highlight an unexpected therapeutic benefit from CIN when paired with maximal macrophage anti-cancer activity: an anti-cancer vaccination-like antibody response that can lead to more durable cures and further potentiate cell-mediated acquired immunity.