bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soybean phenotypic plasticity in response to dark chilling stress
Authors: Elmerich Chloé , Faucon Michel-Pierre , Boulch Guénolé , Jeanson Patrice , Lange Bastien 
Published: May 2024

AbstractThe expansion of soybean cultivation to high-latitude regions is hindered by the adverse effects of dark chilling stress. This study investigates the phenotypic plasticity of soybean in response to dark chilling stress, aiming to identify traits that contribute to adaptation in northern climates. Five soybean cultivars from early maturity groups (000 and 00) were grown in growth chambers set either at 25/18°C or 25/10°C (day/night), and a range of performance and functional traits were measured. The relative distance plasticity index highlighted variations in plasticity across traits and genotypes. Photosynthetic activity recovery traits, shoot growth rate, and tap root elongation rate showed high plasticity and significant differences between cultivars, making them suitable for assessing dark chilling tolerance. Moreover, distinct responses to dark chilling stress were exhibited by different soybean cultivars. For instance, cv. SOPRANA displayed a greater phenotypic plasticity in aboveground performance traits, such as shoot growth, while cv. SULTANA exhibited a greater plasticity in physiological traits like photosynthetic activity recovery. These differing strategies may lead to similar biomass production through distinct mechanisms, highlighting the complexity of soybean’s adaptive responses to dark chilling stress. These findings provide valuable insights for breeders seeking to develop soybean cultivars adapted to high latitudes, meeting the increasing demand for locally produced protein-based food. However, further research in real field conditions is essential to validate the potential benefits of these plastic traits and their role in improving soybean resilience to dark chilling stress. The identified plastic traits offer a promising avenue for screening a broader range of cultivars and enhancing soybean’s suitability for cultivation in northern regions.
The mechanistic rules for species coexistence
Authors: Zhang Zhijie , Becks Lutz 
Published: May 2024

SummaryGlobal biodiversity loss requires effective ecological community management, reliant on accurate predictions of species coexistence and community assembly1-4. Traditional methods, predicting coexistence from the effect of one species on another5-8(i.e., phenomenologically), are sensitive to environmental context9-13. This is because they ignore the fundamental processes that can be applied across environments. While mechanistic approaches offer promise14-17, empirical tests remain rare18,19. Here, we integrated a mechanistic consumer-resource model with the growth of 12 phytoplankton species in monoculture over a range of phosphorous, nitrate or ammonium concentrations. We found that the mechanistic approach accurately predicts the composition of 960 communities across species richness and resource conditions. As confirmed by simulations, species competing for substitutable resources (ammonium vs. nitrate) exhibit greater diversity than those competing for essential resources (phosphorus vs. nitrate), especially when initial species richness is high. This is because when competing for essential resources, each species is likely to consume less of the resource that more limit its growth, violating the mechanistic rule of coexistence (each species must consume more of the resource that more limit it16). Our study highlights the power of the mechanistic approach in understanding and predicting species loss across environments and, ultimately, mitigating its pace.
Hematological Parameters as Predictors of COVID-19 Infection: A Cohort Study Using Brazilian Hospital Data
Authors: Utley James 
Published: May 2024

AbstractObjectivesTo determine if hematology test results can indicate COVID-19 infection.MethodsA cohort study used 2020 Brazilian hospital data for 6,573 patients to run inferential analyses of fourteen red and white blood cell hematology test results, adjusted for age and sex, by patient COVID-19 status.ResultsTen hematological biomarkers were statistically significant predictors of COVID-19 PCR test results; the strongest were Total White Blood Cells: OR=0.90 (0.88-0.93), Basophils: OR=0.97 (0.97-0.98), Total Red Blood Cells: OR=0.88 (0.78-0.99), Hemoglobin: OR=0.93 (0.89-0.97), Hematocrit: OR=0.97 (0.96-0.99). Patient sex was also a strong predictor of COVID-19 PCR test results: OR=1.43 (1.26-1.62).ConclusionsCOVID-19 produces measurable impacts on red and white blood cells that are significant predictors of PCR results. A routine blood draw may offer probabilistic insight as a diagnostic predictor of infection. The virus is associated with impacts in red blood cells’ vital oxygen transport attributes.Public Health ImplicationsA faster diagnostic tool for COVID-19 will assist providers to triage and isolate those with the virus, reducing hospital transmission. Results are being used to develop a predictive model with high sensitivity and specificity.
Cardiovascular disease Multimorbidity is Associated with Decreased Health-Related Quality of Life in Haiti: Findings from a Population-based Cohort
Authors: Sabwa Shalom , Rouzier Vanessa , Sufra Rodney , St. Sauveur Reichling , Mourra Nour , Rasul Rehana , Inddy Joseph , Yan Lily D. , Sterling Madeline , Pinheiro Laura , Deschamps Marie , Pape Jean William , McNairy Margaret L. 
Published: May 2024

AbstractBackgroundMultimorbidity is increasingly prevalent in lower-and middle-income countries (LMICs). Health-related quality of life (HRQOL) has been inversely associated with multimorbidity but is understudied in LMICs. We report cardiovascular disease (CVD) multimorbidity in Haiti and its association with HRQOL.MethodsWe used data from the Haiti CVD Cohort, a population-based longitudinal cohort of adults. CVD multimorbidity was 2+ CVD risk factors/diseases at enrollment. HRQOL was measured using the Short Form-12, yielding physical (PCS)/mental (MCS) component summary scores between 0-100, with higher scores indicating better HRQOL. We used linear regressions to assess the association between CVD multimorbidity and HRQOL and between individual CVD comorbidities and HRQOL. Additionally, we examined how gender and education modified the main effect.ResultsAmong 2,996 participants, the median age was 40 (IQR: 27-55), 58.0% were female, and 70.3% earned <1 USD/day. CVD multimorbidity prevalence was 24.1%; compared to those without CVD multimorbidity, those with CVD multimorbidity were older (median 56.0 [IQR: 47.0, 53.0]) and female (70.5%). Adjusted models revealed CVD multimorbidity was inversely related to PCS (−2.7 [95% CI: −3.8, −1.6]) and MCS (−1.0 [95% CI: −1.8, −0.2]). Heart failure and hypertension showed the strongest CVD morbidities associated with poor HRQOL. In the interaction analysis, among men, CVD multimorbidity was associated with a 4.3-point lower PCS score, and among those with less education, CVD multimorbidity was associated with a 4.6-point lower PCS score than no CVD multimorbidity.ConclusionsOur data are among the first to describe HRQOL data with high CVD multimorbidity in a young population in urban Haiti, and CVD multimorbidity was associated with decreased HRQOL.(https://www.clinicaltrials.gov/ct2/show/NCT03892265, #NCT03892265)Research Perspective–This research raises the question of whether people with CVD multimorbidity in LMICs need specific interventions that are tailored to their high levels of comorbidity and if women and those with low socioeconomic status are at extra risk for experiencing the adverse effects of multimorbidity.–Future research should investigate cut-off points for describing a population average relevant to an LMIC.
Fluid flow overcomes antimicrobial resistance by boosting delivery
Authors: Shuppara Alexander M. , Padron Gilberto C. , Sharma Anuradha , Modi Zil , Koch Matthias D. , Sanfilippo Joseph E. 
Published: May 2024

AbstractAntimicrobial resistance is an emerging global threat to humanity. As resistance outpaces development, new perspectives are required. For decades, scientists have prioritized chemical optimization, while largely ignoring the physical process of delivery. Here, we used biophysical simulations and microfluidic experiments to explore how fluid flow delivers antimicrobials into communities of the highly resistant pathogenPseudomonas aeruginosa. We discover that increasing flow overcomes bacterial resistance towards three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistantP. aeruginosacells generate local zones of depletion by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to regain effectiveness against resistant bacteria. Additionally, we discover that cells on the edge of a community shield internal cells, and cell-cell shielding is abolished in higher flow regimes. Collectively, our quantitative experiments reveal the unexpected result that physical flow and chemical dosage are equally important to antimicrobial effectiveness. Thus, our results should inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials, and could represent a new strategy to combat antimicrobial resistance.
Genomic exploration of the complex journey ofPlasmodium vivaxin Latin America
Authors: Lefebvre M. J. M. , Degrugillier F. , Arnathau C. , Fontecha G. A. , Noya O. , Houzé S. , Severini C. , Pradines B. , Berry A. , Trape J-F. , Sáenz F. E. , Prugnolle F. , Fontaine M. C. , Rougeron V. 
Published: May 2024

AbstractPlasmodium vivax, the predominant malaria parasite in Latin America, has a rich and complex colonization history in the region, with debated hypotheses about its origin. Our study employed cutting-edge population genomic techniques, to collect whole genome sequencing data from 620P. vivaxisolates, including 107 newly sequenced samples, thus representing nearly all potential source populations worldwide. Analyses of the genetic structure, diversity, ancestry, and also, coalescent-based inferences and scenario testing using Approximate Bayesian Computation, have revealed a more complex evolutionary history than previously envisioned. Indeed, according to our analysis, the current AmericanP. vivaxpopulations predominantly stemmed from a now-extinct European lineage, with the potential contribution also from unsampled populations, most likely of West African origin, during post-colonial human migration waves in the late 19th-century. This study provides a fresh perspective onP. vivaxintricate evolutionary journey and brings insights into the possible contribution of West AfricanP. vivaxpopulations to the colonization history of Latin America.
Phylogenomics of novel clones ofAeromonas veroniirecovered from a freshwater lake reveals unique biosynthetic gene clusters
Authors: Lawal Opeyemi U. , Bryan Noah , Parreira Valeria R. , Anderson Rebecca , Chen Yanhong , Precious Melinda , Goodridge Lawrence 
Published: May 2024

ABSTRACTAquatic ecosystems are important reservoirs for clinically relevant pathogens and antimicrobial resistance genes, thus present a significant risk to global health. Here, we assessed the phylogenomics ofAeromonas veronii(A. veronii) recovered from Lake Wilcox in Ontario using a combination of morphological, biochemical, and whole-genome sequencing (WGS) techniques.Eleven distinct bacterial colonies were isolated and identified asA. veronii(n=9), and two otherAeromonasspecies (A. caviaeandA. allosaccharophila), with significant discrepancies noted between biochemical and WGS identification methods. Of note, 67% (n=6/9) ofA. veroniiisolates were human pathogens (Pathogenicity score ≥ 0.50). The genomic analysis revealed high genetic diversity among theA. veroniiisolates, including the discovery of 41 novel alleles and seven new sequence types (ST) suggesting the lake as a reservoir for multiple human pathogenic clones of this bacterium. The comparison of the newly isolated and sequencedA. veroniiwith 214A. veroniigenomes revealed significant genetic diversity and suggests potential broad geographical dissemination of strains. Chromosomal genes (OXA-912andcphA[cphA3, cphA4, cphA7]) genes encoding resistance to β-lactamases were detected in all isolates. Human and non-human pathogenic strains ofA. veroniidiffered in their virulence gene content, with type III secretion systems being associated with human pathogenic isolates. Mobilome analysis revealed the absence of plasmids inA. veroniiisolates and the presence of 13 intact the great majority of which were P22-like (Peduoviridae) phages, and nine different insertion sequence families. Novel biosynthetic gene clusters were identified and characterized, indicating the potential for unique secondary metabolite production inA. veroniiwith different pathogenic potential. Overall, this study underscores the importance of continuous surveillance of aquatic ecosystems for the presence of pathogens, contributing to our understanding of their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements.
Characterization of Tgl2, a putative lipase in yeast mitochondria
Authors: Tiku Vitasta , Tatsuta Takashi , Jung Martin , Rapaport Doron , Dimmer Kai Stefan 
Published: May 2024

AbstractMitochondria derive the majority of their lipids from other organelles through contact sites. These lipids, primarily phosphoglycerolipids, are the main components of mitochondrial membranes. In the cell, neutral lipids like triacylglycerides (TAGs) are stored in lipid droplets, playing an important role in maintaining cellular health. Enzymes like lipases mobilize these TAGs according to cellular needs. Neutral lipids have not yet been reported to play an important role in mitochondria so the presence of a putative TAG lipase – Tgl2, in yeast mitochondria is surprising. Moreover,TGL2andMCP2, a high-copy suppressor for ERMES deficient cells, display genetic interactions suggesting a potential link to lipid metabolism. In this study, we characterize in detail Tgl2. We show that Tgl2 forms dimers through intermolecular disulfide bridges and a cysteine-dependent high molecular weight complex. Furthermore, we could identify the lipase motif and catalytic triad of Tgl2 throughin silicocomparison with other lipases and mutated the catalytically active residues accordingly. Both mutants failed to rescue the growth phenotype ofmcp2Δ/tgl2Δ double deletion strain suggesting that the residues are indeed essential for the protein’s function. Additionally, we discovered that the catalytically active aspartate residue is important for protein stability. Steady state level analyses with non-functional variants of Tgl2 led to the identification of Yme1 as the protease responsible for its quality control. Finally, we provide evidence that the overall increase in TAGs in cells lacking Mcp2 and Tgl2 originates from the mitochondria. Collectively, our study provides new insights into a key player in mitochondrial lipid homeostasis.
Engineering anfgfr4knockout zebrafish to study its role in development and disease
Authors: Harrison Emma N. , Jay Amanda N. , Kent Matthew R. , Sukienik Talia P. , LaVigne Collette A. , Kendall Genevieve C. 
Published: May 2024

AbstractFibroblast growth factor receptor 4 (FGFR4) has a role in many biological processes, including lipid metabolism, tissue repair, and vertebrate development. In recent years, FGFR4 overexpression and activating mutations have been associated with numerous adult and pediatric cancers. As such,FGFR4presents an opportunity for therapeutic targeting which is being pursued in clinical trials. To understand the role of FGFR4 signaling in disease and development, we generated and characterized three alleles offgfr4knockout zebrafish strains using CRISPR/Cas9. To generatefgfr4knockout crispants, we injected single-cell wildtype zebrafish embryos withfgfr4targeting guide RNA and Cas9 proteins, identified adult founders, and outcrossed to wildtype zebrafish to create an F1 generation. The generated mutations introduce a stop codon within the second Ig-like domain of Fgfr4, resulting in a truncated 215, 223, or 228 amino acid Fgfr4 protein compared to 922 amino acids in the full-length protein. All mutant strains exhibited significantly decreasedfgfr4mRNA expression during development, providing evidence for successful knockout offgfr4in mutant zebrafish. We found that, consistent with otherFgfr4knockout animal models, thefgfr4mutant fish developed normally; however, homozygousfgfr4mutant zebrafish were significantly smaller than wildtype fish at three months post fertilization. Thesefgfr4knockout zebrafish lines are a valuable tool to study the role of FGFR4 in vertebrate development and its viability as a potential therapeutic target in pediatric and adult cancers, as well as other diseases.
Intracranial neurophysiological correlates of rumination
Authors: Chen Xiao , Fan Zhen , Chen Dong , Wang Liang , Chen Liang , Yan Chao-Gan 
Published: May 2024

AbstractRumination is a transdiagnostic psychological process that plays a prominent role in many common psychiatric disorders, albeit its neurophysiological basis remains elusive. Existing neuroimaging studies have highlighted the precuneus and hippocampus as two essential brain regions in rumination’s neural underpinnings. Here, we examined the intracranial electroencephalogram (iEEG) recordings from 21 patients with epilepsy during a naturalistic, continuous, active rumination state and measured the slow frequency (1-8 Hz) and high gamma (70-150 Hz) band oscillation powers. We observed enhanced slow frequency power in the precuneus and reduced high gamma power in the hippocampus during the rumination condition compared to the control condition. The hippocampal high gamma power reduction was associated with the self-reported reflection tendency. Our findings provided the first empirical evidence of the neurophysiological underpinnings of rumination and implicated a precuneus-hippocampus coupling across neural oscillation bands during an active rumination state.
Cell Competition Eliminates Aneuploid Human Pluripotent Stem Cells
Authors: Ya Amanda , Deng Chenhui , Godek Kristina M. 
Published: May 2024

SummaryHuman pluripotent stem cells (hPSCs) maintain diploid populations for generations despite a persistently high rate of mitotic errors that cause aneuploidy, or chromosome imbalances. Consequently, to maintain genome stability, aneuploidy must inhibit hPSC proliferation, but the mechanisms are unknown. Here, we surprisingly find that homogeneous aneuploid populations of hPSCs proliferate unlike aneuploid non-transformed somatic cells. Instead, in mosaic populations, cell non-autonomous competition between neighboring diploid and aneuploid hPSCs eliminates less fit aneuploid cells. Aneuploid hPSCs with lower Myc or higher p53 levels relative to diploid neighbors are outcompeted but conversely gain a selective advantage when Myc and p53 relative abundance switches. Thus, although hPSCs frequently missegregate chromosomes and inherently tolerate aneuploidy, Myc- and p53-driven cell competition preserves their genome integrity. These findings have important implications for the use of hPSCs in regenerative medicine and for how diploid human embryos are established despite the prevalence of aneuploidy during early development.
The Rubicon-WIPI axis regulates exosome biogenesis during aging
Authors: Yanagawa Kyosuke , Kuma Akiko , Hamasaki Maho , Kita Shunbun , Yamamuro Tadashi , Nishino Kohei , Nakamura Shuhei , Omori Hiroko , Kaminishi Tatsuya , Oikawa Satoshi , Kato Yoshio , Edahiro Ryuya , Kawagoe Ryosuke , Taniguchi Takako , Tanaka Yoko , Shima Takayuki , Tabata Keisuke , Iwatani Miki , Bekku Nao , Hanayama Rikinari , Okada Yukinori , Akimoto Takayuki , Kosako Hidetaka , Takahashi Akiko , Shimomura Iichiro , Sakata Yasushi , Yoshimori Tamotsu 
Published: May 2024

AbstractCells release intraluminal vesicles (ILVs) in multivesicular bodies as exosomes to communicate with other cells. Although recent studies suggest an intimate link between exosome biogenesis and autophagy, the detailed mechanism is not fully understood. Here we employed comprehensive RNAi screening for autophagy-related factors and discovered that Rubicon, a negative regulator of autophagy, is essential for exosome release. Rubicon recruits WIPI2d to endosomes to promote exosome biogenesis. Interactome analysis of WIPI2d identified the ESCRT components that are required for ILV formation. Notably, we found that Rubicon is required for an age-dependent increase of exosome release in mice. In addition, small RNA sequencing of serum exosomes revealed that Rubicon determines the fate of exosomal microRNAs associated with cellular senescence and longevity pathways. Taken together, our current results suggest that the Rubicon-WIPI axis functions as a key regulator of exosome biogenesis and is responsible for the age-dependent changes in exosome quantity and quality.
Cell type- and layer-specific plasticity of olfactory bulb interneurons following olfactory sensory neuron ablation
Authors: Kunkhyen Tenzin , Brechbill Taryn R. , Berg Sarah P.R. , Pothuri Pranitha , Rangel Alex N , Gupta Ashna , Cheetham Claire E.J. 
Published: May 2024

AbstractLifelong neurogenesis endows the mouse olfactory system with a capacity for regeneration that is unique in the mammalian nervous system. Throughout life, olfactory sensory neurons (OSNs) are generated from olfactory epithelium (OE) stem cells in the nose, while the subventricular zone generates neuroblasts that migrate to the olfactory bulb (OB) and differentiate into multiple populations of inhibitory interneurons. Methimazole (MMZ) selectively ablates OSNs, but OE neurogenesis enables OSN repopulation and gradual recovery of OSN input to the OB within six weeks. However, it is not known how OB interneurons are affected by this loss and subsequent regeneration of OSN input following MMZ treatment. We found that dopaminergic neuron density was significantly reduced 7-14 days post-MMZ but recovered substantially at 35 days. The density of parvalbumin-expressing interneurons was unaffected by MMZ; however, their soma size was significantly reduced at 7-14 days post-MMZ, recovering by 35 days. Surprisingly, we found a transient increase in the density of calretinin-expressing neurons in the glomerular and external plexiform layers, but not the granule cell layer, 7 days post-MMZ. This could not be accounted for by increased neurogenesis but may result from increased calretinin expression. At subsequent time points, calretinin neurons in all three layers showed reduced density at 14 days but recovered to baseline by 35 days. Together, our data demonstrate cell type- and layer-specific changes in OB interneuron density and morphology after MMZ treatment, providing new insight into the range of plasticity mechanisms employed by OB circuits during loss and regeneration of sensory input.