keyword
https://read.qxmd.com/read/38536446/metformin-treatment-reduces-the-incidence-of-osteoporosis-a-two-sample-mendelian-randomized-study
#21
JOURNAL ARTICLE
Yaotian Cai, Gao Jun, Xiaojie Zhuang
UNLABELLED: It remains unclear whether the association between metformin and osteoporosis (OP) risk is causal. This two-sample Mendelian randomization (MR) study suggests a causal relationship between metformin treatment and a decrease in OP and fracture incidence, as well as an increase in bone mineral density (BMD) in the lumbar spine, femoral neck, and heel. Nonetheless, no significant causal effect is observed on forearm BMD. PURPOSE: We utilize a MR approach to investigate the association between metformin treatment and the risk of OP...
March 27, 2024: Osteoporosis International
https://read.qxmd.com/read/38536179/genetic-and-phenotypic-features-of-schizophrenia-in-the-uk-biobank
#22
JOURNAL ARTICLE
Sophie E Legge, Antonio F Pardiñas, Grace Woolway, Elliott Rees, Alastair G Cardno, Valentina Escott-Price, Peter Holmans, George Kirov, Michael J Owen, Michael C O'Donovan, James T R Walters
IMPORTANCE: Large-scale biobanks provide important opportunities for mental health research, but selection biases raise questions regarding the comparability of individuals with those in clinical research settings. OBJECTIVE: To compare the genetic liability to psychiatric disorders in individuals with schizophrenia in the UK Biobank with individuals in the Psychiatric Genomics Consortium (PGC) and to compare genetic liability and phenotypic features with participants recruited from clinical settings...
March 27, 2024: JAMA Psychiatry
https://read.qxmd.com/read/38535342/genome-wide-exploration-of-long-non-coding-rnas-of-helicoverpa-armigera-in-response-to-pyrethroid-insecticide-resistance
#23
JOURNAL ARTICLE
Md-Mafizur Rahman, Celso Omoto, Juil Kim
Genome-wide long non-coding RNAs (lncRNAs) in low, moderate, and high pyrethroid insecticide-resistant and -susceptible strains of Helicoverpa armigera were identified in this study. Using 45 illumina-based RNA-sequencing datasets, 8394 lncRNAs were identified. In addition, a sublethal dose of deltamethrin was administered to a Korean-resistant strain (Kor-T). The average length of lncRNAs was approximately 531 bp, and the expression ratio of lncRNAs was 28% of the total RNA. The identified lncRNAs were divided into six categories-intronic, intergenic, sense, antisense, cis-RNA, and trans-RNA-based on their location and mechanism of action...
February 21, 2024: Insects
https://read.qxmd.com/read/38534448/phylogenetic-analysis-of-pyruvate-ferredoxin-oxidoreductase-a-redox-enzyme-involved-in-the-pharmacological-activation-of-nitro-based-prodrugs-in-bacteria-and-protozoa
#24
JOURNAL ARTICLE
Seth Duwor, Daniela Brites, Pascal Mäser
The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used...
March 9, 2024: Biology
https://read.qxmd.com/read/38533900/ancient-genomes-from-bronze-age-remains-reveal-deep-diversity-and-recent-adaptive-episodes-for-human-oral-pathobionts
#25
JOURNAL ARTICLE
Iseult Jackson, Peter Woodman, Marion Dowd, Linda Fibiger, Lara M Cassidy
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record...
March 1, 2024: Molecular Biology and Evolution
https://read.qxmd.com/read/38533805/genotype-environment-associations-reveal-genes-potentially-linked-to-avian-malaria-infection-in-populations-of-an-endemic-island-bird
#26
JOURNAL ARTICLE
Eleanor C Sheppard, Claudia A Martin, Claire Armstrong, Catalina González-Quevedo, Juan Carlos Illera, Alexander Suh, Lewis G Spurgin, David S Richardson
Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii)...
March 27, 2024: Molecular Ecology
https://read.qxmd.com/read/38532990/causal-associations-between-severe-mental-illness-and-sepsis-a-mendelian-randomization-study
#27
JOURNAL ARTICLE
Ruhao Yang, Hongyu Xiang, Ting Zheng
OBJECTIVE: SMI (severe mental illness) has been identified as a risk factor for sepsis in observational studies; however, the causal association between them has yet to be firmly established. We conducted MR (mendelian randomization) to unveil the causal relationship between SMI and sepsis as well as sepsis mortality. METHODS: GWAS (Genome-wide association) data for major depression and schizophrenia were selected as exposure. GWAS data for sepsis and sepsis mortality were selected as outcome...
2024: Frontiers in Psychiatry
https://read.qxmd.com/read/38532472/association-between-genetic-risk-and-adherence-to-healthy-lifestyle-for-developing-age-related-hearing-loss
#28
JOURNAL ARTICLE
Sang-Hyuk Jung, Young Chan Lee, Manu Shivakumar, Jaeyoung Kim, Jae-Seung Yun, Woong-Yang Park, Hong-Hee Won, Dokyoon Kim
BACKGROUND: Previous studies have shown that lifestyle/environmental factors could accelerate the development of age-related hearing loss (ARHL). However, there has not yet been a study investigating the joint association among genetics, lifestyle/environmental factors, and adherence to healthy lifestyle for risk of ARHL. We aimed to assess the association between ARHL genetic variants, lifestyle/environmental factors, and adherence to healthy lifestyle as pertains to risk of ARHL. METHODS: This case-control study included 376,464 European individuals aged 40 to 69 years, enrolled between 2006 and 2010 in the UK Biobank (UKBB)...
March 26, 2024: BMC Medicine
https://read.qxmd.com/read/38532180/a-diverse-panel-of-755-bread-wheat-accessions-harbors-untapped-genetic-diversity-in-landraces-and-reveals-novel-genetic-regions-conferring-powdery-mildew-resistance
#29
JOURNAL ARTICLE
Rebecca Leber, Matthias Heuberger, Victoria Widrig, Esther Jung, Etienne Paux, Beat Keller, Javier Sánchez-Martín
A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel...
March 27, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://read.qxmd.com/read/38531359/ancestry-dynamics-and-trait-selection-in-a-designer-cat-breed
#30
JOURNAL ARTICLE
Christopher B Kaelin, Kelly A McGowan, Anthony D Hutcherson, John M Delay, Jeremiah H Li, Sarah Kiener, Vidhya Jagannathan, Tosso Leeb, William J Murphy, Gregory S Barsh
The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats...
March 21, 2024: Current Biology: CB
https://read.qxmd.com/read/38528708/strong-prevalence-of-light-regime-specific-qtl-in-arabidopsis-detected-using-automated-high-throughput-phenotyping-in-fluctuating-or-constant-light
#31
JOURNAL ARTICLE
Marc C Heuermann, Rhonda C Meyer, Dominic Knoch, Henning Tschiersch, Thomas Altmann
Plants have evolved and adapted under dynamic environmental conditions, particularly to fluctuating light, but plant research has often focused on constant growth conditions. To quantitatively asses the adaptation to fluctuating light, a panel of 384 natural Arabidopsis thaliana accessions was analyzed in two parallel independent experiments under fluctuating and constant light conditions in an automated high-throughput phenotyping system upgraded with supplemental LEDs. While the integrated daily photosynthetically active radiation was the same under both light regimes, plants in fluctuating light conditions accumulated significantly less biomass and had lower leaf area during their measured vegetative growth than plants in constant light...
2024: Physiologia Plantarum
https://read.qxmd.com/read/38528620/eukaryotic-driven-directed-evolution-of-cas9-nucleases
#32
JOURNAL ARTICLE
Giulia Vittoria Ruta, Matteo Ciciani, Eyemen Kheir, Michele Domenico Gentile, Simone Amistadi, Antonio Casini, Anna Cereseto
BACKGROUND: Further advancement of genome editing highly depends on the development of tools with higher compatibility with eukaryotes. A multitude of described Cas9s have great potential but require optimization for genome editing purposes. Among these, the Cas9 from Campylobacter jejuni, CjCas9, has a favorable small size, facilitating delivery in mammalian cells. Nonetheless, its full exploitation is limited by its poor editing activity. RESULTS: Here, we develop a Eukaryotic Platform to Improve Cas Activity (EPICA) to steer weakly active Cas9 nucleases into highly active enzymes by directed evolution...
March 25, 2024: Genome Biology
https://read.qxmd.com/read/38528503/periodontitis-and-sjogren-s-syndrome-a-bidirectional-two-sample-mendelian-randomization-study
#33
JOURNAL ARTICLE
Yixuan Liu, Nuozhou Liu, Peiyan Sun, Yi Liu, Wei Hua
OBJECTIVES: Observational studies indicated a controversial relationship between periodontitis (PD) and Sjogren's syndrome (SS). To overcome restrictions in conventional observational studies, we conducted a two-sample Mendelian randomization (MR) analysis to assess the potential bidirectional relationship between PD and SS. METHODS: We utilized the largest available genome-wide association study (GWAS) of European ancestry on both PD (17,353 cases-28,210 controls) and SS (2495 cases-365,533 controls) for MR genetic instrument selection...
March 25, 2024: BMC Oral Health
https://read.qxmd.com/read/38528244/exploring-genomic-inbreeding-and-selection-signatures-in-a-commercial-brangus-herd-through-functional-annotation
#34
JOURNAL ARTICLE
Gabriel A Zayas, Eduardo E Rodriguez, Aakilah S Hernandez, Fernanda M Rezende, Raluca G Mateescu
Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year...
March 25, 2024: Journal of Applied Genetics
https://read.qxmd.com/read/38527083/phenotypic-screening-reveals-a-highly-selective-phthalimide-based-compound-with-antileishmanial-activity
#35
JOURNAL ARTICLE
Farnaz Zahedifard, Meenakshi Bansal, Neha Sharma, Sumit Kumar, Siqi Shen, Priyamvada Singh, Brijesh Rathi, Martin Zoltner
Pharmacophores such as hydroxyethylamine (HEA) and phthalimide (PHT) have been identified as potential synthons for the development of compounds against various parasitic infections. In order to further advance our progress, we conducted an experiment utilising a collection of PHT and HEA derivatives through phenotypic screening against a diverse set of protist parasites. This approach led to the identification of a number of compounds that exhibited significant effects on the survival of Entamoeba histolytica, Trypanosoma brucei, and multiple life-cycle stages of Leishmania spp...
March 25, 2024: PLoS Neglected Tropical Diseases
https://read.qxmd.com/read/38525798/comparative-genomic-analyses-reveal-evidence-for-adaptive-a-to-i-rna-editing-in-insect-adar-gene
#36
JOURNAL ARTICLE
Caiqing Zheng, Ling Ma, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan
Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking...
December 2024: Epigenetics: Official Journal of the DNA Methylation Society
https://read.qxmd.com/read/38525495/assessing-the-role-of-cortisol-in-anxiety-major-depression-and-neuroticism-a-mendelian-randomization-study-using-serpina6-serpina1-variants
#37
JOURNAL ARTICLE
Io Ieong Chan, Anise M S Wu
BACKGROUND: Previous evidence informed by the toxic stress model suggests that higher cortisol causes anxiety and major depression, but clinical success is lacking. To clarify the role of cortisol, we used Mendelian randomization to estimate its associations with anxiety, major depression, and neuroticism, leveraging the largest available genome-wide association studies including from the Psychiatric Genomics Consortium, the UK Biobank, and FinnGen. METHODS: After meta-analyzing 2 genome-wide association studies on morning plasma cortisol ( n  = 32,981), we selected single nucleotide polymorphisms (SNPs) at p < 5 × 10-8 and r 2 < 0...
May 2024: Biol Psychiatry Glob Open Sci
https://read.qxmd.com/read/38525152/the-effect-of-marker-types-and-density-on-genomic-prediction-and-gwas-of-key-performance-traits-in-tetraploid-potato
#38
JOURNAL ARTICLE
Trine Aalborg, Elsa Sverrisdóttir, Heidi Thorgaard Kristensen, Kåre Lehmann Nielsen
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38523595/alcohol-drinking-dna-methylation-and-psychiatric-disorders-a-multi-omics-mendelian-randomization-study-to-investigate-causal-pathways
#39
JOURNAL ARTICLE
Xiaoqiang Shi, Meng Li, Jianhua Yao, Ming D Li, Zhongli Yang
BACKGROUND AND AIMS: Whether alcohol-related DNA methylation has a causal effect on psychiatric disorders has not been investigated. Furthermore, a comprehensive investigation into the causal relationship and underlying mechanisms linking alcohol consumption and psychiatric disorders has been lacking. This study aimed to evaluate the causal effect of general alcohol intake and pathological drinking behaviors on psychiatric disorders, alcohol-associated DNA methylation on gene expression and psychiatric disorders, and gene expression on psychiatric disorders...
March 25, 2024: Addiction
https://read.qxmd.com/read/38521585/production-of-the-anti-g-quadruplex-antibody-bg4-for-efficient-genome-wide-analyses-from-plasmid-quality-control-to-antibody-validation
#40
JOURNAL ARTICLE
Ilaria Maurizio, Beatrice Tosoni, Irene Gallina, Emanuela Ruggiero, Irene Zanin, Sara N Richter
G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that can form at guanine-rich sequences of DNA and RNA in every kingdom of life. At the DNA level, G4s can form throughout genomes but they are prevalently found in promoter regions and at telomeres, and they have been attributed functions spanning from transcriptional regulation, to control of DNA replication, to maintenance of chromosome ends. Our understanding of the functions of G4s in cells has greatly improved with the development of specific anti-G4 antibodies, which allow the visualization of G4s by immunofluorescence but also the mapping of these secondary DNA structures genome wide...
2024: Methods in Enzymology
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