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JOURNAL ARTICLE
Shiwen Zhang, Shengqing Wu, Zhiqi Jia, Junhong Zhang, Ying Li, Xingyun Ma, Bingli Fan, Panqiao Wang, Yanna Gao, Zhibiao Ye, Wei Wang
Tomato (Solanum lycopersicum) stands as one of the most valuable vegetable crops globally, and fruit firmness significantly impacts storage and transportation. To identify genes governing tomato firmness, we scrutinized the firmness of 266 accessions from core collections. Our study pinpointed an ethylene receptor gene, SlEIN4, located on chromosome 4 through a genome-wide association study (GWAS) of fruit firmness in the 266 tomato core accessions. A single-nucleotide polymorphism (SNP) (A → G) of SlEIN4 distinguished lower (AA) and higher (GG) fruit firmness genotypes...
April 16, 2024: Plant Biotechnology Journal
#2
JOURNAL ARTICLE
Laxmi, Pougang Golmei, Shriyansh Srivastava, Sachin Kumar
Primary hypertension is a multiplex and multifactorial disease influenced by various strong components including genetics. Extensive research such as Genome-wide association studies and candidate gene studies have revealed various single nucleotide polymorphisms (SNPs) related to hypertension, providing insights into the genetic basis of the condition. This review summarizes the current status of SNP research in primary hypertension, including examples of hypertension-related SNPs, their location, function, and frequency in different populations...
April 13, 2024: European Journal of Pharmacology
#3
JOURNAL ARTICLE
Aradhana Sachdev, Kamaljot Gill, Maria Sckaff, Alisha M Birk, Olubankole Aladesuyi Arogundade, Katherine A Brown, Runvir S Chouhan, Patrick Oliver Issagholian-Lewin, Esha Patel, Hannah L Watry, Mylinh T Bernardi, Kathleen C Keough, Yu-Chih Tsai, Alec Simon Tulloch Smith, Bruce R Conklin, Claire Dudley Clelland
Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes...
April 23, 2024: Proceedings of the National Academy of Sciences of the United States of America
#4
JOURNAL ARTICLE
Shilpa Sonti, Sheridan H Littleton, Matthew C Pahl, Amber J Zimmerman, Alessandra Chesi, Justin Palermo, Chiara Lasconi, Elizabeth B Brown, James A Pippin, Andrew D Wells, Fusun Doldur-Balli, Allan I Pack, Phillip R Gehrman, Alex C Keene, Struan F A Grant
Although genome wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' GWAS locus...
April 4, 2024: Sleep
#5
JOURNAL ARTICLE
Jack B Roberts, Olivia L G Boldvig, Guillaume Aubourg, S Tanishq Kanchenapally, David J Deehan, Sarah J Rice, John Loughlin
BACKGROUND: Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism (SNP) rs34195470 (A > G). The OA risk-conferring G allele of this SNP associates with increased DNA methylation (DNAm) at two CpG dinucleotides within WWP2...
April 3, 2024: Arthritis Research & Therapy
#6
JOURNAL ARTICLE
Matthew S H Lau, Abubakar Madika, Ying Zhang, Nigel P Minton
The relentless increase in atmospheric greenhouse gas concentrations as a consequence of the exploitation of fossil resources compels the adoption of sustainable routes to chemical and fuel manufacture based on biological fermentation processes. The use of thermophilic chassis in such processes is an attractive proposition; however, their effective exploitation will require improved genome editing tools. In the case of the industrially relevant chassis Parageobacillus thermoglucosidasius , CRISPR/Cas9-based gene editing has been demonstrated...
March 22, 2024: ACS Synthetic Biology
#7
JOURNAL ARTICLE
Sushuang Liu, Zhan Xu, Jemaa Essemine, Yanmin Liu, Chundong Liu, Feixue Zhang, Zubair Iqbal, Mingnan Qu
Inorganic phosphorus (Pi) deficiency significantly impacts plant growth, development and photosynthetic efficiency (Asat ). This study evaluated 206 rice accessions from a MiniCore population under both Pi sufficient (Pi+ ) and Pi starvation (Pi- ) conditions in the field to assess photosynthetic phosphorus use efficiency (PPUE), defined as the ratio of Asat Pi- to Asat Pi+ . A genome-wide association study (GWAS) and differential gene expression analyses identified an acid phosphatase (ACP2) gene that responds strongly to phosphate availability...
March 19, 2024: Plant communications
#8
JOURNAL ARTICLE
Floris Huider, Yuri Milaneschi, Jouke-Jan Hottenga, Mariska Bot, M Liset Rietman, Almar A L Kok, Tessel E Galesloot, Leen M 't Hart, Femke Rutters, Marieke T Blom, Didi Rhebergen, Marjolein Visser, Ingeborg Brouwer, Edith Feskens, Catharina A Hartman, Albertine J Oldehinkel, Eco J C de Geus, Lambertus A Kiemeney, Martijn Huisman, H Susan J Picavet, W M Monique Verschuren, Hanna M van Loo, Brenda W J H Penninx, Dorret I Boomsma
In this cohort profile article we describe the lifetime major depressive disorder (MDD) database that has been established as part of the BIObanks Netherlands Internet Collaboration (BIONIC). Across the Netherlands we collected data on Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition ( DSM-5 ) lifetime MDD diagnosis in 132,850 Dutch individuals. Currently, N = 66,684 of these also have genomewide single nucleotide polymorphism (SNP) data. We initiated this project because the complex genetic basis of MDD requires large population-wide studies with uniform in-depth phenotyping...
March 18, 2024: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
#9
Daniel R Barnes, Jonathan P Tyrer, Joe Dennis, Goska Leslie, Manjeet K Bolla, Michael Lush, Amber M Aeilts, Kristiina Aittomäki, Nadine Andrieu, Irene L Andrulis, Hoda Anton-Culver, Adalgeir Arason, Banu K Arun, Judith Balmaña, Elisa V Bandera, Rosa B Barkardottir, Lieke P V Berger, Amy Berrington de Gonzalez, Pascaline Berthet, Katarzyna Białkowska, Line Bjørge, Amie M Blanco, Marinus J Blok, Kristie A Bobolis, Natalia V Bogdanova, James D Brenton, Henriett Butz, Saundra S Buys, Maria A Caligo, Ian Campbell, Carmen Castillo, Kathleen B M Claes, Sarah V Colonna, Linda S Cook, Mary B Daly, Agnieszka Dansonka-Mieszkowska, Miguel de la Hoya, Anna deFazio, Allison DePersia, Yuan Chun Ding, Susan M Domchek, Thilo Dörk, Zakaria Einbeigi, Christoph Engel, D Gareth Evans, Lenka Foretova, Renée T Fortner, Florentia Fostira, Maria Cristina Foti, Eitan Friedman, Megan N Frone, Patricia A Ganz, Aleksandra Gentry-Maharaj, Gord Glendon, Andrew K Godwin, Anna González-Neira, Mark H Greene, Jacek Gronwald, Aliana Guerrieri-Gonzaga, Ute Hamann, Thomas V O Hansen, Holly R Harris, Jan Hauke, Florian Heitz, Frans B L Hogervorst, Maartje J Hooning, John L Hopper, Chad D Huff, David G Huntsman, Evgeny N Imyanitov, Louise Izatt, Anna Jakubowska, Paul A James, Ramunas Janavicius, Esther M John, Siddhartha Kar, Beth Y Karlan, Catherine J Kennedy, Lambertus A L M Kiemeney, Irene Konstantopoulou, Jolanta Kupryjanczyk, Yael Laitman, Ofer Lavie, Kate Lawrenson, Jenny Lester, Fabienne Lesueur, Carlos Lopez-Pleguezuelos, Phuong L Mai, Siranoush Manoukian, Taymaa May, Iain A McNeish, Usha Menon, Roger L Milne, Francesmary Modugno, Jennifer M Mongiovi, Marco Montagna, Kirsten B Moysich, Susan L Neuhausen, Finn C Nielsen, Catherine Noguès, Edit Oláh, Olufunmilayo I Olopade, Ana Osorio, Laura Papi, Harsh Pathak, Celeste L Pearce, Inge S Pedersen, Ana Peixoto, Tanja Pejovic, Pei-Chen Peng, Beth N Peshkin, Paolo Peterlongo, C Bethan Powell, Darya Prokofyeva, Miquel Angel Pujana, Paolo Radice, Muhammad U Rashid, Gad Rennert, George Richenberg, Dale P Sandler, Naoko Sasamoto, Veronica W Setiawan, Priyanka Sharma, Weiva Sieh, Christian F Singer, Katie Snape, Anna P Sokolenko, Penny Soucy, Melissa C Southey, Dominique Stoppa-Lyonnet, Rebecca Sutphen, Christian Sutter, Manuel R Teixeira, Kathryn L Terry, Liv Cecilie V Thomsen, Marc Tischkowitz, Amanda E Toland, Toon Van Gorp, Ana Vega, Digna R Velez Edwards, Penelope M Webb, Jeffrey N Weitzel, Nicolas Wentzensen, Alice S Whittemore, Stacey J Winham, Anna H Wu, Siddhartha Yadav, Yao Yu, Argyrios Ziogas, Andrew Berchuck, Fergus J Couch, Ellen L Goode, Marc T Goodman, Alvaro N Monteiro, Kenneth Offit, Susan J Ramus, Harvey A Risch, Joellen M Schildkraut, Mads Thomassen, Jacques Simard, Douglas F Easton, Michelle R Jones, Georgia Chenevix-Trench, Simon A Gayther, Antonis C Antoniou, Paul D P Pharoah
BACKGROUND: Nineteen genomic regions have been associated with high-grade serous ovarian cancer (HGSOC). We used data from the Ovarian Cancer Association Consortium (OCAC), Consortium of Investigators of Modifiers of BRCA1/BRCA2 (CIMBA), UK Biobank (UKBB), and FinnGen to identify novel HGSOC susceptibility loci and develop polygenic scores (PGS). METHODS: We analyzed >22 million variants for 398,238 women. Associations were assessed separately by consortium and meta-analysed...
March 4, 2024: medRxiv
#10
JOURNAL ARTICLE
Marcos E Jaso-Vera, Shohei Takaoka, Ishika Patel, Xiangbo Ruan
Long non-coding RNA (lncRNA) genes represent a large class of transcripts that are widely expressed across species. As most human lncRNAs are non-conserved, we recently employed a unique humanized liver mouse model to study lncRNAs expressed in human livers. We identified a human hepatocyte-specific lncRNA, hLMR1 (human lncRNA metabolic regulator 1), which is induced by feeding and promotes hepatic cholesterol synthesis. Recent genome-wide association studies (GWAS) found that several single-nucleotide polymorphisms (SNPs) from the hLMR1 gene locus are associated with blood lipids and markers of liver damage...
March 17, 2024: Human Genetics
#11
JOURNAL ARTICLE
Oliver M Moore, Yuriana Aguilar-Sanchez, Satadru K Lahiri, Mohit M Hulsurkar, J Alberto Navarro-Garcia, Tarah A Word, Joshua A Keefe, Dean Barazi, Elda M Munivez, Charles T Moore, Vaidya Parthasarathy, Jaysón Davidson, William R Lagor, So Hyun Park, Gang Bao, Christina Y Miyake, Xander H T Wehrens
INTRODUCTION: Heterozygous autosomal-dominant single nucleotide variants in RYR2 account for 60% of cases of catecholaminergic polymorphic ventricular tachycardia (CPVT), an inherited arrhythmia disorder associated with high mortality rates. CRISPR/Cas9-mediated genome editing is a promising therapeutic approach that can permanently cure the disease by removing the mutant RYR2 allele. However, the safety and long-term efficacy of this strategy have not been established in a relevant disease model...
January 2024: The journal of cardiovascular aging
#12
Lloyd D Harvey, Mona Alotaibi, Hee-Jung Janice Kim, Yi-Yin Tai, Ying Tang, Wei Sun, Wadih El Khoury, Chen-Shan C Woodcock, Yassmin Al Aaraj, Claudette M St Croix, Donna B Stolz, Jiyoung Lee, Mary Hongying Cheng, Tae-Hwi Schwantes-An, Ankit A Desai, Michael W Pauciulo, William C Nichols, Amy Webb, Robert Lafyatis, Mehdi Nouraie, Haodi Wu, Jeffrey G McDonald, Caroline Chauvet, Susan Cheng, Ivet Bahar, Thomas Bertero, Raymond L Benza, Mohit Jain, Stephen Y Chan
Vascular inflammation critically regulates endothelial cell (EC) pathophenotypes, particularly in pulmonary arterial hypertension (PAH). Dysregulation of lysosomal activity and cholesterol metabolism have known inflammatory roles in disease, but their relevance to PAH is unclear. In human pulmonary arterial ECs and in PAH, we found that inflammatory cytokine induction of the nuclear receptor coactivator 7 (NCOA7) both preserved lysosomal acidification and served as a homeostatic brake to constrain EC immunoactivation...
March 1, 2024: bioRxiv
#13
JOURNAL ARTICLE
Taehyeung Kim, Marta Martínez-Bonet, Qiang Wang, Nicolaj Hackert, Jeffrey A Sparks, Yuriy Baglaenko, Byunghee Koh, Roxane Darbousset, Raquel Laza-Briviesca, Xiaoting Chen, Vitor R C Aguiar, Darren J Chiu, Harm-Jan Westra, Maria Gutierrez-Arcelus, Matthew T Weirauch, Soumya Raychaudhuri, Deepak A Rao, Peter A Nigrovic
Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors...
March 9, 2024: Nature Communications
#14
JOURNAL ARTICLE
Kenichiro Mori, Koji Tanase, Katsutomo Sasaki
A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis...
March 6, 2024: Planta
#15
JOURNAL ARTICLE
Shijun You, Gaoke Lei, Huiling Zhou, Jianyu Li, Shaoping Chen, Jieling Huang, Liette Vasseur, Geoff M Gurr, Minsheng You, Yanting Chen
Understanding a population's fitness heterogeneity and genetic basis of thermal adaptation is essential for predicting the responses to global warming. We examined the thermotolerance and genetic adaptation of Plutella xylostella to exposure to hot temperatures. The population fitness parameters of the hot-acclimated DBM strains varied in the thermal environments. Using genome scanning and transcription profiling, we find a number of genes potentially involved in thermal adaptation of DBM. Editing two ABCG transporter genes, PxWhite and PxABCG , confirmed their role in altering cuticle permeability and influencing thermal responses...
March 15, 2024: IScience
#16
JOURNAL ARTICLE
Chung-Chieh Hung, Ying-Chin Ko, Chia-Min Chung
Betel quid (BQ) is the fourth most popular psychoactive substance in the world, and BQ use disorder (BUD) is prevalent in Asian countries. Although the mechanisms underlying BUD remain unclear, studies have reported influences from monoamine oxidase inhibitor. We enrolled 50 patients with BUD and assessed their BQ consumption habits, emotional conditions, and the clinical severity of addiction-assessed using the Diagnostic and Statistical Manual of Mental Disorders [Fifth Edition] ( DSM-5 ) criteria, Substance Use Severity Rating Scale, and Yale-Brown Obsessive Compulsive Disorder Rating Scale for BQ...
January 23, 2024: Current Issues in Molecular Biology
#17
JOURNAL ARTICLE
Mehdi Fazel-Najafabadi, Loren L Looger, Harikrishna Reddy Rallabandi, Swapan K Nath
OBJECTIVES: Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWAS) have revealed multiple SLE susceptibility loci and associated single nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown. METHODS: Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping...
February 19, 2024: Arthritis & Rheumatology
#18
JOURNAL ARTICLE
Casimiro Castillejo-López, José Ramón Bárcenas-Walls, Marco Cavalli, Anders Larsson, Claes Wadelius
BACKGROUND: Genome-wide association studies (GWAS) have identified genetic variants linked to fat metabolism and related traits, but rarely pinpoint causative variants. This limitation arises from GWAS not considering functional implications of noncoding variants that can affect transcription factor binding and potentially regulate gene expression. The aim of this study is to investigate a candidate noncoding functional variant within a genetic locus flagged by a GWAS SNP associated with non-alcoholic fatty liver disease (NAFLD), a condition characterized by liver fat accumulation in non-alcohol consumers...
February 16, 2024: Lipids in Health and Disease
#19
JOURNAL ARTICLE
Jitendra K Mohanty, Virevol Thakro, Antima Yadav, Harsh Nayyar, Girish P Dixit, Pinky Agarwal, Swarup K Parida, Uday Chand Jha
Chickpea (Cicer arietinum) is a cool season grain legume experiencing severe yield loss during heat stress due to the intensifying climate changes and its associated gradual increase of mean temperature. Hence, understanding the genetic architecture regulating heat stress tolerance has emerged as an important trait to be addressed for enhancing yield and productivity of chickpea under heat stress. The present study is intended to identify the major genomic region(s) governing heat stress tolerance in chickpea...
February 16, 2024: Plant Molecular Biology
#20
JOURNAL ARTICLE
Daisuke Matsumoto, Erina Matsugi, Kanae Kishi, Yuto Inoue, Kiyomi Nigorikawa, Wataru Nomura
In genome editing, it is important to avoid off-target mutations so as to reduce unexpected side effects, especially for therapeutic applications. Recently, several high-fidelity versions of SpCas9 have been developed to reduce off-target mutations. In addition to reducing off-target effects, highly efficient intended target gene correction is also essential to rescue protein functions that have been disrupted by single nucleotide polymorphisms. Homology-directed repair (HDR) corrects genes precisely using a DNA template...
March 12, 2024: Molecular Therapy. Nucleic Acids
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