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JOURNAL ARTICLE
Xiaoqing Wu, Zetian Cui, Xinyi Li, Zehuai Yu, Pingping Lin, Li Xue, Abdullah Khan, Cailan Ou, Zuhu Deng, Muqing Zhang, Wei Yao, Fan Yu
BACKGROUND: Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense...
April 30, 2024: BMC genomic data
#42
JOURNAL ARTICLE
Wentao Cai, Jian Hu, Yunsheng Zhang, Zhanbao Guo, Zhengkui Zhou, Shuisheng Hou
BACKGROUND: Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential candidate genes and causal DNA variants vital to complex traits in human and many farm animals. However, eQTL mapping has not been conducted in ducks. It is desirable to know whether eQTLs within GWAS signals contributed to duck economic traits. RESULTS: In this study, we conducted an eQTL analysis using publicly available RNA sequencing data from 820 samples, focusing on liver, muscle, blood, adipose, ovary, spleen, and lung tissues...
April 30, 2024: BMC Genomics
#43
JOURNAL ARTICLE
Jake Adolf V Montecillo, Merell P Billacura, Maria Distressa G Billacura
The genus Aestuariicella has been recently reclassified as a member of the family Cellvibrionaceae. However, the taxonomic position of the genus as a distinct member of the family has not been clarified. In the present study, we performed multilayered analyses anchored on genome sequences to clarify the relationship between the genera Aestuariicella and Pseudomaricurvus within the family Cellvibrionaceae. Phylogenetic analyses based on 16S rRNA gene, RNA polymerase beta subunit (RpoB) protein, and core gene sequences showed a well-supported tight cluster formed by the members of the two genera...
April 30, 2024: Current Microbiology
#44
REVIEW
Daniel P Agustinho, Yilei Fu, Vipin K Menon, Ginger A Metcalf, Todd J Treangen, Fritz J Sedlazeck
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads...
April 30, 2024: Nature Methods
#45
REVIEW
Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance.
Matthew J Shepherd, Taoran Fu, Niamh E Harrington, Anastasia Kottara, Kendall Cagney, James D Chalmers, Steve Paterson, Joanne L Fothergill, Michael A Brockhurst
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages...
April 30, 2024: Nature Reviews. Microbiology
#46
JOURNAL ARTICLE
Amin Tajerian
Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting over 3% of those over 65. It's caused by reduced dopaminergic neurons and Lewy bodies, leading to motor and non-motor symptoms. The relationship between COMT gene polymorphisms and PD is complex and not fully elucidated. Some studies have reported associations between certain COMT gene variants and PD risk, while others have not found significant associations. This study investigates how COMT gene variations impact cortical thickness changes in PD patients over time, aiming to link genetic factors, especially COMT gene variations, with PD progression...
April 30, 2024: Scientific Reports
#47
JOURNAL ARTICLE
Anzaan Dippenaar, Nabila Ismail, Tim H Heupink, Melanie Grobbelaar, Johannes Loubser, Annelies Van Rie, Robin M Warren
Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix Xdrop-instrument and sequenced alongside a control sample using standard Illumina protocols followed by MAGMA-analysis...
April 30, 2024: Scientific Reports
#48
JOURNAL ARTICLE
Jacob M Keaton, Zoha Kamali, Tian Xie, Ahmad Vaez, Ariel Williams, Slavina B Goleva, Alireza Ani, Evangelos Evangelou, Jacklyn N Hellwege, Loic Yengo, William J Young, Matthew Traylor, Ayush Giri, Zhili Zheng, Jian Zeng, Daniel I Chasman, Andrew P Morris, Mark J Caulfield, Shih-Jen Hwang, Jaspal S Kooner, David Conen, John R Attia, Alanna C Morrison, Ruth J F Loos, Kati Kristiansson, Reinhold Schmidt, Andrew A Hicks, Peter P Pramstaller, Christopher P Nelson, Nilesh J Samani, Lorenz Risch, Ulf Gyllensten, Olle Melander, Harriette Riese, James F Wilson, Harry Campbell, Stephen S Rich, Bruce M Psaty, Yingchang Lu, Jerome I Rotter, Xiuqing Guo, Kenneth M Rice, Peter Vollenweider, Johan Sundström, Claudia Langenberg, Martin D Tobin, Vilmantas Giedraitis, Jian'an Luan, Jaakko Tuomilehto, Zoltan Kutalik, Samuli Ripatti, Veikko Salomaa, Giorgia Girotto, Stella Trompet, J Wouter Jukema, Pim van der Harst, Paul M Ridker, Franco Giulianini, Veronique Vitart, Anuj Goel, Hugh Watkins, Sarah E Harris, Ian J Deary, Peter J van der Most, Albertine J Oldehinkel, Bernard D Keavney, Caroline Hayward, Archie Campbell, Michael Boehnke, Laura J Scott, Thibaud Boutin, Chrysovalanto Mamasoula, Marjo-Riitta Järvelin, Annette Peters, Christian Gieger, Edward G Lakatta, Francesco Cucca, Jennie Hui, Paul Knekt, Stefan Enroth, Martin H De Borst, Ozren Polašek, Maria Pina Concas, Eulalia Catamo, Massimiliano Cocca, Ruifang Li-Gao, Edith Hofer, Helena Schmidt, Beatrice Spedicati, Melanie Waldenberger, David P Strachan, Maris Laan, Alexander Teumer, Marcus Dörr, Vilmundur Gudnason, James P Cook, Daniela Ruggiero, Ivana Kolcic, Eric Boerwinkle, Michela Traglia, Terho Lehtimäki, Olli T Raitakari, Andrew D Johnson, Christopher Newton-Cheh, Morris J Brown, Anna F Dominiczak, Peter J Sever, Neil Poulter, John C Chambers, Roberto Elosua, David Siscovick, Tõnu Esko, Andres Metspalu, Rona J Strawbridge, Markku Laakso, Anders Hamsten, Jouke-Jan Hottenga, Eco de Geus, Andrew D Morris, Colin N A Palmer, Ilja M Nolte, Yuri Milaneschi, Jonathan Marten, Alan Wright, Eleftheria Zeggini, Joanna M M Howson, Christopher J O'Donnell, Tim Spector, Mike A Nalls, Eleanor M Simonsick, Yongmei Liu, Cornelia M van Duijn, Adam S Butterworth, John N Danesh, Cristina Menni, Nicholas J Wareham, Kay-Tee Khaw, Yan V Sun, Peter W F Wilson, Kelly Cho, Peter M Visscher, Joshua C Denny, Daniel Levy, Todd L Edwards, Patricia B Munroe, Harold Snieder, Helen R Warren
Hypertension affects more than one billion people worldwide. Here we identify 113 novel loci, reporting a total of 2,103 independent genetic signals (P < 5 × 10-8 ) from the largest single-stage blood pressure (BP) genome-wide association study to date (n = 1,028,980 European individuals). These associations explain more than 60% of single nucleotide polymorphism-based BP heritability. Comparing top versus bottom deciles of polygenic risk scores (PRSs) reveals clinically meaningful differences in BP (16...
April 30, 2024: Nature Genetics
#49
JOURNAL ARTICLE
Zhili Zheng, Shouye Liu, Julia Sidorenko, Ying Wang, Tian Lin, Loic Yengo, Patrick Turley, Alireza Ani, Rujia Wang, Ilja M Nolte, Harold Snieder, Jian Yang, Naomi R Wray, Michael E Goddard, Peter M Visscher, Jian Zeng
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyze 50 complex traits and diseases using ∼7 million common single-nucleotide polymorphisms (SNPs) and 96 annotations...
April 30, 2024: Nature Genetics
#50
JOURNAL ARTICLE
Lisa Bachmann, Laura Weber, Wendy Liermann, Harald M Hammon, Cora Delling, Franziska Dengler, Katharina Schaufler, Michael Schwabe, Elias Eger, Karsten Becker, Anne Schütz, Timo Homeier-Bachmann
The aim of the present study was to determine if colostrum and the equipment for harvesting and feeding colostrum are sources of fecal ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-E. coli) in calves. Therefore, 15 male calves fed with pooled colostrum on a dairy farm and held individually in an experimental barn, the colostrum pool and the equipment for harvesting and feeding colostrum were sampled and analyzed for the occurrence of ESBL/AmpC-E. coli. The ESBL-AmpC-E. coli suspicious isolates were subjected to whole-genome sequence analysis...
April 30, 2024: Scientific Reports
#51
JOURNAL ARTICLE
Xu-Sheng Liu, Ya-Lan Chen, Yu-Xuan Chen, Rui-Min Wu, Fan Tan, Ya-Lan Wang, Zi-Yue Liu, Yan Gao, Zhi-Jun Pei
RAB3B is essential for the transportation and secretion within cells. Its increased expression is linked to the development and progression of various malignancies. However, understanding of RAB3B's involvement in carcinogenesis is mostly limited to specific cancer subtypes. Hence, exploring RAB3B's regulatory roles and molecular mechanisms through comprehensive cancer datasets might offer innovative approaches for managing clinical cancer. To examine the potential involvement of RAB3B in the development of cancer, we analyzed data from various sources including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), cBioPortal, HPA, UALCAN, and tissue microarray (TAM)...
April 30, 2024: Scientific Reports
#52
JOURNAL ARTICLE
Céline Antoine, Fanny Laforêt, Abdoulaye Fall, Bob Blasdel, Véronique Delcenserie, Damien Thiry
AIMS: Understanding bacterial phage resistance mechanisms has implications for developing phage-based therapies. This study aimed to explore the development of phage resistance in Escherichia coli K1 isolates' to K1-ULINTec4, a K1-dependent bacteriophage. METHODS AND RESULTS: Resistant colonies were isolated from two different strains (APEC 45 and C5), both previously exposed to K1-ULINTec4. Genome analysis and several parameters were assessed, including growth capacity, phage adsorption, phenotypic impact at capsular level, biofilm production and virulence in the in-vivo Galleria mellonella larvae model...
April 30, 2024: Journal of Applied Microbiology
#53
JOURNAL ARTICLE
Lu Xiao, Weina Li, Fawei Li, Xingjuan Chen, Yun Xu, Ying Hu, Yingkun Fu, Ling Feng
BACKGROUND: Observational studies show that patients with chronic obstructive pulmonary disease (COPD) tend to be sedentary during leisure time. Physical activity (PA) may reduce the risk of COPD, but the causal relationship is unclear. We used a Mendelian randomisation (MR) method to elucidate the association of leisure sedentary behaviours (LSB) and PA with lung function and COPD. METHODS: Data on LSB (n=422 218), PA (n=608 595), COPD (n=299 929) and lung function (n=79 055) were obtained from the large-scale genome-wide association study...
April 30, 2024: BMJ Open Respiratory Research
#54
REVIEW
Georgios Leotsakos, Ioannis Katafigiotis, Ioannis Leotsakos, Fiori Kousta, Aristeidis Molympakis, Aikaterini Perimeni, Michael Koutsilieris
Psoriasis continues to affect a large percentage of patients worldwide and strongly appears to be a systematic disease. Efforts are being made to understand its etiology, which have led to research extended to genomic analysis with a focus on the role of pro-inflammatory cytokines, which play a major role in the pathogenesis of the disease. Plasma proteomic analysis in various diseases has provided promising results for choosing the right treatment for psoriasis, suggesting that it could play a key role in the prevention, prognosis, and treatment of the disease by individualizing treatment choices based on the proteomic profile of each patient...
2024: In Vivo
#55
JOURNAL ARTICLE
Wenmin Zhang, Tianyuan Lu, Robert Sladek, Yue Li, Hamed Najafabadi, Josée Dupuis
MOTIVATION: Colocalization analysis is commonly used to assess whether two or more traits share the same genetic signals identified in genome-wide association studies (GWAS), and is important for prioritizing targets for functional follow-up of GWAS results. Existing colocalization methods can have suboptimal performance when there are multiple causal variants in one genomic locus. RESULTS: We propose SharePro to extend the COLOC framework for colocalization analysis...
April 30, 2024: Bioinformatics
#56
JOURNAL ARTICLE
Zulema Rodriguez-Hernandez, Mathias Gorski, Maria Tellez Plaza, Pascal Schlosser, Matthias Wuttke
SUMMARY: This paper introduces the metaGWASmanager, which streamlines genome-wide association studies within large-scale meta-analysis consortia. It is a toolbox for both the central consortium analysis group and participating studies to generate homogeneous phenotypes, minimize unwanted variability from inconsistent methodologies, ensure high-quality association results, and implement time-efficient quality control workflows. The toolbox features a plug-in-based approach for customization of association testing...
April 30, 2024: Bioinformatics
#57
JOURNAL ARTICLE
Chiao-Hsu Ke, Pan-Yun Lai, Feng-Yang Hsu, Po-Ren Hsueh, Ming-Tang Chiou, Chao-Nan Lin
Actinobacillus pleuropneumoniae infection causes a high mortality rate in porcine animals. Antimicrobial resistance poses global threats to public health. The current study aimed to determine the antimicrobial susceptibilities and probe the resistome of A. pleuropneumoniae in Taiwan. Herein, 133 isolates were retrospectively collected; upon initial screening, 38 samples were subjected to next-generation sequencing (NGS). Over the period 2017-2022, the lowest frequencies of resistant isolates were found for ceftiofur, cephalexin, cephalothin, and enrofloxacin, while the highest frequencies of resistant isolates were found for oxytetracycline, streptomycin, doxycycline, ampicillin, amoxicillin, kanamycin, and florfenicol...
December 2024: Veterinary Quarterly
#58
JOURNAL ARTICLE
Carine Ngo, Sophie Cotteret, Imène Deneche, Maria Kfoury, Randa Chehab, Alicia Tran-Dien, Julien Vibert, Alexandra Leary, Sébastien Gouy, Amandine Maulard, Philippe Morice, Jean-Yves Scoazec, Patricia Pautier, Catherine Genestie
Mullerian adenosarcoma is a rare malignant biphasic tumor. The mesenchymal component may be low or high grade, with or without sarcomatous overgrowth (SO). Little is known about the molecular heterogeneity of these tumors. In this study, we aim to reclassify a large retrospective monocentric cohort of uterine adenosarcomas according to tumor grade and SO, to evaluate the clinical significance of pathological classification and to correlate with copy-number variations inferred from single nucleotide polymorphism array...
April 28, 2024: Human Pathology
#59
JOURNAL ARTICLE
Yuanyuan Li, Ning Wang, Guoyue Yang
BACKGROUND: Patients with head and neck squamous cell carcinoma (HNSCC) exhibit unfavorable clinical outcomes, accompanied by high morbidity/mortality. In recent years, the management of HNSCC has encountered a significant obstacle. Z-DNA binding protein 1 (ZBP1) exerts crucial biological functions in chronic inflammatory disease and cancer. The aim of this research was to identify the possible function of ZBP1 in HNSCC. METHODS: The Cancer Genome Atlas (TCGA) database was used to collect the gene expression profile and corresponding clinical data...
April 28, 2024: Journal of Stomatology, Oral and Maxillofacial Surgery
#60
JOURNAL ARTICLE
Xinmin Deng, Wen Chang, Jingyi Zhu, Xiaofeng Lv, Rui Lai, Yu Cai, Shanshan Liu, Jingtao Liang
BACKGROUND: The association between hypothyroidism and stroke remains controversial and the association between hypothyroidism and stroke subtypes has not been satisfactorily researched. This study aimed to explore the causal effect of hypothyroidism on the risk of stroke and its subtypes by Mendelian randomization (MR) analysis. METHODS: Single nucleotide polymorphisms (SNPs) were selected from published genome-wide association studies (GWAS) meta-analysis as instrumental variables (IVs) for hypothyroidism...
April 28, 2024: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
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