bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserving genetic diversity during climate change: Niche marginality and discrepant monitoring capacity in Europe
Authors: Pearman Peter B. , Broennimann Olivier , Albayrak Tamer , Alves Paulo Célio , Bertola Laura D. , Biedrzycka Aleksandra , Buzan Elena , Cubric-Curik Vlatka , Fedorca Ancuta , Godoy José A. , Hvilsom Christina , Klinga Peter , Konopiński Maciej K. , Kopatz Alexander , Laikre Linda , Lopez Fernandez Margarida , Mergeay Joachim , Neophytou Charalambos , Pálsson Snæbjörn , Paz-Vinas Ivan , Posledovich Diana , Rolečková Barbora , Ruņģis Dainis , Segelbacher Gernot , Kavčič Sonnenschein Katja , Thurfjell Henrik , Träger Sabrina , Vernesi Cristiano , Vilà Carles , Westergren Marjana , Zachos Frank E. , Guisan Antoine , Bruford Michael 
Published: March 2023

AbstractGenetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. Genetic monitoring supports the conservation and management of fisheries, game, and threatened populations. It also can contribute to the assessment of predicted and realized impacts of climate change, and their management. We report the first accounting of genetic monitoring efforts among countries in Europe (their ‘genetic monitoring capacity’, GMC) to determine where GMC suggests the combination of national infrastructure, political support and resources for continued and expanded monitoring. Overlaying GMC with areas where species ranges approach current and future climate niche limits (i.e., niche marginality) helps identify whether GMC coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area extent, financial resources, and conservation policy influence GMC, high values of which inconsistently match joint species patterns of climate niche marginality. Populations at niche margins likely hold genetic diversity that is important to adaptation to changing climate, and our results illuminate the need in Europe for expanded genetic monitoring across the climate gradients occupied by species, a need arguably greatest in southeastern European countries.
VRK3 depletion induces cell cycle arrest and metabolic reprogramming of Pontine Diffuse Midline Glioma (DMG)-K27 altered cells
Authors: Menez Virginie , Kergrohen Thomas , Shasha Tal , Silva-Evangelista Claudia , Ledret Ludivine , Auffret Lucie , Subecz Chloé , Lancien Manon , Ajlil Yassine , Beccaria Kévin , Blauwblomme Thomas , Oberlin Estelle , Grill Jacques , Castel David , Debily Marie-Anne 
Published: March 2023

AbstractWe previously identified VRK3 as a specific vulnerability in DMG-H3K27M cells in a synthetic lethality screen targeting the whole kinome. The aim of the present study was to elucidate the mechanisms by which VRK3 depletion impact DMG-K27M cell fitness. Gene expression studies afterVRK3knockdown emphasized the inhibition of genes involved in G1/S transition of the cell cycle resulting in growth arrest in G1. Additionally, a massive modulation of genes involved in chromosome segregation was observed, concomitantly with a reduction in the level of phosphorylation of serine 10 and serine 28 of histone H3 supporting the regulation of chromatin condensation during cell division. This last effect could be partly due to a concomitant decrease of the chromatin kinase VRK1 in DMG followingVRK3knock-down. Furthermore, a metabolic switch specific to VRK3 function was observed towards increased oxidative phosphorylation without change in mitochondria content, that we hypothesized would represent a cell rescue mechanism. This study further explored the vulnerability of DMG-H3K27M cells to VRK3 depletion suggesting potential therapeutic combinations,e.g.with the mitochondrial ClpP protease activator ONC201.
Beyond the reference: gene expression variation and transcriptional response to RNAi inC. elegans
Authors: Bell Avery Davis , Chou Han Ting , Paaby Annalise B. 
Published: March 2023

AbstractA universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic studies that do evaluate wild strains typically rely on the reference strain genome for read alignment, leading to the possibility of biased inferences based on incomplete or inaccurate mapping; the extent of reference bias can be difficult to quantify. As an intermediary between genome and organismal traits, gene expression is well positioned to describe natural variability across genotypes generally and in the context of environmental responses, which can represent complex adaptive phenotypes.C. eleganssits at the forefront of investigation into small-RNA gene regulatory mechanisms, or RNA interference (RNAi), and wild strains exhibit natural variation in RNAi competency following environmental triggers. Here, we examine how genetic differences among five wild strains affect theC. eleganstranscriptome in general and after inducing RNAi responses to two germline target genes. Approximately 34% of genes were differentially expressed across strains; 411 genes were not expressed at all in at least one strain despite robust expression in others, including 49 genes not expressed in reference strain N2. Despite the presence of hyper-diverse hotspots throughout theC. elegansgenome, reference mapping bias was of limited concern: over 92% of variably expressed genes were robust to mapping issues. Overall, the transcriptional response to RNAi was strongly strain-specific and highly specific to the target gene, and the laboratory strain N2 was not representative of the other strains. Moreover, the transcriptional response to RNAi was not correlated with RNAi phenotypic penetrance; the two germline RNAi incompetent strains exhibited substantial differential gene expression following RNAi treatment, indicating an RNAi response despite failure to reduce expression of the target gene. We conclude that gene expression, both generally and in response to RNAi, differs acrossC. elegansstrains such that choice of strain may meaningfully influence scientific conclusions. To provide a public, easily accessible resource for querying gene expression variation in this dataset, we introduce an interactive website athttps://wildworm.biosci.gatech.edu/rnai/.
Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)
Authors: Biello Roberto , Ghirotto Silvia , Schmidt Daniel J. , Fuselli Silvia , Roberts David T. , Espinoza Tom , Hughes Jane M. , Bertorelle Giorgio 
Published: March 2023

ABSTRACTThe Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution for this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs, and 5,196 nuclear SNPs) using the Approximate Bayesian Computation algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model amongst the simulated datasets (where the model was known), but different markers typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is present in the Brisbane and North Pine Rivers where past translocations are documented. These results will inform ongoing conservation efforts for this endangered and iconic species and warrant careful consideration of future genetic management of the Australian lungfish populations.
Continuous Multiplexed Phage Genome Editing Using Recombitrons
Authors: Fishman Chloe B. , Crawford Kate D. , Bhattarai-Kline Santi , Zhang Karen , González-Delgado Alejandro , Shipman Seth L. 
Published: March 2023

ABSTRACTBacteriophages, which naturally shape bacterial communities, can be co-opted as a biological technology to help eliminate pathogenic bacteria from our bodies and food supply1. Phage genome editing is a critical tool to engineer more effective phage technologies. However, editing phage genomes has traditionally been a low efficiency process that requires laborious screening, counter selection, orin vitroconstruction of modified genomes2. These requirements impose limitations on the type and throughput of phage modifications, which in turn limit our knowledge and potential for innovation. Here, we present a scalable approach for engineering phage genomes using recombitrons: modified bacterial retrons3that generate recombineering donor DNA paired with single stranded binding and annealing proteins to integrate those donors into phage genomes. This system can efficiently create genome modifications in multiple phages without the need for counterselection. Moreover, the process is continuous, with edits accumulating in the phage genome the longer the phage is cultured with the host, and multiplexable, with different editing hosts contributing distinct mutations along the genome of a phage in a mixed culture. In lambda phage, as an example, recombitrons yield single-base substitutions at up to 99% efficiency and up to 5 distinct mutations installed on a single phage genome, all without counterselection and only a few hours of hands-on time.
Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization
Authors: Palumbieri Maria Dilia , Merigliano Chiara , Acosta Daniel González , von Känel Thomas , Welter Bettina , Stoy Henriette , Krietsch Jana , Ulferts Svenja , Sanchi Andrea , Grosse Robert , Chiolo Irene , Lopes Massimo 
Published: March 2023

AbstractCells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
Parasite hybridization promotes spreading of endosymbiotic viruses
Authors: Heeren Senne , Maes Ilse , Sanders Mandy , Lye Lon-Fye , Arevalo Jorge , Llanos-Cuentas Alejandro , Garcia Lineth , Lemey Philippe , Beverley Stephen M , Cotton James A , Dujardin Jean-Claude , Van den Broeck Frederik 
Published: March 2023

ABSTRACTViruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis ofLeishmania braziliensisparasites and their endosymbioticLeishmaniaRNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.
Glioblastoma induces the recruitment and differentiation of hybrid neutrophils from skull bone marrow
Authors: Lad By Meeki , Beniwal Angad S. , Jain Saket , Shukla Poojan , Jung Jangham , Shah Sumedh S. , Yagnik Garima , Babikir Husam , Nguyen Alan T. , Gill Sabraj , Young Jacob S. , Lui Austin , Salha Diana , Diaz Aaron , Aghi Manish K. 
Published: March 2023

SUMMARYTumor-associated neutrophil (TAN) effects on glioblastoma biology remain under-characterized. We show here that ‘hybrid’ neutrophils with dendritic features – including morphological complexity, expression of antigen presentation genes, and the ability to process exogenous peptide and stimulate MHCII-dependent T cell activation – accumulate intratumorally and suppress tumor growthin vivo. Trajectory analysis of patient TAN scRNA-seq identifies this phenotype as a polarization state which is distinct from canonical cytotoxic TANs and differentiates intratumorally from immature precursors absent in circulation. Rather, these hybrid-inducible immature neutrophils – which we identified in patient and murine glioblastomas – arise from local skull marrow. Through labeled skull flap transplantation and targeted ablation, we characterize calvarial marrow as a potent contributor of antitumoral myeloid APCs, including hybrid TANs and dendritic cells, which elicit T cell cytotoxicity and memory. As such, agents augmenting neutrophil egress from skull marrow – such as intracalvarial AMD3100 whose survival prolonging-effect in GBM we demonstrate – present therapeutic potential.
BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference
Authors: Ghosal Sayan , Schatz Michael C. , Venkataraman Archana 
Published: March 2023

AbstractWe introduce a novel framework BEATRICE to identify putative causal variants from GWAS statistics. Identifying causal variants is challenging due to their sparsity and high correlation in the nearby regions. To account for these challenges, we rely on a hierarchical Bayesian model that imposes a binary concrete prior on the set of causal variants. We derive a variational algorithm for this fine-mapping problem by minimizing the KL divergence between an approximate density and the posterior probability distribution of the causal configurations. Correspondingly, we use a deep neural network as an inference machine to estimate the parameters of our proposal distribution. Our stochastic optimization procedure allows us to simultaneously sample from the space of causal configurations. We use these samples to compute the posterior inclusion probabilities and determine credible sets for each causal variant. We conduct a detailed simulation study to quantify the performance of our framework against two state-of-the-art baseline methods across different numbers of causal variants and different noise paradigms, as defined by the relative genetic contributions of causal and non-causal variants. We demonstrate that BEATRICE achieves uniformly better coverage with comparable power and set sizes, and that the performance gain increases with the number of causal variants. We also show the efficacy BEATRICE in finding causal variants from the GWAS study of Alzheimer’s disease. In comparison to the baselines, only BEATRICE can successfully find the APOEϵ2 allele, a commonly associated variant of Alzheimer’s. Thus, we show that BEATRICE is a valuable tool to identify causal variants from eQTL and GWAS summary statistics across complex diseases and traits.
Apigenin exerts anti-cancer effects in colon cancer possibly by regulating Heat shock protein 90 alpha family class A member 1 (HSP90AA1)
Authors: Sain Arindam , Khamrai Dipshikha , Kandasamy Thirukumaran , Naskar Debdut 
Published: March 2023

ABSTRACTApigenin, a natural flavonoid, has shown early promise in colon cancer (CC); thus, exploring potential mechanisms of apigenin in CC is obligatory. In this study, shared targets of apigenin and CC were identified through different online tools and subjected to functional enrichment analyses like Gene Ontology and KEGG. Further, the protein-protein interaction network of the shared targets was developed (via STRING); hub/core targets were identified (MCODE application). The top targets of apigenin in CC were identified by molecular docking; further investigated for differential gene and protein expression in CC and their influence on CC patient survival (using TCGA data). Based on the docking score of the 13 hub genes, the top 3 targets (HSP90AA1, MMP9, PTGS2) were selected, and their expression was significantly elevated and related to poor overall survival in CC (exceptPTGS2). Molecular dynamics simulation further validated protein-ligand interactions and selected HSP90AA1 as the best target of apigenin in CC. Finally, apigenin was found to be involved in the cytotoxicity of CC cells (COLO-205) by reducingHSP90AA1expression. The results of this study identified HSP90AA1 as one of the prime targets of apigenin in CC, and apigenin might act on HSP90AA1 to exert its anti-cancer mechanism.
Hierarchical Clustering and Omics Analysis Revealed Massive Molecular Shifts in a Tree under Combined Hypoxia and Salinity
Authors: Cisse El-Hadji Malick , Jiang Bai-Hui , Yin Li-Yan , Miao Ling-Feng , Zhou Jing-Jing , Mekontso Francine Ngaffo , Li Da-Dong , Xiang Li-Shan , Yang Fan 
Published: March 2023

AbstractField and Greenhouse studies that attempted to describe the molecular responses of trees under waterlogging (WL) combined with salinity (ST) are quasi-inexistent. To dissect plant-specific molecular responses and patterns under SWL, we integrated transcriptional and metabolic analyses involving common differentially expressed genes (DEGs) and metabolites (DMs) patterns inDalbergia odoriferaleaflets. SWL-treated seedlings exhibited an impressively high number of DEGs and DMs compared to ST or WL. Although the main common DEGs and DMs showed a neutral pattern, gene ontology enrichment following the classification in different functional categories of SWL-transcripts displayed a predominant synergistic pattern mode. Hierarchical and silhouette analysis regrouped different morpho-physiological clusters following the treatment, SWL was mainly grouped with both single stress. SWL induced a massive shutdown of the photosynthesis apparatus throughLHCBs- andPSA-related genes. Starch and plastoglobuli synthesis appeared to be drastically affected by SWL, while ABA content confirmed by ABA synthesis related-genes (ABF,ABA1andNCED) variations showed a less-needed role.NXN(Nucleoredoxin) genes are the main factors that sustain the antioxidant system under SWL. Here we provide the first molecular responses, characterization and patterns of a tree under SWL that would significantly shed light on our understanding of the molecular mechanisms underlying combined stress.
Spatial and temporal variation in abundance of introduced African fig fly (Zaprionus indianus) (Diptera: Drosophilidae) in the eastern United States
Authors: Rakes Logan M. , Delamont Megan , Cole Christine , Yates Jillian A. , Blevins Lynsey Jo , Hassan Fatima Naureen , Bergland Alan O. , Erickson Priscilla A. 
Published: March 2023

AbstractThe African fig fly,Zaprionus indianus(Gupta), has spread globally from its native range in tropical Africa, becoming an invasive crop pest in select areas such as Brazil.Z. indianuswas first reported in the United States in 2005 and has since been documented as far north as Canada. As a tropical species,Z. indianusis expected to have low cold tolerance, likely limiting its ability to persist at northern latitudes. In North America, the geographic regions whereZ. indianuscan thrive and seasonal fluctuations in its abundance are not well understood. The purpose of this study was to characterize the temporal and spatial variation inZ. indianusabundance to better understand its invasion of the eastern United States. We sampled drosophilid communities over the growing season at two orchards in Virginia from 2020-2022 and several locations along the East Coast during the fall of 2022. Virginia abundance curves showed similar seasonal dynamics across years with individuals first detected around July and becoming absent around December. Massachusetts was the northernmost population and noZ. indianuswere detected in Maine. Variation inZ. indianusrelative abundance was high between nearby orchards and across different fruits within orchards but was not correlated with latitude. Fitness of wild-caught females decreased later in the season and at higher latitudes. The patterns ofZ. indianusabundance shown here demonstrate an apparent susceptibility to cold and highlight a need for systematic sampling to accurately characterize the range and spread ofZ. indianus.
Morphological Attributes ofGlycine max(Soybean)
Authors: Bashir Gazala 
Published: March 2023

AbstractHeavy metal like lead and chromium present in environment in large quantities cause a severe environmental concern. Significant risks to the environment and agriculture are posed by heavy metal contamination of the air, water, and soil as a result of increased urbanisation and industrialization. Heavy metal pollution in soils can harm nearby ecosystems, groundwater, agricultural productivity, and human health because of its persistence and high toxicity. Heavy metals are accumulated in the tissues of plants growing in metal-contaminated soil, which can have a negative impact on the morphology of the plant. The present study was carried out to determine the effect of different concentrations (50ml, 100ml, 150ml and 200ml) of chromium and lead on morphological attributes of three varieties (JS:335, JS:80-21, JS:75-46) of soybean(Glycine max). The result of the present study showed that the exposure ofGlycine maxto Pb and Cr resulted in a decrease in total length, number of nodes and number of leaves of a plant. The shape of leaves in case of treated plants was also changed from ovoid to heart and oval shapes, at higher concentration of heavy metals. Among the three different varieties (JS:335, JS:80-21, JS:75-46) ofGlycine. max(soybean)JS:335showed maximum reduction and theJS:80-21showed least reduction in the growth of a plant. Lead treatment proved more toxic than chromium treatment for all the three different varieties (JS:335, JS:80-21, JS:75-46) ofGlycine max.