bluuebunny/crossref_metadata_2025 huggingface dataset:
The discovery of genome-wide mutational dependence in naturally evolving
populations
Authors: Green Anna G. , Vargas Roger , Marin Maximillian G. , Freschi Luca , Xie Jiaqi , Farhat Maha R.
Published: April 2023

Background

Evolutionary pressures on bacterial pathogens can result in phenotypic
change including increased virulence, drug resistance, and transmissibility.
Understanding the evolution of these phenotypes in nature and the multiple
genetic changes needed has historically been difficult due to sparse and
contemporaneous sampling. A complete picture of the evolutionary routes
frequently travelled by pathogens would allow us to better understand
bacterial biology and potentially forecast pathogen population
shifts.

Methods

In this work, we develop a phylogeny-based method to assess evolutionary
dependency between mutations. We apply our method to a dataset of
31,428Mycobacterium tuberculosiscomplex
(MTBC) genomes, a globally prevalent bacterial pathogen with increasing
levels of antibiotic resistance.

Results

We find evolutionary dependency within simultaneously- and
sequentially-acquired variation, and identify that genes with dependent
sites are enriched in antibiotic resistance and antigenic function. We
discover 20 mutations that potentiate the development of antibiotic
resistance and 1,003 dependencies that evolve as a consequence antibiotic
resistance. Varying by antibiotic, between 9% and 80% of resistant strains
harbor a dependent mutation acquired after a resistance-conferring variant.
We demonstrate that mutational dependence can not only improve prediction of
phenotype (e.g. antibiotic resistance), but can also detect sequential
environmental pressures on the pathogen (e.g. the pressures imposed by
sequential antibiotic exposure during the course of standard
multi-antibiotic treatment). Taken together, our results demonstrate the
feasibility and utility of detecting dependent events in the evolution of
natural populations.

Data and code available at:https://github.com/farhat-lab/DependentMutations
Knowledge of COVID-19 Symptoms, Transmission, and Prevention: Evidence from Health and Demographic Surveillance in Southern Mozambique
Authors: Nhacolo Ariel Q. , Madewell Zachary J. , Muir Jonathan A. , Sacoor Charfudin N. , Xerinda Elisio G. , Matsena Teodimiro , Bassat Quique , Whitney Cynthia G. , Mandomando Inácio M. , Cunningham Solveig A.
Published: April 2023

Over 230,000 COVID-19 cases and over 2,200 deaths have been reported in Mozambique though May 2023. Understanding community members’ knowledge of SARS-CoV-2 transmission and prevention is essential for directing public health interventions to reduce disease spread and improve vaccination coverage. Here, we describe knowledge of COVID-19 transmission, prevention, and symptoms among community residents in Mozambique. We conducted a cross-sectional survey among 33,087 households in a Health and Demographic Surveillance System in Manhiça, Mozambique. Participants were recruited at the tail end of the Delta variant wave in September 2021 to the peak of Omicron cases in January 2022. Principal components analysis was used to create scores representing knowledge of COVID-19 symptoms, transmission, and prevention. Multiple imputation and quasi-Poisson regression were used to examine associations between demographic characteristics and sources of COVID-19 information, and knowledge of COVID-19 symptoms, transmission, and prevention. We examined whether sources of COVID-19 information mediated the relationship between educational attainment and knowledge of symptoms, transmission, and prevention. Across this rural community, 98.2%, 97.0%, and 85.1% of respondents reported knowing how COVID-19 could be prevented, that SARS-CoV-2 can cause disease, and how SARS-CoV-2 is transmitted, respectively. Most cited symptoms were cough (51.2%), headaches (44.9%), and fever (44.5%); transmission mechanisms were droplets (50.5%) or aerosol (<5 µm diameter) (46.9%) from an infected person; and prevention measures were handwashing (91.9%) and mask-wearing (91.8%). Characteristics associated with greater knowledge of symptoms, transmission, and prevention included having at least primary education, older age, employment, higher wealth, and Christian religion. Respondents who had had COVID-19 symptoms were also more likely to have knowledge of symptoms, transmission, and prevention. Gathering information from TV, WhatsApp, radio, and hospital mediated the relationship between educational attainment and knowledge scores. These findings support the need for outreach and for community-engaged messaging to promote prevention measures, particularly among people with low education.
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

Cerebral 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

We 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

Understanding 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

The 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.
Small time delay approximation in replicator dynamics
Authors: Miȩkisz Jacek , Mohamadichamgavi Javad , Vardanyan Raffi
Published: April 2023

We present a microscopic model of replicator dynamics with strategy-dependent time delays. In such a model, new players are born from parents who interacted and received payoffs in the past. In the case of small delays, we use Taylor expansion to get ordinary differential equations for frequencies of strategies with time delays as parameters. We apply our technique to get analytic expressions for interior stationary states in two games: Snowdrift and Stag-hunt. We show that interior stationary states depend continuously upon time delays. Our analytic formulas for stationary states approximate well exact numerical results for small time delays.
In silicopredictions of the hepatic metabolic clearance in humans for 10 drugs with highly variablein vitropharmacokinetics
Authors: Fagerholm Urban
Published: April 2023

Abstract

Challenges/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

Programmed 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

Antibody 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

Thedilute 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

Wet 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

Knowledge 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

Bacteria 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.

Significance

Many 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

Chromosomal 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.
Genome size, genetic diversity, and phenotypic variability imply the effect of genetic variation instead of ploidy on trait plasticity in the cross-pollinated tree species of mulberry
Authors: Gnanesh Belaghihalli N , Mondal Raju , Arunakumar GS , Manojkumar HB , Singh Pradeep , Bhavya MR , Sowbhagya P , Burji Shreyas M , Mogili T , Sivaprasad V
Published: April 2023

Genome size, genetic diversity, and phenotypic vitiation were estimated to develop a model-based population structure and identify ploidy-associated traits of a wide collection of cross-pollinated, highly heterozygous tree species ofMorus.

Elucidation of genome size (GS), genetic and phenotypic variation is the fundamental aspect of crop improvement programs. Mulberry is a cross-pollinated, highly heterozygous tree eudicot, and comprised of huge ploidy variation with great adaptability across the world. However, because of inadequate information on GS, ploidy-associated traits, as well as the correlation between genetic and phenotypic variation hinder the further improvement of mulberry. In this present research, a core set of 157 germplasm accessions belonging to eight accepted species ofMorusincluding promising functional varieties were chosen to represent the genetic spectrum from the whole germplasm collection. To estimate the GS, accessions were subjected to flow cytometry (FCM) analysis and the result suggested that four different ploidies (2n=2x, 3x, 4x, and 6x) with GS ranging from 0.72±0.005 (S-30) to 2.89±0.015 (M. serrata), accounting ∼4.01 fold difference. The predicted polyploidy was further confirmed with metaphase chromosome count. In addition, the genetic variation was estimated by selecting a representative morphologically, diverse population of 82 accessions comprised of all ploidy variations using simple sequence repeats (SSR). The estimated average Polymorphism Information Content (PIC) and expected heterozygosity showed high levels of genetic diversity. Additionally, three populations were identified by the model-based population structure (k=3) with a moderate level of correlation between the populations and different species of mulberry, which imply the effect of genetic variation instead of ploidy on trait plasticity that could be a consequence of the high level of heterozygosity imposed by natural cross-pollination. Further, the correlation between ploidies, especially diploid and triploid with selected phenotypic traits was identified, however, consistency could not be defined with higher ploidy levels (>3x). Moreover, incite gained here can serve as a platform for future omics approaches to the improvement of mulberry traits.
Lectins in pistils play a key role in self-incompatibility in the heterostylousLinum perenne
Authors: Levchuk Hanna , Makhno Yuliia , Costa Maria Manuela Ribeiro , Lenhard Michael
Published: April 2023

Self-incompatibility is one of the mechanisms preventing inbreeding in populations, based on the failure of pollen grains to germinate or of pollen tubes to grow normally in incompatible crosses. A unique model for studying this process are heterostylous species, in which self-incompatibility alleles are closely linked to flower morphological traits. One such species isL. perenne, a classic distylous species with reciprocal herkogamy and complete self-incompatibility strongly linked. The mechanism of self-pollen recognition is poorly understood in most heterostylous species, includingL. perenne. As self-incompatibility in other systems is based on protein-protein interactions and many extracellular proteins are glycosylated, one of the possible participants in this process may be lectins. Therefore, we aimed to investigate the lectin activity in pistils and stamens ofL. perenneL-morph and S-morph plants and to establish whether these lectins take part in self-incompatibility. We show that pistil-derived galactose-specific Ca2+-independent lectins from the respective other morph can overcome self-incompatibility in heterostylousL. perenne. This may be due to the presence of some lectins that are specific for arabinose and xylose. Our results suggest that lectins participate in signaling pathways for recognition at the pollen-stigma interface and are involved in the regulation of the self-incompatibility process inL. perenne.
A hybrid demultiplexing strategy that improves performance and robustness of cell hashing
Authors: Li Lei , Sun Jiayi , Fu Yanbin , Changrob Siriruk , McGrath Joshua J.C. , Wilson Patrick C.
Published: April 2023

Recent advances in single cell RNA sequencing allow users to pool multiple samples and demultiplex in downstream analysis, which greatly increase experimental efficiency and cost-effectiveness. Among all the demultiplexing methods, nucleotide barcode-based cell hashing has gained widespread popularity due to its compatibility and simplicity. Despite these advantages, certain issues of this technic remain to be solved, such as challenges in distinguishing true positive from background, high reagent cost for samples with large cell numbers, and unpredictable false negative and false doublet rates. Here, we propose a hybrid demultiplexing strategy that increases calling accuracy and cell recovery of cell hashing without adding experimental cost. In this approach, we computationally cluster all single cells based on their natural genetic variations and assign donor identity by finding the dominant hashtag in each genotype cluster. This hybrid strategy assigns donor identity to any cell that is identified as singlet by either genotype clustering or cell hashing, which allows us to demultiplex most majority of cells even if only a small fraction of cells are labeled with hashtags. When comparing its performance with cell hashing on multiple real-world datasets, this hybrid approach consistently generates reliable demultiplexing results with increased cell recovery and accuracy.

Key Points

The improved cut-off calling tool, HTOreader, accurately distinguishes true positive from background signal for each individual hashtag.

The hybrid demultiplexing strategy increases cell recovery of cell hashing by increasing cut-off calling accuracy and decreasing false negative and false double rates.

The hybrid strategy enhances cost-effectiveness of cell hashing and consistently produces reliable demultiplexing results, regardless of hashtag staining quality.

The hybrid strategy can be seamlessly integrated into a variety of single-cell experimental protocols and analytic pipelines.
Guadalupe fur seal alopecia: a metabolic syndrome associated to climatic anomalies?
Authors: Guzmán-Solís Ariadna A. , Elorriaga-Verplancken Fernando R. , Acevedo-Whitehouse Karina A.
Published: April 2023

Alopecia is characterized by the thinning and loss of hair or fur, and has been observed in different marine carnivores. Until recently, there were no records of alopecia in marine mammals from the Northeast Pacific Ocean. However, sightings of juvenile male Guadalupe fur seals with patchy alopecia in the ventral body have been reported in the San Benito Archipelago. This is concerning given that the species is considered endangered under Mexican law and has only started to recover from near extinction less than a century ago. We captured 13 fur seals at San Benito Archipelago during the summer of 2017 and 2018 and collected fur samples for common dermatological analysis, as well as scanning electron microscopy and X-ray spectroscopy. We found marked damage to the structure of guard fur, with loss of integrity, medullary damage and perforations. Damage to secondary underfur hair was less common. We found no evidence of dermatophyte microorganisms or ectoparasites commonly associated with alopecia. We suggest that the damage is caused by metabolic alterations secondary to nutritional stress that is consequential to high sea surface temperatures that alter prey availability. This is the first study of alopecia in an otariid pinniped of the Northeast Pacific Ocean.
Beyond gene-disease validity: capturing structured data on inheritance, allelic-requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions
Authors: Josephs Katherine S , Roberts Angharad M , Theotokis Pantazis , Walsh Roddy , Ostrowski Philip J , Edwards Matthew , Fleming Andrew , Thaxton Courtney , Roberts Jason D , Care Melanie , Zareba Wojciech , Adler Arnon , Sturm Amy C , Tadros Rafik , Novelli Valeria , Owens Emma , Bronicki Lucas , Jarinova Olga , Callewaert Bert , Peters Stacey , Lumbers Tom , Jordan Elizabeth , Asatryan Babken , Krishnan Neesha , Hershberger Ray E , Chahal C. Anwar A. , Landstrom Andrew P. , James Cynthia , McNally Elizabeth M , Judge Daniel P , van Tintelen Peter , Wilde Arthur , Gollob Michael , Ingles Jodie , Ware James S
Published: April 2023

Background

As availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including as secondary findings.

Methods

We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering.

Results

For 36/65 gene-disease pairs, loss-of-function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using CardiacG2P as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches.

Conclusions

Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is pre-requisite for scalable genomic testing.
A rapid review of what organisational level factors support or inhibit the scale and spread of innovations in children’s social care
Authors: Mann Mala , Lifford Kate , O’Connell Susan , Weightman Alison , Searchfield Lydia , Lewis Ruth , Cooper Alison , Edwards Adrian
Published: April 2023

Innovation may provide a means for tackling challenges facing childrens social care, some of them deep-rooted and many exacerbated by COVID-19. Welsh Government has recently committed to a significant 3-year investment to support innovation in adults and childrens social care. The delivery of social care in Wales has a complex and multi-faceted approach, involving collaborative working between a range of organisations, which will likely affect decisions around implementation and scale-up of new and/or existing interventions. The aim of the review was to identify any factors (barriers and enablers) that affect the implementation and scale up of an innovation in childrens social care organisations.

Ten studies were identified, comprising three secondary studies (reviews) and seven primary studies. Factors potentially influencing scale and spread of innovation were extracted and categorised. The domains (and sub-domains) covered by included studies were; adopters (staff role/identity; carer input), organisation (capacity to innovate; readiness for change; nature of adoption/funding; extent of change needed; work needed to implement), and wider system (political/policy; regulatory/legal; professional; socio-cultural).

Enablers for which a clear consensus seems to be emerging across the literature included: specific training and support for professional staff, support and mutual respect within inter-professional and professional-carer relationships, senior management/leadership buy-in and support, multi-disciplinary communication and joint working, and developing compatible data systems to support joint working/collaboration. Barriers for which a clear consensus seems to be emerging across the literature were: short term or lack of funding (the need for funding was presented as an enabler in some studies), and implementation difficulties (e.g. multiple priorities and changing structures).

Policy Implications: This review highlights the complexity of the social care models but provides some clear pointers for policy and practice. The findings indicate the need for: senior management buy-in and support, short and longer term funding, multi-disciplinary communication and joint working, good professional (and professional-carer) relationships with support and mutual respect, and specific training and support for professional staff.

The confidence in the evidence is uncertain as the study designs included non-systematic reviews and service evaluations; most studies did not use a formal methodology and all had some quality limitations.
SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration
Authors: Hartmann Jakob , Bajaj Thomas , Otten Joy , Klengel Claudia , Gellner Anne-Kathrin , Junglas Ellen , Hafner Kathrin , Anderzhanova Elmira A , Tang Fiona , Missig Galen , Rexrode Lindsay , Li Katelyn , Pöhlmann Max L , Heinz Daniel E , Lardenoije Roy , Dedic Nina , McCullough Kenneth M , Próchnicki Tomasz , Rhomberg Thomas , Martinelli Silvia , Payton Antony , Robinson Andrew C. , Stein Valentin , Latz Eicke , Carlezon William A , Schmidt Mathias V , Murgatroyd Chris , Berretta Sabina , Klengel Torsten , Pantazopoulos Harry , Ressler Kerry J , Gassen Nils C
Published: April 2023

High levels of proinflammatory cytokines induce neurotoxicity and catalyze inflammation-driven neurodegeneration, but the specific release mechanisms from microglia remain elusive. We demonstrate that secretory autophagy (SA), a non-lytic modality of autophagy for secretion of vesicular cargo, regulates neuroinflammation-mediated neurodegeneration via SKA2 and FKBP5 signaling. SKA2 inhibits SA-dependent IL-1β release by counteracting FKBP5 function. HippocampalSka2knockdown in mice hyperactivates SA resulting in neuroinflammation, subsequent neurodegeneration and complete hippocampal atrophy within six weeks. The hyperactivation of SA increases IL-1β release, initiating an inflammatory feed-forward vicious cycle including NLRP3-inflammasome activation and Gasdermin D (GSDMD)-mediated neurotoxicity, which ultimately drives neurodegeneration. Results from protein expression and co-immunoprecipitation analyses of postmortem brains demonstrate that SA is hyperactivated in Alzheimer’s disease. Overall, our findings suggest that SKA2-regulated, hyperactive SA facilitates neuroinflammation and is linked to Alzheimer’s disease, providing new mechanistic insight into the biology of neuroinflammation.
Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling
Authors: Potter Alisa , Cabrera-Orefice Alfredo , Spelbrink Johannes N.
Published: April 2023

Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimised this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multi-protein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically-induced mtDNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
Efflux pumps mediate changes to fundamental bacterial physiology via membrane potential
Authors: Whittle Emily E , Orababa Oluwatosin , Osgerby Alexander , Element Sarah J , Blair Jessica MA , Overton Tim W
Published: April 2023

Efflux pumps are well known to be an important mechanism for removing noxious substances such as antibiotics from bacteria. Given that many antibiotics function by accumulating inside bacteria, efflux pumps contribute to resistance. Efflux pump inactivation is a potential strategy to combat antimicrobial resistance, as bacteria would not be able to pump out antibiotics. We recently discovered that the impact of loss of efflux function is only apparent in actively growing cells. We demonstrated that the global transcriptome ofSalmonellaTyphimurium is drastically altered during slower growth leading to stationary phase cells having a re-modelled, less permeable, envelope that prevents antibiotics entering the cell. Here, we investigated the effects of deleting the major efflux pump ofSalmonellaTyphimurium, AcrB, on global gene transcription across growth. We revealed that anacrBknockout entered stationary phase later than the wild type strain SL1344, and displayed increased and prolonged expression of genes responsible for anaerobic energy metabolism. We devised a model linking efflux and membrane potential, whereby deactivation of AcrB prevents influx of protons across the inner membrane and thereby hyperpolarisation. Knockout or deactivation of AcrB was demonstrated to increase membrane potential. We propose that the global transcription regulator ArcBA senses changes to the redox state of the quinol pool (linked to the membrane potential of the bacterium) and coordinates the shift from exponential to stationary phase via the key master regulators RpoS, Rsd, and Rmf. Inactivation of efflux pumps therefore influences the fundamental physiology ofSalmonella, with likely impacts on multiple phenotypes.

Importance

We demonstrate for the first time that deactivation of efflux pumps brings about changes to gross bacterial physiology and metabolism. Rather than simply being a response to noxious substances, efflux pumps appear to play a key role in maintenance of membrane potential and thereby energy metabolism. This discovery suggests that efflux pump inhibition or inactivation might have unforeseen positive consequences on antibiotic activity. Given that stationary phase bacteria are more resistant to antibiotic uptake, late entry into stationary phase would prolong antibiotic accumulation by bacteria. Furthermore, membrane hyperpolarisation could result in increased generation of reactive species proposed to be important for the activity of some antibiotics. Finally, changes in gross physiology could also explain the decreased virulence of efflux mutants.
APPLICATION OF PLANTS BASED MATERIAL FOR THE MANUFACTURING OF MOSQUITO REPELLENT SURFACE COATING
Authors: Iftikhar Tehreema , Majeed Hammad , Abid Rida , Khan Faheem. A.
Published: April 2023

Mosquitos have been a malice and source of many diseases in humans. Later on, humans understood they learned that plants also possess mosquito-repellent properties. Different insectrepellent coatings are present in the market which are chemically prepared and can be harmful to humans and the environment. Different plants have insect-repellent properties which have been utilized in this research to make a nature-based insect-repellent surface coating.Moringa oleiferaL. andMentha piperitaL. are naturally insect-repellent plants. Nanoparticles increase the surface area and efficiency of extracts of plants. Thus, ZnONP ofMoringa olieferaL. andMentha piperitaL. plants were made characterization was done through UV-vis spectroscopy, FTIR, and PSA. The UV-visible spectrum showed absorption peaks for ZnO nanoparticles at 350nm forMentha piperitaL. and 356nm forMoringa oleiferaL. The particle size analysis indicated the variable sizes of ZnONPs for both plants. FTIR showed vibration peaks from 3341 to 650cm-1forMoringa oleiferaL. and 3393 to 700 cm-1forMentha piperitaL. ZnONPs were used in paint along with water extracts of plants to make the paint insect-repellent in nature. Mosquito repellent activity of paint formulations was also tested againstAedes aegypti.