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JOURNAL ARTICLE
Nico Seeger, Stefan Gutknecht, Irin Zschokke, Isabella Fleischmann, Nadja Roth, Jürg Metzger, Markus Weber, Stefan Breitenstein, Lukasz Filip Grochola
BACKGROUND: Single nucleotide polymorphisms (SNPs) are inherited genetic variants that can be easily determined in everyday clinical practice using a simple blood or even saliva test. They have the potential to serve as non-invasive biomarkers to predict cancer-specific patient outcomes after resection of pancreatic ductal adenocarcinoma (PDAC). Specifically, two recent analyses led to the identification and validation of three SNPs in the CD44 and CHI3L2 genes (SNPrs187115, SNPrs353630, SNPrs684559) that can be utilised as predictive biomarkers to help select patients who are likely to benefit from pancreatic resection...
April 2, 2024: JMIR Research Protocols
#2
JOURNAL ARTICLE
Tatiana Kasinsky, Natalia Rosciano, Juliana A Vianna, Pablo Yorio, Leonardo Campagna
The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia...
2024: PloS One
#3
JOURNAL ARTICLE
Amine Bouchareb, Daniel Biggs, Samy Alghadban, Christopher Preece, Benjamin Davies
Integration of a point mutation to correct or edit a gene requires the repair of the CRISPR-Cas9-induced double-strand break by homology-directed repair (HDR). This repair pathway is more active in late S and G2 phases of the cell cycle, whereas the competing pathway of nonhomologous end-joining (NHEJ) operates throughout the cell cycle. Accordingly, modulation of the cell cycle by chemical perturbation or simply by the timing of gene editing to shift the editing toward the S/G2 phase has been shown to increase HDR rates...
April 2024: CRISPR Journal
#4
JOURNAL ARTICLE
Ying Wang, Yalan Sun, Mingjuan Tan, Xin Lin, Ping Tai, Xiaoqin Huang, Qing Jin, Dan Yuan, Tao Xu, Bangshun He
Breast cancer risk have been discussed to be associated with polymorphisms in genes as well as abnormal DNA damage repair function. This study aims to assess the relationship between genes single nucleotide polymorphisms (SNPs) related to DNA damage repair and female breast cancer risk in Chinese population. A case-control study containing 400 patients and 400 healthy controls was conducted. Genotype was identified using the sequence MassARRAY method and expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2) in tumor tissues was analyzed by immunohistochemistry assay...
April 17, 2024: DNA and Cell Biology
#5
JOURNAL ARTICLE
Bowei Chen, Min Wang, Yile Guo, Zihui Zhang, Wei Zhou, Lesheng Cao, Tianxu Zhang, Shahid Ali, Linan Xie, Yuhua Li, Gaurav Zinta, Shanwen Sun, Qingzhu Zhang
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs...
April 18, 2024: Molecular Ecology
#6
JOURNAL ARTICLE
Niccolo' Tesi, Sven van der Lee, Marc Hulsman, Natasja M van Schoor, Martijn Huisman, Yolande Pijnenburg, Wiesje M van der Flier, Marcel Reinders, Henne Holstege
BACKGROUND: Alzheimer's disease (AD) prevalence increases with age, yet a small fraction of the population reaches ages > 100 years without cognitive decline. We studied the genetic factors associated with such resilience against AD. METHODS: Genome-wide association studies identified 86 single nucleotide polymorphisms (SNPs) associated with AD risk. We estimated SNP frequency in 2281 AD cases, 3165 age-matched controls, and 346 cognitively healthy centenarians...
April 18, 2024: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
#7
JOURNAL ARTICLE
Hanna Puolakka, Anssi Solismaa, Leo-Pekka Lyytikäinen, Merja Viikki, Niko Seppälä, Nina Mononen, Terho Lehtimäki, Olli Kampman
OBJECTIVE: Sialorrhea is a common and uncomfortable adverse effect of clozapine, and its severity varies between patients. The aim of the study was to select broadly genes related to the regulation of salivation and study associations between sialorrhea and dry mouth and polymorphisms in the selected genes. METHODS: The study population consists of 237 clozapine-treated patients, of which 172 were genotyped. Associations between sialorrhea and dry mouth with age, sex, BMI, smoking, clozapine dose, clozapine and norclozapine serum levels, and other comedication were studied...
April 18, 2024: Acta Neuropsychiatrica
#8
JOURNAL ARTICLE
Lin-Lin Wang, Ping-Shan Pan, Hui Ma, Chun He, Zai-Long Qin, Wei He, Jing Huang, Shu-Yin Tan, Da-Hua Meng, Hong-Wei Wei, Ai-Hua Yin
BACKGROUND: Malformations of cortical development (MCD) are a group of congenital disorders characterized by structural abnormalities in the brain cortex. The clinical manifestations include refractory epilepsy, mental retardation, and cognitive impairment. Genetic factors play a key role in the etiology of MCD. Currently, there is no curative treatment for MCD. Phenotypes such as epilepsy and cerebral palsy cannot be observed in the fetus. Therefore, the diagnosis of MCD is typically based on fetal brain magnetic resonance imaging (MRI), ultrasound, or genetic testing...
April 2024: Molecular Genetics & Genomic Medicine
#9
JOURNAL ARTICLE
Glenn Ramsey, Christina M Barriteau
BACKGROUND: For patients with weak or discrepant RhD RBC phenotypes, RHD genotyping is employed to determine need for RhD-negative management. However, many RHD variants are type D-negative or D-positive. Serological recognition rates (RRs) of weak and partial RHD variants are poorly characterized. STUDY DESIGN AND METHODS: Four US studies employing RHD genotyping for weak or discrepant RhD phenotypes provided data for race/ethnicity-specific serological recognition...
April 18, 2024: Transfusion
#10
JOURNAL ARTICLE
Jian Xiong, Yuxin Sun, Hui Huang, Yu Liu, Fayang Ling, Yin Wei, Qianhua Zheng, Wenchuan Qi, Fanrong Liang
PURPOSE: Two-sample Mendelian randomization (MR) was conducted to assess the causal relationship between angina pectoris and gout. Material and Methods . Based on genome-wide association studies, single nucleotide polymorphisms (SNPs) that were closely associated with gout were selected from the UK Biobank-Neale Lab (ukb-a-107) as genetic instrumental variables. Considering that gout is characterized by elevated blood uric acid levels, SNPs related to blood uric acid levels were screened from BioBank Japan (bbj-a-57) as auxiliary gene instrumental variables...
2024: Pain Research & Management
#11
Marijne Vandebergh, Eliana Marisa Ramos, Nick Corriveau-Lecavalier, Vijay K Ramanan, John Kornak, Carly Mester, Tyler Kolander, Danielle Brushaber, Adam M Staffaroni, Daniel Geschwind, Amy Wolf, Kejal Kantarci, Tania F Gendron, Leonard Petrucelli, Marleen Van den Broeck, Sarah Wynants, Matthew C Baker, Sergi Borrego-Écija, Brian Appleby, Sami Barmada, Andrea Bozoki, David Clark, R Ryan Darby, Bradford C Dickerson, Kimiko Domoto-Reilly, Julie A Fields, Douglas R Galasko, Nupur Ghoshal, Neill Graff-Radford, Ian M Grant, Lawrence S Honig, Ging-Yuek Robin Hsiung, Edward D Huey, David Irwin, David S Knopman, Justin Y Kwan, Gabriel C Léger, Irene Litvan, Joseph C Masdeu, Mario F Mendez, Chiadi Onyike, Belen Pascual, Peter Pressman, Aaron Ritter, Erik D Roberson, Allison Snyder, Anna Campbell Sullivan, M Carmela Tartaglia, Dylan Wint, Hilary W Heuer, Leah K Forsberg, Adam L Boxer, Howard J Rosen, Bradley F Boeve, Rosa Rademakers
BACKGROUND AND OBJECTIVES: TMEM106B has been proposed as a modifier of disease risk in FTLD-TDP, particularly in GRN mutation carriers. Furthermore, TMEM106B has been investigated as a disease modifier in the context of healthy aging and across multiple neurodegenerative diseases. The objective of this study is to evaluate and compare the effect of TMEM106B on gray matter volume and cognition in each of the common genetic FTD groups and in sporadic FTD patients. METHODS: Participants were enrolled through the ARTFL/LEFFTDS Longitudinal Frontotemporal Lobar Degeneration (ALLFTD) study, which includes symptomatic and presymptomatic individuals with a pathogenic mutation in C9orf72, GRN, MAPT, VCP, TBK1, TARDBP, symptomatic non-mutation carriers, and non-carrier family controls...
April 5, 2024: medRxiv
#12
JOURNAL ARTICLE
Xuejiao Wei, Mengtuan Long, Zhongyu Fan, Yue Hou, Liming Yang, Zhihui Qu, Yujun Du
BACKGROUND: The morbidity and mortality of chronic kidney disease (CKD) are increasing worldwide, making it a serious public health problem. Although a potential correlation between body water content and CKD progression has been suggested, the presence of a causal association remains uncertain. This study aimed to determine the causal effect of body water content on kidney function. METHODS: Genome-wide association study summary data sourced from UK Biobank were used to evaluate single-nucleotide polymorphisms (SNPs) associated with whole-body water mass (BWM)...
2024: Frontiers in Endocrinology
#13
JOURNAL ARTICLE
Charlotte E Eriksson, Gretchen H Roffler, Jennifer M Allen, Alex Lewis, Taal Levi
Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting on sea otters and other marine resources without ungulate prey, violating this long-held assumption. We address questions about these wolves regarding their origin and fate, degree of isolation, risk of inbreeding depression, and diet specialization by individual and sex. We applied DNA metabarcoding and genotyping by amplicon sequencing using 957 scats collected from 2016 to 2022, and reduced representation sequencing of tissue samples to establish a detailed understanding of Pleasant Island wolf ecology and compare them with adjacent mainland wolves...
April 2024: Ecology and Evolution
#14
JOURNAL ARTICLE
Dongyan Zhao, Manoj Sapkota, Meng Lin, Craig Beil, Moira Sheehan, Stephanie Greene, Brian M Irish
Annual medic ( Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized...
2024: Frontiers in Plant Science
#15
JOURNAL ARTICLE
Yiling Pan, Yujia Luo, Jingkai Bao, Cuiyun Wu, Jiurui Wang, Mengjun Liu, Fenfen Yan
INTRODUCTION: Fruit size is an important economic trait affecting jujube fruit quality, which has always been the focus of marker-assisted breeding of jujube traits. However, despite a large number of studies have been carried out, the mechanism and key genes regulating jujube fruit size are mostly unknown. METHODS: In this study, we used a new analysis method Quantitative Trait Loci sequencing (QTL-seq) (bulked segregant analysis) to screen the parents 'Yuhong' and 'Jiaocheng 5' with significant phenotypic differences and mixed offspring group with extreme traits of large fruit and small fruit, respectively, and, then, DNA mixed pool sequencing was carried out to further shortening the QTL candidate interval for fruit size trait and excavated candidate genes for controlling fruit size...
2024: Frontiers in Plant Science
#16
JOURNAL ARTICLE
Yanjing Chen, Ping Liu, Zhiyi Zhang, Yingling Ye, Sijie Yi, Chunhua Fan, Wei Zhao, Jun Liu
BACKGROUND: The existence of chronic pain increases susceptibility to virus and is now widely acknowledged as a prominent feature recognized as a major manifestation of long-term coronavirus disease 2019 (COVID-19) infection. Given the ongoing COVID-19 pandemic, it is imperative to explore the genetic associations between chronic pain and predisposition to COVID-19. METHODS: We conducted genetic analysis at the single nucleotide polymorphism (SNP), gene, and molecular levels using summary statistics of genome-wide association study (GWAS) and analyzed the drug targets by summary data-based Mendelian randomization analysis (SMR) to alleviate the multi-site chronic pain in COVID-19...
2024: Frontiers in Immunology
#17
JOURNAL ARTICLE
Bihui Su, Guanghong Du, Shuiping Hou, Zongqiu Chen, Xiaoying Wu, Gang He, Jun Yuan, Chaojun Xie
WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: S. 1,4,[5],12:i:- and S. Rissen are emerging serotypes of Salmonella that require close monitoring for antimicrobial resistance and containment of their spread. WHAT IS ADDED BY THIS REPORT?: The study aimed to identify antimicrobial resistance genes (ARGs) in S. 1,4,[5],12:i:- and S. Rissen strains isolated from environmental sewage in Guangzhou City, Guangdong Province, China. A phylogenetic tree was constructed using single nucleotide polymorphism data to assess genetic relatedness among strains, offering insights for Salmonella infection outbreak investigations in the future...
March 29, 2024: China CDC weekly
#18
JOURNAL ARTICLE
Eman Ebissy, Asmaa Darwish, Amani A Hafez, Ahmed Ateya, Ahmed El-Sayed
BACKGROUND: Mastitis in goats is unquestionably a grave concern, with far-reaching implications for both animal well-being and productivity, while also presenting a potential threat to public health. AIM: The study aimed to compare culture methods and multiplex PCR (m-PCR) in the detection of the most three common mastitis-causing pathogens ( Staphylococcus aureus , Escherichia coli , and Streptococcus spp.) and investigate the gene expression, single nucleotide polymorphisms (SNPs), serum concentrations of immunological and antioxidant indicators linked to mastitis in Shami goats...
January 2024: Open Veterinary Journal
#19
JOURNAL ARTICLE
Lyne Touchette, Julie Godbout, Manuel Lamothe, Ilga Porth, Nathalie Isabel
Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa , a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach...
April 2024: Evolutionary Applications
#20
JOURNAL ARTICLE
Matuszkiewicz Mateusz, Grądzielewska Agnieszka, Święcicka Magdalena, Ozturk Alperen, Mokrzycka Monika, Igbari Aramide Dolapo, Song Jie, Kilian Andrzej, Rakoczy-Trojanowska Monika
BACKGROUND: Leaf rust (LR) is among the most destructive fungal diseases of rye (Secale cereale L.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. RESULTS: A genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye...
April 17, 2024: BMC Plant Biology
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