bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated glycoprotein acetyl levels in adolescence and early adulthood predict adverse cardiometabolic profiles and risk of metabolic syndrome in up to 10 year follow-up
Authors: Chiesa Scott T. , Charakida Marietta , Georgiopoulos Georgios , Roberts Justin D. , Stafford Simon J. , Park Chloe , Mykkänen Juha , Kähönen Mika , Lehtimäki Terho , Ala-Korpela Mika , Raitakari Olli , Hughes Alun D. , Sattar Naveed , Timpson Nicholas J. , Deanfield John E. 
Published: October 2020

ABSTRACTObjectiveLow-grade inflammation in the young may contribute to the early development of adverse cardiometabolic risk profiles. We assessed whether measures of glycoprotein acetylation (GlycA) were better able to detect the development of these changes compared to the more commonly used biomarker high-sensitivity C-reactive protein (CRP), and investigated whether these relationships differed in an adolescent compared to young adult cohort.Research Design and MethodsA total of 3306 adolescents (Avon Longitudinal Study of Parents and Children - ALSPAC; mean age 15.4±0.3; n=1750) and young adults (Cardiovascular Risk in Young Finns Study - YFS; mean age 32.1±5.0; n=1556) were included. Inflammatory biomarkers (GlycA/CRP), body composition (BMI / waist circumference) and cardiometabolic risk factors (blood pressure, triglycerides, HDL-c, glucose, insulin, and homeostasis model of insulin resistance [HOMA_IR]), were measured at baseline and again in 9-10 year follow-up. Metabolic Syndrome (MetS) was defined using adolescent-specific National Cholesterol Education Programme (NCEP) guidelines in ALSPAC and standard NCEP guidelines in YFS.ResultsGlycA levels showed greater within-subject correlation over the 9-10 year duration of follow-up in both cohorts when compared to CRP, particularly in the younger adolescent group. In adjusted models, only GlycA was found to increase in line with cardiometabolic risk factor burden at baseline, and to predict adverse changes in several cardiometabolic risk factors in follow-up. In both cohorts, GlycA predicted future risk of MetS (OR [95%CI] for Q4 vs. Q1 = 1.95 [1.08,3.53] and 2.74 [1.30,5.73] for ALSPAC and YFS, respectively), whereas CRP showed a neutral or even negative relationship in fully-adjusted models (OR [95%CI] = 0.50 [0.29,0.86] and 0.93 [0.53,1.64]).ConclusionsChronic inflammation is associated with adverse cardiometabolic risk profiles from as early as adolescence and predicts risk of future cardiometabolic risk and MetS in up to 10 year follow-up. GlycA may be a more sensitive inflammatory biomarker to CRP for detecting early cardiometabolic and cardiovascular risk in the young.
Missed opportunities of flu vaccination in Italian target categories: insights from the online EPICOVID 19 survey
Authors: Giacomelli Andrea , Galli Massimo , Maggi Stefania , Pagani Gabriele , Incalzi Raffaele Antonelli , Pedone Claudio , di Bari Mauro , Noale Marianna , Trevisan Caterina , Bianchi Fabrizio , Tavio Marcello , Andreoni Massimo , Mastroianni Claudio , Sojic Aleksandra , Prinelli Federica , Adorni Fulvio 
Published: October 2020

AbstractWe aimed to assess the reported rate of flu vaccination in the season 2019/2020 in respondents to the Italian nationwide online EPICOVID 19 survey. A national convenience sample of volunteers aged 18 or older was assessed between 13th April and 2nd June 2020. Flu vaccine rates were calculated for all classes of age. The association between the independent variables and the flu vaccine was assessed by applying a multivariable binary logistic regression model. Of the 198,822 respondents 41,818 (21.0%) reported to have received a flu vaccination shot during the last influenza season. In particular, 15,009 (53.4%) subjects aged 65 years or older received a flu vaccination shot. Being 65 years aged or older (aOR 3.06, 95%CI 2.92-3.20) and having a high education level (aOR 1.34. 95%CI 1.28-1.41) were independently associated to flu vaccination. Heart and lung diseases were the morbidities associated with the higher odds of being vaccinated [aOR 1.97 (95%CI 1.86-2.09) and aOR 1.92 (95%CI 1.84-2.01), respectively]. Nursing home residents aged ≥ 65 years showed a lower odds of being vaccinated [aOR 0.39 (95%CI 0.28-0.54)]. Our data claims for an urgent public heath effort to fill the gap of missed vaccination opportunities reported in the past flu seasons.
In vivo amygdala nuclei volumes in schizophrenia and bipolar disorders
Authors: Barth Claudia , Nerland Stener , de Lange Ann-Marie G. , Wortinger Laura A. , Hilland Eva , Andreassen Ole A. , Jørgensen Kjetil N. , Agartz Ingrid 
Published: October 2020

AbstractBackgroundAbnormalities in amygdala volume are well-established in schizophrenia and commonly reported in bipolar disorders. However, the specificity of volumetric differences in individual amygdala nuclei is largely unknown.MethodsPatients with schizophrenia disorders (SCZ, n=452, including schizophrenia, schizoaffective and other psychotic disorders, mean age 30.7±9.2 (SD), females 44.4%), bipolar disorders (BP, n=316, including bipolar I and II, 33.7±11.4, 58.5%) and healthy controls (n=753, 34.1±9.1, 40.9%) underwent T1-weighted magnetic resonance imaging. Total amygdala and nuclei volumes as well as intracranial volume (ICV) were estimated with Freesurfer (v6.0.0). Analysis of covariance and multiple linear regression models, adjusting for age, age2, ICV and sex, were fitted to examine diagnostic group and subgroup differences in volume, respectively.ResultsBilateral total amygdala and all nuclei volumes, except the medial and central nuclei, were significantly smaller in patients relative to controls. The largest effect sizes were found for the basal nucleus, accessory basal nucleus and cortico-amygdaloid transition area (partial η2 > 0.02). The diagnostic subgroup analysis showed that reductions in amygdala nuclei volume were most widespread in schizophrenia, with the lateral, cortical, paralaminar and central nuclei being solely reduced in this disorder. The right accessory basal nucleus was marginally smaller in SCZ relative to BP (t = 2.32, p = 0.05).ConclusionsOur study is the first to demonstrate distinct patterns of amygdala nuclei volume reductions in a well-powered sample of patients with schizophrenia and bipolar disorders. Volume differences in the basolateral complex (lateral, basal, accessory basal nuclei) may be putative neuroimaging markers for differentiating schizophrenia and bipolar disorders.
Potential Spreading Dynamics of COVID-19 with Temporary Immunity – A Mathematical Modeling Study
Authors: Shayak B , Sharma Mohit M 
Published: October 2020

AbstractCOVID-19 is caused by a hitherto nonexistent pathogen, hence the immune response to the disease is currently unknown. Studies conducted over the past few weeks have found that the antibody titre levels in the blood plasma of infected patients decrease over time, as is common for acute viral infections. Fully documented reinfection cases from Hong Kong, India, Belgium and USA, as well as credible to anecdotal evidence of second-time cases from other countries, bring into sharp focus the question of what profile the epidemic trajectories may take if immunity were really to be temporary in a significant fraction of the population. Here we use mathematical modeling to answer this question, constructing a novel delay differential equation model which is tailored to accommodate different kinds of immune response. We consider two immune responses here : (a) where a recovered case becomes completely susceptible after a given time interval following infection and (b) where a first-time recovered case becomes susceptible to a lower virulence infection after a given time interval following recovery, and becomes permanently immunized by a second infection. We find possible solutions exhibiting large number of waves of disease in the first situation and two to three waves in the second situation. Interestingly however, these multiple wave solutions are manifest only for some intermediate values of the reproduction number R, which is governed by public health intervention measures. For sufficiently low as well as sufficiently high R, we find conventional single-wave solutions despite the short-lived immunity. Our results cast insight into the potential spreading dynamics of the disease and might also be useful for analysing the spread after a vaccine is invented, and mass vaccination programs initiated.
Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures
Authors: N’Guessan Arnaud , Brito Ilana Lauren , Serohijos Adrian W.R. , Shapiro B. Jesse 
Published: October 2020

AbstractPangenomes – the cumulative set of genes encoded by a species – arise from evolutionary forces including horizontal gene transfer (HGT), drift, and selection. The relative importance of drift and selection in shaping pangenome structure has been recently debated, and the role of sequence evolution (point mutations) within mobile genes has been largely ignored, with studies focusing mainly on patterns of gene presence or absence. The effects of drift, selection, and HGT on pangenome evolution likely depends on the time scale being studied, ranging from ancient (e.g., between distantly related species) to recent (e.g., within a single animal host), and the unit of selection being considered (e.g., the gene, whole genome, microbial species, or human host). To shed light on pangenome evolution within microbiomes on relatively recent time scales, we investigate the selective pressures acting on mobile genes using a dataset that previously identified such genes in the gut metagenomes of 176 Fiji islanders. We mapped the metagenomic reads to mobile genes to call single nucleotide variants (SNVs) and calculate population genetic metrics that allowed us to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village membership, suggesting that selection at the level of gene function is most relevant on these short time scales. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation, without the need to invoke an adaptive advantage of mobile genes to their bacterial host genome. This suggests that, at least on short time scales, a majority of the pangenome need not be adaptive. On the other hand, a subset of gene functions including defense mechanisms and secondary metabolism showed an aberrant pattern of molecular evolution, consistent with species-specific selective pressures or negative frequency-dependent selection not seen in prophages, transposons, or other gene categories. That mobile genes of different functions behave so differently suggests stronger selection at the gene level, rather than at the genome level. While pangenomes may be largely adaptive to their bacterial hosts on longer evolution time scales, here we show that, on shorter “human” time scales, drift and gene-specific selection predominate.
MAP kinase Slt2p attenuates cell wall mRNA decay by downregulating the RNA-binding protein Rbp1p in response to stress
Authors: Chang Lin-Chun , Wu Yu-Chieh , Chang Yu-Yun , Lee Fang-Jen 
Published: October 2020

AbstractThe yeast cell wall integrity (CWI) MAPK pathway is a signaling cascade function in maintaining cell wall integrity under stressful environmental conditions. Recently, the activity and signaling of Slt2p (Mpk1p) MAP kinase has been shown to control assembly of the processing body (P-body) upon cell wall stresses, implicating its posttranscriptional role in decay of cell wall mRNAs. However, how Slt2p MAP kinase directly regulates the stability of cell wall transcripts during cell wall stress remains unclear. Here, we reported that the RNA-binding protein Rbp1p (Ngr1p) is a downstream effector and target of Slt2p MAP kinase during activation of the cell wall stress signaling cascade. In addition to the well-defined target mitochondrial porin mRNA, we found that Rbp1p also negatively regulates the stability of a subset of Slt2p-regulated cell wall transcripts. Deletion ofRBP1increases the level of cell wall transcripts and partially suppresses the hypersensitivity of theslt2Δdeletion strain to cell wall damage. Slt2p is necessary for cell wall stress-induced stabilization of cell wall transcripts. Deletion ofRBP1compromises the destabilization of cell wall transcripts inslt2Δmutants under cell wall stress. Notably, C-terminal deleted Slt2p impairs its function in promoting turnover of the Rbp1p protein and fails to stabilize cell wall transcripts, although it can complement the growth defect of theslt2Δstrain upon cell wall stress. Altogether, our results demonstrate that MAP kinase Slt2p attenuates CWI mRNA decay in response to cell wall damage by downregulating the activity of the RNA-binding protein Rbp1p.
A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions
Authors: Masonbrink Rick E , Alt David , Bayles Darrel O. , Boggiatto Paola , Edwards William , Tatum Fred , Williams Jeffrey , Wilson-Welder Jenny , Zimin Aleksey , Severin Andrew , Olsen Steven 
Published: October 2020

AbstractRocky Mountain elk (Cervus canadensis) is a major reservoir forBrucella abortusin the Greater Yellowstone area, which has significant economic implications to the cattle industry. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and HiC sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing nine putative gene losses in elk.Author SummaryBrucellosis, also known as contagious abortion, is a bacterial disease that commonly affects livestock and remains prevalent in Rocky Mountain elk (Cervus canadensis). Since the 1920’s the USDA has led a program to eradicate Brucellosis from cattle, yet wild Rocky Mountain elk continue to be a source of transmission. Attempts to vaccinate wild elk herds have been unsuccessful, due to a poor and short-lived immune response. To investigate the genetic basis for this inherent difference, we created the first genome and annotation for the Rocky Mountain elk. This genome assembly is of the highest quality and contains single linear sequences for all 35 chromosomes. In order to generate gene models, an array of RNA-Seq data and proteins from many different organ tissues and cells were used in gene prediction software. Specifically, we compare cattle immune system genes with the Rocky Mountain elk, revealing the putative loss of nine immune-system related genes in elk.
Host range projection of SARS-CoV-2: South Asia perspective
Authors: Ahmed Rasel , Hasan Rajnee , Siddiki A.M.A.M Zonaed , Islam Md. Shahidul 
Published: October 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causing agent of Coronavirus Disease-2019 (COVID-19), is likely to be originated from bat and transmitted through intermediate hosts. However, the immediate source species of SARS-CoV-2 has not yet been confirmed. Here, we used diversity analysis of the angiotensin I converting enzyme 2 (ACE2) that serves as cellular receptor for SARS-CoV-2 and transmembrane protease serine 2 (TMPRSS2), which has been proved to be utilized by SARS-CoV-2 for spike protein priming. We also simulated the structure of receptor binding domain of SARS-CoV-2 spike protein (SARS-CoV-2 S RBD) with the ACE2s to investigate their binding affinity to determine the potential intermediate animal hosts that could spread the SARS-CoV-2 virus to humans in South Asia. We identified cow, buffalo, goat and sheep, which are predominant species in the household farming system in South Asia that can potentially be infected by SARS-CoV-2. All the bird species studied along with rat and mouse were considered less potential to interact with SARS-CoV-2. The interaction interfaces of SARS-CoV-2 S RBD and ACE2 protein complex suggests pangolin as a potential intermediate host in SARS-CoV-2. Our results provide a valuable resource for the identification of potential hosts for SARS-CoV-2 in South Asia and henceforth reduce the opportunity for a future outbreak of COVID-19.
Soil microbial diversity impacts plant microbiota more than herbivory
Authors: Malacrinò Antonino , Karley Alison J. , Schena Leonardo , Bennett Alison E. 
Published: October 2020

AbstractInteractions between plants and microbiomes play a key role in ecosystem functioning and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, we tested and quantified the effect of different factors driving the diversity and composition of plant-associated microbial communities. We manipulated soil microbial diversity (high or low diversity), plant species (Solanum tuberosumorSolanum vernei), and herbivory (presence or absence of a phloem-feeding insectMacrosiphum euphorbiae), and found that soil microbial diversity influenced the herbivore-associated microbiome composition, but also plant species and herbivory influenced the soil microbiome composition. We quantified the relative strength of these effects and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems.
Momilactone B inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling
Authors: Wu Jianxin , Long Jun , Lin Xianhui , Chang Zhenyi , Baerson Scott R. , Ding Chaohui , Wu Xiaoyan , Pan Zhiqiang , Song Yuanyuan , Zeng Rensen 
Published: October 2020

AbstractIn competition for limited resources, many plants release allelochemicals to inhibit the growth of neighboring plants. Momilactone B (MB) is a major allelochemical produced by rice (Oryza sativa), however its mode of action is currently unknown. We used Arabidopsis (Arabidopsis thaliana) as a model system to evaluate potential mechanisms underlying the inhibitory effects of MB on seed germination, seedling establishment and root growth through the use of confocal microscopy and the examination of transcriptional responses in MB-treated seedlings. In response to MB treatment, transcript levels for genes encoding several key ABA biosynthetic enzymes and signaling components, including the transcription factor ABA-INSENSITIVE 4 (ABI4), were dramatically increased. Additionally,ABA insensitive 4(abi4) mutant seedlings exhibited reduced susceptibility to exogenously-provided MB. Although the transcript levels ofDELLAgenes, which negatively regulate GA signaling, were significantly increased upon MB exposure, exogenous GA application did not reverse the inhibitory effects of MB on Arabidopsis germination and seedling development. Moreover, a reduction in seedling root meristematic activity, associated with reduced expression of auxin biosynthetic genes and efflux transporters, and apparent lowered auxin content, was observed in MB-treated root tips. Exogenous auxin applications partially rescued the inhibitory effects of MB observed in root growth. Our results indicate that MB suppresses Arabidopsis seed germination and root growth primarily via disruption of ABA and auxin signaling. These findings underscore the crucial roles played by phytohormones in mediating responses to allelochemical exposure.One-sentence summaryMomilactone B, the key allelochemical of rice, inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling, suggesting the crucial roles of phytohormones in plant allelopathy
Screening bacterial isolates for phosphate Solubilizing capability in a ferruginous ultisol in Benin City, Edo State Nigeria
Authors: Musa S.I. , Ikhajiagbe Beckley 
Published: October 2020

AbstractPhosphorus is a major growth-limiting nutrient which plays important biochemical role in photosynthesis, respiration and several other processes in the living plant. It is widely distributed in minerals as phosphates. It reacts easily with Fe3+in ferruginous ultisols and therefore not bioavailable for plant usage. Many bacteria have the ability to solubilize phosphate minerals and make it bioavailable to plants. Thus this research investigates the culturable bacterial composition of ferruginous ultisol, comparative to control soils as well as the phosphate solubilizing capabilities of the isolates for future use in soil improvements. Six soil samples of different ferruginous levels and a control were assayed for physicochemical parameters prior to the experiment. Culturable bacteria as well as the phosphate solubilizing bacteria (PSB) were assayed in Pikovskaya’s medium at 27°C with 7.5 pH for 7days. Six distinct isolates were observed which proved to beProteus spp.,Pseudomonas spp.,Klebsiella spp.,Salmonella spp.,Bacillus spp. and Serratia spp. based on biochemical and morphological characteristics. Of these six isolates, three isolates (EMBF2-Klebsiellaspp, BCAF1-Proteusspp and BCAC2-Bacillusspp) were identify to solubilize phosphate by releasing a considerable amount of phosphate (12.01-21.23 ppm) and lowering the pH of the media. The three isolates showed tolerance to acidic and alkaline media and also showed plant growth promoting capabilities by releasing IAA and siderophores. The result revealed that the three isolates had potential to chelate the ion bond in Fe3+in ferruginous ultisol by releasing low molecular weight organic acid, making phosphate to be bioavailable for plant usage. This will serve as biofertilizer in improving yield of crops in ferruginous ultisol and improve soil fertility.
Fluorescence-free quantification of protein/nucleic-acid binding through single-molecule kinetic locking
Authors: Rieu Martin , Valle-Orero Jessica , Ducos Bertrand , Allemand Jean-François , Croquette Vincent 
Published: October 2020

ABSTRACTFluorescence-free micro-manipulation of nucleic acids (NA) allows the functional characterization of DNA/RNA processing proteins, without the interference of labels, but currently fails to detect and quantify their binding. To overcome this limitation, we developed a new method based on single-molecule force spectroscopy, called kinetic locking, that allows a direct in vitro visualization of protein binding while avoiding any kind of chemical disturbance of the protein’s natural function. We validate kinetic locking by measuring accurately the hybridization energy of ultrashort nucleotides (5,6,7 bases) and use it to measure the dynamical interactions of E. coli RecQ helicase with its DNA substrate.