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REVIEW
Rexhina Vlashi, Xingen Zhang, Haibo Li, Guiqian Chen
Osteoarthritis (OA) is an incapacitating and one of the most common physically degenerative conditions with an assorted etiology and a highly complicated molecular mechanism that to date lacks an efficient treatment. The capacity to design biological networks and accurately modify existing genomic sites holds an apt potential for applications across medical and biotechnological sciences. One of these highly specific genomes editing technologies is the CRISPR/Cas9 mechanism, referred to as the clustered regularly interspaced short palindromic repeats, which is a defense mechanism constituted by CRISPR associated protein 9 (Cas9) directed by small non-coding RNAs (sncRNA) that bind to target DNA through Watson-Crick base pairing rules where subsequent repair of the target DNA is initiated...
December 6, 2023: Reviews in Endocrine & Metabolic Disorders
#22
JOURNAL ARTICLE
Amy Braddel, Melanie Watson
Nurses represent the largest professional group within the National Health Service (NHS) and are therefore central to the successful integration of mainstreaming genomics into routine healthcare. Inherited cardiac conditions (ICC) nurse roles have been developed in recent years to streamline the care for patients and families affected by an ICC. Like many nurse specialists, ICC nurses' prior exposure to genomics and the wider implications surrounding inherited conditions is limited. The aim of the study was to explore the education needs and support required for ICC nurses to fulfill their role within the genomic medicine era...
November 27, 2023: Journal of Genetic Counseling
#23
Artem Mikelov, George Nefediev, Alexander Tashkeev, Oscar L Rodriguez, Diego A Ortmans, Valeriia Skatova, Mark Izraelson, Alexey Davydov, Stanislav Poslavsky, Souad Rahmouni, Corey T Watson, Dmitriy Chudakov, Scott D Boyd, Dmitry Bolotin
Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), has been shown to be of critical importance for immune responses to pathogens and vaccines. In recent years, B cell and T cell receptor repertoire sequencing (Rep-Seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci in different populations...
November 17, 2023: bioRxiv
#24
REVIEW
Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops.
Qamar U Zaman, Ali Raza, Jorge Lozano-Juste, Li Chao, Michael G K Jones, Hua-Feng Wang, Rajeev K Varshney
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits...
November 21, 2023: Trends in Biotechnology
#25
JOURNAL ARTICLE
Jennifer L Goldstein, Jennifer McGlaughon, Dona Kanavy, Shelly Goomber, Yinghong Pan, Brett Deml, Taraka Donti, Liz Kearns, Bryce A Seifert, Miriam Schachter, Rachel G Son, Courtney Thaxton, Rupa Udani, Deeksha Bali, Heather Baudet, Michele Caggana, Christina Hung, Lianna Kyriakopoulou, Lynne Rosenblum, Robert Steiner, Filippo Pinto E Vairo, Yang Wang, Michael Watson, Raquel Fernandez, Meredith Weaver, Lorne Clarke, Catherine Rehder
Accurate determination of the clinical significance of genetic variants is critical to the integration of genomics in medicine. To facilitate this process, the NIH-funded Clinical Genome Resource (ClinGen) has assembled Variant Curation Expert Panels (VCEPs), groups of experts and biocurators which provide gene- and disease- specifications to the American College of Medical Genetics & Genomics and Association for Molecular Pathology's (ACMG/AMP) variation classification guidelines. With the goal of classifying the clinical significance of GAA variants in Pompe disease (Glycogen storage disease, type II), the ClinGen Lysosomal Diseases (LD) VCEP has specified the ACMG/AMP criteria for GAA...
2023: Molecular Genetics and Metabolism
#26
Belle A Moyers, Jacob M Loupe, Stephanie A Felker, James M J Lawlor, Ashlyn G Anderson, Ivan Rodriguez-Nunez, William E Bunney, Blynn G Bunney, Preston M Cartagena, Adolfo Sequeira, Stanley J Watson, Huda Akil, Eric M Mendenhall, Gregory M Cooper, Richard M Myers
Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors...
October 9, 2023: bioRxiv
#27
JOURNAL ARTICLE
Jerry Guintivano, Enda M Byrne, Jacqueline Kiewa, Shuyang Yao, Anna E Bauer, Karolina A Aberg, Mark J Adams, Archie Campbell, Megan L Campbell, Karmel W Choi, Elizabeth C Corfield, Alexandra Havdahl, Donald Hucks, Nastassja Koen, Yi Lu, Merete L Mægbæk, Jimmy Mullaert, Roseann E Peterson, Laura M Raffield, Hannah M Sallis, Julia M Sealock, Alicia Walker, Hunna J Watson, Ying Xiong, Jessica M K Yang, Richard J L Anney, Katherine Gordon-Smith, Leon Hubbard, Lisa A Jones, Raluca Mihaescu, Mette Nyegaard, Antonio F Pardiñas, Amy Perry, Nazmus Saquib, Aladdin H Shadyab, Alexander Viktorin, Ole A Andreassen, Tim B Bigdeli, Lea K Davis, Cindy-Lee Dennis, Arianna Di Florio, Caroline Dubertret, Yen-Chen A Feng, Benicio N Frey, Sophie Grigoriadis, Emilie Gloaguen, Ian Jones, James L Kennedy, Holly Krohn, Theodora Kunovac Kallak, Yun Li, Nicholas G Martin, Andrew M McIntosh, Jeannette Milgrom, Trine Munk-Olsen, Tim Oberlander, Catherine M Olsen, Nicolas Ramoz, Ted Reichborn-Kjennerud, Emma Robertson Blackmore, David Rubinow, Alkistis Skalkidou, Jordan W Smoller, Dan J Stein, Zachary N Stowe, Valerie Taylor, Sarah Tebeka, Martin Tesli, Ryan J Van Lieshout, Edwin J C G van den Oord, Simone N Vigod, Thomas Werge, Lars T Westlye, David C Whiteman, Heather J Zar, Naomi Wray, Samantha Meltzer-Brody, Patrick Sullivan
OBJECTIVE: Postpartum depression (PPD) is a common subtype of major depressive disorder (MDD) that is more heritable, yet is understudied in psychiatric genetics. The authors conducted meta-analyses of genome-wide association studies (GWASs) to investigate the genetic architecture of PPD. METHOD: Meta-analyses were conducted on 18 cohorts of European ancestry (17,339 PPD cases and 53,426 controls), one cohort of East Asian ancestry (975 cases and 3,780 controls), and one cohort of African ancestry (456 cases and 1,255 controls), totaling 18,770 PPD cases and 58,461 controls...
December 1, 2023: American Journal of Psychiatry
#28
JOURNAL ARTICLE
Chunyan Liu, Yaxin Yue, Yanfen Xue, Cheng Zhou, Yanhe Ma
BACKGROUND: Halophiles possess several unique properties and have broad biotechnological applications including industrial biotechnology production. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), some proteins, small molecular compounds, organic acids, and has the potential to become a chassis cell for the next-generation of industrial biotechnology (NGIB) owing to its simple culture, fast growth, contamination-resistant, low production cost, and high production value...
October 14, 2023: Microbial Cell Factories
#29
JOURNAL ARTICLE
Joshua Watson, Tianfang Wang, Kun-Lin Ho, Yuan Feng, Tanakamol Mahawan, Kevin K Dobbin, Shaying Zhao
BACKGROUND: About 20% of breast cancers in humans are basal-like, a subtype that is often triple-negative and difficult to treat. An effective translational model for basal-like breast cancer is currently lacking and urgently needed. To determine whether spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. METHODS: We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data...
October 3, 2023: Breast Cancer Research: BCR
#30
JOURNAL ARTICLE
Anna R Docherty, Niamh Mullins, Allison E Ashley-Koch, Xuejun Qin, Jonathan R I Coleman, Andrey Shabalin, JooEun Kang, Balasz Murnyak, Frank Wendt, Mark Adams, Adrian I Campos, Emily DiBlasi, Janice M Fullerton, Henry R Kranzler, Amanda V Bakian, Eric T Monson, Miguel E Rentería, Consuelo Walss-Bass, Ole A Andreassen, Chittaranjan Behera, Cynthia M Bulik, Howard J Edenberg, Ronald C Kessler, J John Mann, John I Nurnberger, Giorgio Pistis, Fabian Streit, Robert J Ursano, Renato Polimanti, Michelle Dennis, Melanie Garrett, Lauren Hair, Philip Harvey, Elizabeth R Hauser, Michael A Hauser, Jennifer Huffman, Daniel Jacobson, Ravi Madduri, Benjamin McMahon, David W Oslin, Jodie Trafton, Swapnil Awasthi, Wade H Berrettini, Martin Bohus, Xiao Chang, Hsi-Chung Chen, Wei J Chen, Erik D Christensen, Scott Crow, Philibert Duriez, Alexis C Edwards, Fernando Fernández-Aranda, Hanga Galfalvy, Michael Gandal, Philip Gorwood, Yiran Guo, Jonathan D Hafferty, Hakon Hakonarson, Katherine A Halmi, Akitoyo Hishimoto, Sonia Jain, Stéphane Jamain, Susana Jiménez-Murcia, Craig Johnson, Allan S Kaplan, Walter H Kaye, Pamela K Keel, James L Kennedy, Minsoo Kim, Kelly L Klump, Daniel F Levey, Dong Li, Shih-Cheng Liao, Klaus Lieb, Lisa Lilenfeld, Christian R Marshall, James E Mitchell, Satoshi Okazaki, Ikuo Otsuka, Dalila Pinto, Abigail Powers, Nicolas Ramoz, Stephan Ripke, Stefan Roepke, Vsevolod Rozanov, Stephen W Scherer, Christian Schmahl, Marcus Sokolowski, Anna Starnawska, Michael Strober, Mei-Hsin Su, Laura M Thornton, Janet Treasure, Erin B Ware, Hunna J Watson, Stephanie H Witt, D Blake Woodside, Zeynep Yilmaz, Lea Zillich, Rolf Adolfsson, Ingrid Agartz, Martin Alda, Lars Alfredsson, Vivek Appadurai, María Soler Artigas, Sandra Van der Auwera, M Helena Azevedo, Nicholas Bass, Claiton H D Bau, Bernhard T Baune, Frank Bellivier, Klaus Berger, Joanna M Biernacka, Tim B Bigdeli, Elisabeth B Binder, Michael Boehnke, Marco P Boks, David L Braff, Richard Bryant, Monika Budde, Enda M Byrne, Wiepke Cahn, Enrique Castelao, Jorge A Cervilla, Boris Chaumette, Aiden Corvin, Nicholas Craddock, Srdjan Djurovic, Jerome C Foo, Andreas J Forstner, Mark Frye, Justine M Gatt, Ina Giegling, Hans J Grabe, Melissa J Green, Eugenio H Grevet, Maria Grigoroiu-Serbanescu, Blanca Gutierrez, Jose Guzman-Parra, Marian L Hamshere, Annette M Hartmann, Joanna Hauser, Stefanie Heilmann-Heimbach, Per Hoffmann, Marcus Ising, Ian Jones, Lisa A Jones, Lina Jonsson, René S Kahn, John R Kelsoe, Kenneth S Kendler, Stefan Kloiber, Karestan C Koenen, Manolis Kogevinas, Marie-Odile Krebs, Mikael Landén, Marion Leboyer, Phil H Lee, Douglas F Levinson, Calwing Liao, Jolanta Lissowska, Fermin Mayoral, Susan L McElroy, Patrick McGrath, Peter McGuffin, Andrew McQuillin, Divya Mehta, Ingrid Melle, Philip B Mitchell, Esther Molina, Gunnar Morken, Caroline Nievergelt, Markus M Nöthen, Michael C O'Donovan, Roel A Ophoff, Michael J Owen, Carlos Pato, Michele T Pato, Brenda W J H Penninx, James B Potash, Robert A Power, Martin Preisig, Digby Quested, Josep Antoni Ramos-Quiroga, Andreas Reif, Marta Ribasés, Vanesa Richarte, Marcella Rietschel, Margarita Rivera, Andrea Roberts, Gloria Roberts, Guy A Rouleau, Diego L Rovaris, Alan R Sanders, Peter R Schofield, Thomas G Schulze, Laura J Scott, Alessandro Serretti, Jianxin Shi, Lea Sirignano, Pamela Sklar, Olav B Smeland, Jordan W Smoller, Edmund J S Sonuga-Barke, Maciej Trzaskowski, Ming T Tsuang, Gustavo Turecki, Laura Vilar-Ribó, John B Vincent, Henry Völzke, James T R Walters, Cynthia Shannon Weickert, Thomas W Weickert, Myrna M Weissman, Leanne M Williams, Naomi R Wray, Clement C Zai, Esben Agerbo, Anders D Børglum, Gerome Breen, Ditte Demontis, Annette Erlangsen, Joel Gelernter, Stephen J Glatt, David M Hougaard, Hai-Gwo Hwu, Po-Hsiu Kuo, Cathryn M Lewis, Qingqin S Li, Chih-Min Liu, Nicholas G Martin, Andrew M McIntosh, Sarah E Medland, Ole Mors, Merete Nordentoft, Catherine M Olsen, David Porteous, Daniel J Smith, Eli A Stahl, Murray B Stein, Danuta Wasserman, Thomas Werge, David C Whiteman, Virginia Willour, Hilary Coon, Jean C Beckham, Nathan A Kimbrel, Douglas M Ruderfer
OBJECTIVE: Suicidal behavior is heritable and is a major cause of death worldwide. Two large-scale genome-wide association studies (GWASs) recently discovered and cross-validated genome-wide significant (GWS) loci for suicide attempt (SA). The present study leveraged the genetic cohorts from both studies to conduct the largest GWAS meta-analysis of SA to date. Multi-ancestry and admixture-specific meta-analyses were conducted within groups of significant African, East Asian, and European ancestry admixtures...
October 1, 2023: American Journal of Psychiatry
#31
JOURNAL ARTICLE
Alizhah J Watson, Michaela L Shaffer, Renee A Bouley, Ruben C Petreaca
Homologous recombination (HR) is the major mechanism of rescue of stalled replication forks or repair of DNA double-strand breaks (DSBs) during S phase or mitosis. In human cells, HR is facilitated by the BRCA2-BRCA1-PALB2 module, which loads the RAD51 recombinase onto a resected single-stranded DNA end to initiate repair. Although the process is essential for error-free repair, unrestrained HR can cause chromosomal rearrangements and genome instability. F-box DNA Helicase 1 (FBH1) antagonizes the role of BRCA2-BRCA1-PALB2 to restrict hyper-recombination and prevent genome instability...
September 6, 2023: Cancers
#32
JOURNAL ARTICLE
Jennifer A Karlow, Erica C Pehrsson, Xiaoyun Xing, Mark Watson, Siddhartha Devarakonda, Ramaswamy Govindan, Ting Wang
Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment outcome. To determine the potential contribution of DNA methylation alterations to tumor phenotype in non-small cell lung cancer (NSCLC) in both smoker and never-smoker patients, we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary assays methylation DNA immunoprecipitation (MeDIP-seq) and methylation sensitive restriction enzyme digestion followed by sequencing (MRE-seq)...
September 22, 2023: Genomics, Proteomics & Bioinformatics
#33
JOURNAL ARTICLE
Marcela Sandoval-Velasco, Anuradha Jagadeesan, Jazmín Ramos-Madrigal, María C Ávila-Arcos, Cesar A Fortes-Lima, Judy Watson, Erna Johannesdóttir, Diana I Cruz-Dávalos, Shyam Gopalakrishnan, J Víctor Moreno-Mayar, Jonas Niemann, Gabriel Renaud, Katharine A Robson Brown, Helena Bennett, Andrew Pearson, Agnar Helgason, M Thomas P Gilbert, Hannes Schroeder
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown...
September 7, 2023: American Journal of Human Genetics
#34
JOURNAL ARTICLE
Kevin Morey, Tyler Thomas-Fenderson, Al Watson, Jacob Sebesta, Christie Peebles, Claudia Gentry Weeks
Recent world events have led to an increased interest in developing rapid and inexpensive clinical diagnostic platforms for viral detection. Here, the development of a cell-free toehold switch-based biosensor, which does not require upstream amplification of target RNA, is described for the detection of RNA viruses. Toehold switches were designed to avoid interfering secondary structure in the viral RNA binding region, mutational hotspots, and cross-reacting sequences of other coronaviruses. Using these design criteria, toehold switches were targeted to a low mutation region of the SARS-CoV-2 genome nonstructural protein 2...
August 28, 2023: Biotechnology Journal
#35
JOURNAL ARTICLE
S Hayward, J Norton, L Bownass, C Platt, H Campbell, E Watson, N Forrester, S Smithson, A Menon
BACKGROUND: The majority of cases of Dent's disease are caused by pathogenic variants in the CLCN5 gene, which encodes a voltage-gated chloride ion channel (ClC-5), resulting in proximal tubular dysfunction. We present three members of the same family and one unrelated paediatric patient with the same insertion-deletion CLCN5 variant. The identification of these patients and positive familial segregation led to the re-classification of this variant from one of unknown significance to one of likely pathogenicity...
August 28, 2023: BMC Nephrology
#36
JOURNAL ARTICLE
Janet E Alexander, Serina Filler, Philip J Bergman, Claire E Bowring, Laura Carvell-Miller, Brenda Fulcher, Richard Haydock, Teresa Lightfoot, Darren W Logan, Talon S McKee, Tracy Mills, JoAnn Morrison, Phillip Watson, Colby Woodruff
BACKGROUND: The veterinary care of cats and dogs is increasingly embracing innovations first applied to human health, including an increased emphasis on preventative care and precision medicine. Large scale human population biobanks have advanced research in these areas; however, few have been established in veterinary medicine. The MARS PETCARE BIOBANK™ (MPB) is a prospective study that aims to build a longitudinal bank of biological samples, with paired medical and lifestyle data, from 20,000 initially healthy cats and dogs (10,000 / species), recruited through veterinary hospitals over a ten-year period...
August 17, 2023: BMC Veterinary Research
#37
JOURNAL ARTICLE
Erica L Lyons, Daniel Watson, Mohammad S Alodadi, Sharie J Haugabook, Gregory J Tawa, Fady Hannah-Shmouni, Forbes D Porter, Jack R Collins, Elizabeth A Ottinger, Uma S Mudunuri
BACKGROUND: Approximately 4-8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved therapies. Genetic sequencing has the potential to shorten the current diagnostic process, increase mechanistic understanding, and facilitate research on therapeutic approaches but is limited by the difficulty of novel variant pathogenicity interpretation and the communication of known causative variants. It is unknown how many published rare disease variants are currently accessible in the public domain...
August 16, 2023: BMC Genomics
#38
JOURNAL ARTICLE
Ayelet Peres, William D Lees, Oscar L Rodriguez, Noah Y Lee, Pazit Polak, Ronen Hope, Meirav Kedmi, Andrew M Collins, Mats Ohlin, Steven H Kleinstein, Corey T Watson, Gur Yaari
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes...
August 7, 2023: Nucleic Acids Research
#39
Jessica Tyler, Rhiannon Aguilar, Nina Arslanovic, Kaylah Birmingham, Kritika Kaliwal, Ujani Chakraborty, Spike Postnikoff, Allison Hickman, Laiba Kahn, Rachel Watson, Ryan Ezell, Hannah Willis, Martis Cowles, Matthew Marunde, Michael-C Keogh, Ignacio Gutierrez, Abraham Shim, Richard Garner
Tardigrades are remarkable in their ability to survive extreme environments. The damage suppressor (Dsup) protein is thought responsible for their extreme resistance to reactive oxygen species (ROS) generated by irradiation. Here we show that expression of Ramazzottius varieornatus Dsup in Saccharomyces cerevisiae reduces oxidative DNA damage and extends the lifespan of budding yeast exposed to chronic oxidative genotoxicity. This protection from ROS requires either the Dsup HMGN-like domain or sequences C-terminal to same...
July 28, 2023: Research Square
#40
JOURNAL ARTICLE
Diedre Reitz, Yasmina Djeghmoum, Ruth A Watson, Pallavi Rajput, Juan Lucas Argueso, Wolf-Dietrich Heyer, Aurèle Piazza
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies...
August 4, 2023: Genes & Development
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