bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance
Authors: Grant Trudy-Ann , López-Pérez Mario , Almagro-Moreno Salvador 
Published: October 2022

ABSTRACTAntimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU, is a porin that makes up to 60% of the outer membrane ofVibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of the bacterium and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmentalV. choleraeand established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a uniqueompUallele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes.AUTHOR SUMMARYAntimicrobial resistance (AMR) is one of the major threats to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here we developed an approach that uses genetic diversity from environmental populations to decode emergent phenotypes such as AMR. Specifically, we examined naturally occurring allelic variants of an outer membrane porin, OmpU, inVibrio choleraeand established associations between genotype and phenotype. Using this approach, we identified and characterized the functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Our perspective towards disentangling the emergence of AMR can be naturally extended to other proteins and bacterial pathogens.
Deletion of the ion channelTrpm4increases cardiac inflammatory markers and fibrosis after myocardial infarction in mice
Authors: Boukenna Mey , Rougier Jean-Sébastien , Aghagolzadeh Parisa , Pradervand Sylvain , Guichard Sabrina , Hämmerli Anne-Flore , Pedrazzini Thierry , Abriel Hugues 
Published: October 2022

ABSTRACTBACKGROUNDThe first cause of mortality worldwide is ischemic heart disease. In myocardial infarction (MI), the ischemic event causes cell death, which triggers a large inflammatory response responsible for removing necrotic material and inducing tissue repair. Endothelial cells, immune cells and fibroblasts play a key role in orchestrating this healing process. TRPM4 is a Ca2+-activated ion channel permeable to monovalent cations and its silencing or knocking out was shown to critically modify cellular functions of these non-myocytic cell types.OBJECTIVEOur aims were to 1) evaluate the role of TRPM4 on mice survival and cardiac function after MI; and 2) investigate the role of TRPM4 in the post-MI acute and chronic inflammatory response.METHODSWe performed ligation of the left anterior descending coronary artery or sham intervention on 154Trpm4WT or KO male mice and monitored survival for up to 5 weeks as well as cardiac function using echocardiography at 72h and five weeks. We drew blood at different acute time points (6h, 12h, 24h) and performed time-of-flight mass spectrometry to analyze the sera proteomes. Further, we sacrificed sub-groups of mice at 24h and 72h after surgery and performed single-cell RNA sequencing on the non-myocytic cells. Lastly, we assessed fibrosis and angiogenesis at five weeks using type I collagen and CD31 immunostaining respectively.RESULTSWe observed no significant differences in survival or cardiac function post-MI between both genotypes. However, our serum proteomics data showed significantly decreased tissue injury markers such as creatine kinase M and VE-Cadherin in KO compared to WT 12h after MI. On the other hand, inflammation characterized by serum amyloid P component in the serum, as well as higher number of recruited granulocytes, M1 macrophages, M1 monocytes, Mac-6 macrophages, and expression of pro-inflammatory genes such asIl1b, Lyz2andS100a8/a9was significantly higher in endothelial cells, macrophages and fibroblasts of KO than of WT. This correlated with increased cardiac fibrosis and angiogenesis 5 weeks after MI in KO.CONCLUSIONOur data suggest that knocking outTrpm4drastically increases acute inflammation post-MI, is associated with increased chronic fibrosis and does not improve survival at 5 weeks post-MI. Thus, targeting TRPM4 in the context of MI should be pondered carefully and approaches that nuance the timing of the inhibition or cellular target may be required.
Knockout of ribosomal protein RpmJ leads to zinc resistance inEscherichia coli
Authors: Shirakawa Riko , Ishikawa Kazuya , Furuta Kazuyuki , Kaito Chikara 
Published: October 2022

AbstractZinc is an essential metal for cells, but excess amounts are toxic. Other than by regulating the intracellular zinc concentration by zinc uptake or efflux, the mechanisms underlying bacterial resistance to excess zinc are unknown. In the present study, we searched for zinc-resistant mutant strains from the Keio collection, a gene knockout library ofEscherichia coli, a model gram-negative bacteria. We found that knockout mutant of RpmJ, a 50S ribosomal protein, exhibited zinc resistance. TherpmJmutant was sensitive to protein synthesis inhibitors and had altered translation fidelity, indicating ribosomal dysfunction. In therpmJmutant, the intracellular zinc concentration was decreased under excess zinc conditions. RNA sequence analysis revealed thatrpmJknockout decreased the expression of synthetic genes for iron-sulfur cluster proteins, which are toxic targets for zinc. These findings suggest that knocking out RpmJ causes zinc resistance by decreasing zinc targets and lowering the intracellular zinc concentration. Knockouts of other ribosomal proteins, including RplA, RpmE, RpmI, and RpsT, also led to a zinc-resistant phenotype, suggesting that deletion of ribosomal proteins is closely related to zinc resistance.
Quantifying metal ion specificity of the nickel-binding proteinCcNikZ-II fromClostridium carboxidivoransin the presence of competing metal ions
Authors: Diep Patrick , Kell Brayden , Yakunin Alexander , Hilfinger Andreas , Mahadevan Radhakrishnan 
Published: October 2022

AbstractMany proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins,in vivometal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteinsin vitroto purify specific metal ions from wastewater, where specificity is dictated by the protein’s metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein’s specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding kinetics. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate kinetic models in multi-metal solutions forCcNikZ-II, a nickel-binding protein fromClostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models forCcNikZ-II. We further demonstrate that principles for improving specificity through changes in binding affinity are qualitatively different depending on the competing metals, highlighting the power of mechanistic models to guide metalloprotein engineering targets.
Citrus genomic resources unravel putative genetic determinants of Huanglongbing, a pathogen-triggered immune disease
Authors: Gao Yuxia , Xu Jin , Li Zhilong , Zhang Yunzeng , Riera Nadia , Xiong Zhiwei , Ouyang Zhigang , Liu Xinjun , Lu Zhanjun , Seymour Danelle , Zhong Balian , Wang Nian 
Published: October 2022

SummaryCitrus is one of the most important tree crops worldwide and citrus production is threatened by Huanglongbing (HLB), a devasting citrus disease caused byCandidatusLiberibacter. HLB is a pathogen-triggered immune disease, in which the pathogen initiates systemic and chronic immune responses including the excessive production of reactive oxidative species, which subsequently lead to cell death of phloem tissues and HLB disease symptoms. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. To enable these analyses we first developed a phased diploid assembly ofCitrus sinensis‘Newhall’ genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 sequenced accessions for genome-wide association mapping of the HLB response. Genes with HLB pathogenicity were associated with the host immune response, ROS production, and antioxidants. Overall, this study has provided a significant recourse of citrus genomic data and we have identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity and to generate HLB resistant/tolerant citrus varieties.
Metformin attenuates hyperglycaemia-stimulated pro-fibrotic gene expression in vascular adventitial fibroblasts via inhibition of Discoidin Domain Receptor 2
Authors: Titus Allen Sam , Ushakumary Mereena George , Venugopal Harikrishnan , Wang Mingyi , Lakatta Edward G. , Kailasam Shivakumar 
Published: October 2022

AbstractMolecular mechanisms underlying the diverse therapeutic effects of anti-diabetic metformin, beyond its anti-hyperglycaemic effects, remain largely unclear. Metformin is reported to reduce the long-term complications of diabetes, including cardiovascular fibrosis and remodelling. Our recent investigations show that Discoidin Domain Receptor 2 (DDR2), a collagen receptor tyrosine kinase, has an obligate regulatory role in collagen type I gene expression in cardiac and vascular adventitial fibroblasts, and that it may be a molecular link between arterial fibrosis and metabolic syndrome in rhesus monkeys. Using gene knockdown and over-expression approaches, the present study examined whether DDR2 is a target of metformin, and whether, by targeting DDR2, it inhibits fibronectin and collagen expression in vascular adventitial fibroblasts exposed to hyperglycaemic conditions. Metformin was found to attenuate hyperglycaemia-induced increase in DDR2 mRNA and protein expression by inhibiting TGF-β1/ Smad2/3 signalling that mediates the stimulatory effect of hyperglycaemia on DDR2 expression. Metformin also inhibited DDR2-dependent expression of fibronectin and collagen, indicating that it regulates these matrix proteins via DDR2 inhibition. The findings identify DDR2, a major mediator of cardiovascular remodelling, as a molecular target of metformin, thereby uncovering the molecular basis of its protective role in vascular fibrosis, and possibly, cardiac fibrosis associated with diabetic cardiomyopathy.
Genes associated with depression and coronary artery disease are enriched for inflammation and cardiomyopathy-associated pathways
Authors: Singh Kritika , Lee Hyunjoon , Sealock Julia M , Miller-Flemming Tyne , Straub Peter , Cox Nancy J. , Wells Quinn S. , Smoller Jordan W. , Hodges Emily C. , Davis Lea K. 
Published: October 2022

AbstractBackgroundDepression and Coronary Artery Disease (CAD) are highly comorbid conditions. Approximately 40% of individuals who have one diagnosis will also develop the other within their lifetime. Prior research indicates that polygenic risk for depression increases the odds of developing CAD even in the absence of clinical depression. However, the specific genes and pathways involved in comorbid depression-CAD remain unknown.ResultsWe identified genes that are significantly associated with both depression and CAD, and are enriched for pathways involved in inflammation and for previous association with cardiomyopathy. We observed increased rate of prevalent, but not incident, cardiomyopathy cases in individuals with comorbid depression-CAD compared to those with CAD alone in three electronic large health record (EHR) datasets.ConclusionsThe results of our study implicate genetically regulated inflammatory mechanisms in depression-CAD. Our results also raise the hypothesis that depression-associated CAD may be enriched for cardiomyopathy.Clinical PerspectiveWhat’s New?Gene associations shared between depression and CAD are enriched for prior association with cardiomyopathy phenotypes.Cardiomyopathy is significantly more prevalent in individuals with comorbid depression-CAD than in CAD or depression alone.What are the Clinical Implications?Our work suggests that individuals with comorbid depression-CAD may benefit from screening for cardiomyopathy.
East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease
Authors: He Yunye , Koido Masaru , Sutoh Yoichi , Shi Mingyang , Otsuka-Yamasaki Yayoi , Munter Hans Markus , Morisaki Takayuki , Nagai Akiko , Murakami Yoshinori , Tanikawa Chizu , Hachiya Tsuyoshi , Matsuda Koichi , Shimizu Atsushi , Kamatani Yoichiro 
Published: October 2022

AbstractPeptic ulcer disease (PUD) refers to acid-induced injury of the digestive tract, occurring mainly in the stomach (gastric ulcer; GU) or duodenum (duodenal ulcer; DU). We conducted a large-scale cross-ancestry meta-analysis of PUD combining genome-wide association studies with four Japanese and two European studies (52,032 cases and 905,344 controls), and discovered 25 novel loci highly concordant across ancestries. Based on these loci, an examination of similarities and differences in genetic architecture between GU and DU demonstrated that GU shared the same risk loci as DU, although with smaller genetic effect sizes and higher polygenicity than DU, indicating higher heterogeneity of GU.H. pylori(HP)-stratified analysis found an HP-related host genetic locus, marking its role in HP-mediated PUD etiology. Integrative analyses using bulk and single-cell transcriptome profiles highlighted the genetic factors of PUD to be enriched in the highly expressed genes in stomach tissues, especially in somatostatin-producing D cells. Our results provide genetic evidence that gastrointestinal cell differentiations and hormone regulations are critical in PUD etiology.
Effects of the COVID-19 pandemic on hospital admissions and inpatient mortality in Kenya
Authors: Ogero M , Isaaka L , Mumelo L , Kimego D , Njoroge T , Mbevi G , Wanyama C , Lucinde R , Gathuri H , Otiende M , Nzioki C , Wachira A , Mumbi F , Oeri G , Mwangi N , Gitari R , Mugambi D , Namu S , Ithondeka A , Kariuki H , Kiama Z , Mwende L , Jowi E , Muthui B , Kaara A , Sitienei E , Thuranira L , Oginga I , Njagi J , Kamau E , Namulala E , Oketch G , Wandera O , Adhiambo S , Adem A , Ochieng M , Otedo A , Otiende K , Odondi A , Makokha F , Lubanga D , Nyikui J , Masoso W , Manyonge M , Inginia R , Manuthu E , Wafula D , Agutu C , Malangachi R , Biko S , Simiyu  , Obare J , Kimutai D , Gituma B , Kyalo J , Timbwa M , Otieno J , Liru M , Nyabinda C , Otieno S , Aman R , Mwangangi M , Amoth P , Were I , Mwangi C , Kasera K , Ng’ang’a W , Tsegaye A , Sherry C , Singa B , Tickell K , Walson J , Berkley J , Were F , Mturi N , Hamaluba M , Tsofa B , Mwangangi J , Bejon P , Barasa E , English M , Nyaguara A , Kagucia EW , Scott JAG , Akech S , Etyang AO , Agweyu A 
Published: October 2022

AbstractBackgroundThe impact of COVID-19 in Africa remains poorly defined. We sought to describe trends in hospitalisation due to all medical causes, pneumonia-specific admissions, and inpatient mortality in Kenya before and during the first five waves of the COVID-19 pandemic in Kenya.MethodsWe conducted a hospital-based, multi-site, longitudinal observational study of patients admitted to 13 public referral facilities in Kenya from January 2018 to December 2021. The pre-COVID population included patients admitted before 1 March 2020. We fitted time series models to compare observed and predicted trends for each outcome. To estimate the impact of the COVID-19 pandemic, we calculated incidence rate ratios (IRR) and corresponding 95% confidence intervals (CI) from negative binomial mixed-effects models.ResultsOut of 302,703 patients hospitalised across the 13 surveillance sites (range 11547 to 57011), 117642 (39%) were admitted to adult wards. Compared with the pre-COVID period, hospitalisations declined markedly among adult (IRR 0.68, 95% CI 0.63 to 0.73) and paediatric (IRR 0.67, 95% CI 0.62 to 0.73) patients. Adjusted in-hospital mortality also declined among both adult (IRR 0.83, 95% CI 0.77 to 0.89) and paediatric (IRR 0.85, 95% CI 0.77 to 0.94) admissions. Pneumonia-specific admissions among adults increased during the pandemic (IRR 1.75, 95% CI 1.18 to 2.59). Paediatric pneumonia cases were lower than pre-pandemic levels in the first year of the pandemic and elevated in late 2021 (IRR 0.78, 95% CI 0.51 to 1.20).ConclusionsContrary to initial predictions, the COVID-19 pandemic was associated with lower hospitalisation rates and in-hospital mortality, despite increased pneumonia admissions among adults. These trends were sustained after the withdrawal of containment measures that disrupted essential health services, suggesting a role for additional factors that warrant further investigation.
Tackling the challenges of group network inference from intracranial EEG data
Authors: Pidnebesna Anna , Sanda Pavel , Kalina Adam , Hammer Jiri , Marusic Petr , Vlcek Kamil , Hlinka Jaroslav 
Published: October 2022

ABSTRACTIntracranial EEG (iEEG) data is a powerful way to map brain function, characterized by high temporal and spatial resolution, allowing the study of interactions among neuronal populations that orchestrate cognitive processing. However, the statistical inference and analysis of brain networks using iEEG data faces many challenges related to its sparse brain coverage, and its inhomogeneity across patients. We review these challenges and develop a methodological pipeline for estimation of network structure not obtainable from any single patient, illustrated on the inference of the interaction among visual streams using a dataset of 27 human iEEG recordings from a visual experiment employing visual scene stimuli. 100 ms sliding window and multiple band-pass filtered signals are used to provide temporal and spectral resolution. For the connectivity analysis we showcase two connectivity measures reflecting different types of interaction between regions of interest (ROI): Phase Locking Value as a symmetric measure of synchrony, and Directed Transfer Function - asymmetric measure describing causal interaction. For each two channels, initial uncorrected significance testing at p<0.05 for every time-frequency point is carried out by comparison of the data-derived connectivity to a baseline surrogate-based null distribution, providing a binary time-frequency connectivity map. For each ROI pair, a connectivity density map is obtained by averaging across all pairs of channels spanning them, effectively agglomerating data across relevant channels and subjects. Finally, the difference of the mean map value after and before the stimulation is compared to the same statistic in surrogate data to assess link significance.The analysis confirmed the function of the parieto-medial temporal pathway, mediating visuospatial information between dorsal and ventral visual streams during visual scene analysis. Moreover, we observed the anterior hippocampal connectivity with more posterior areas in the medial temporal lobe, and found the reciprocal information flow between early processing areas and medial place area. To summarize, we developed an approach for estimating network connectivity, dealing with the challenge of sparse individual coverage of intracranial EEG electrodes. Its application provided new insights into the interaction between the dorsal and ventral visual streams, one of the iconic dualities in human cognition.
Expansion Spatial Transcriptomics
Authors: Fan Yuhang , Andrusivová Žaneta , Wu Yunming , Chai Chew , Larsson Ludvig , He Mengxiao , Luo Liqun , Lundeberg Joakim , Wang Bo 
Published: October 2022

AbstractCapture array-based spatial transcriptomics methods have been widely used to resolve gene expression in diverse tissue contexts, however, their spatial resolution is limited by array density. We present Expansion Spatial Transcriptomics (Ex-ST) to overcome this limitation by clearing and expanding tissue prior to capturing the entire transcriptome. This approach allows us to achieve near cellular resolution and higher capture efficiency of lowly-expressed genes, which we demonstrate using mouse brain samples.