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JOURNAL ARTICLE
Nicola J Wyatt, Hannah Watson, Carl A Anderson, Nicholas A Kennedy, Tim Raine, Tariq Ahmad, Dean Allerton, Michelle Bardgett, Emma Clark, Dawn Clewes, Cristina Cotobal Martin, Mary Doona, Jennifer A Doyle, Katherine Frith, Helen C Hancock, Ailsa L Hart, Victoria Hildreth, Peter M Irving, Sameena Iqbal, Ciara Kennedy, Andrew King, Sarah Lawrence, Charlie W Lees, Robert Lees, Laura Letchford, Trevor Liddle, James O Lindsay, Rebecca H Maier, John C Mansfield, Julian R Marchesi, Naomi McGregor, Rebecca E McIntyre, Jasmin Ostermayer, Tolulope Osunnuyi, Nick Powell, Natalie J Prescott, Jack Satsangi, Shriya Sharma, Tara Shrestha, Ally Speight, Michelle Strickland, James Ms Wason, Kevin Whelan, Ruth Wood, Gregory R Young, Xinyue Zhang, Miles Parkes, Christopher J Stewart, Luke Jostins-Dean, Christopher A Lamb
INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients...
April 17, 2024: BMJ Open
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JOURNAL ARTICLE
Jack M Shireman, Quinn White, Zijian Ni, Chitrasen Mohanty, Yujia Cai, Lei Zhao, Namita Agrawal, Nikita Gonugunta, Xiaohu Wang, Liam Mccarthy, Varshitha Kasulabada, Akshita Pattnaik, Atique U Ahmed, James Miller, Charles Kulwin, Aaron Cohen-Gadol, Troy Payner, Chih-Ta Lin, Jesse J Savage, Brandon Lane, Kevin Shiue, Aaron Kamer, Mitesh Shah, Gopal Iyer, Gordon Watson, Christina Kendziorski, Mahua Dey
Stereotactic radiosurgery (SRS) has been shown to be efficacious for the treatment of limited brain metastasis (BM); however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis on resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis...
April 19, 2024: IScience
#3
Alexander R Leydon, Benjamin Downing, Janet Solano Sanchez, Raphael Loll-Krippleber, Nathan M Belliveau, Ricard A Rodriguez-Mias, Andrew Bauer, Isabella J Watson, Lena Bae, Judit Villén, Grant W Brown, Jennifer L Nemhauser
The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model Saccharomyces cerevisiae to localize repressive function to two distinct domains. Here, we employed two unbiased whole genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5 and SPT6 as necessary for repression with the SPT4 subunit acting as a bridge connecting TPL to SPT5 and SPT6...
April 1, 2024: bioRxiv
#4
John S A Mattick, Robin E Bromley, Kaylee J Watson, Ricky S Adkins, Christopher I Holt, Jarrett F Lebov, Benjamin C Sparklin, Tyonna S Tyson, David A Rasko, Julie C Dunning Hotopp
Transcripts are potential therapeutic targets, yet bacterial transcripts remain biological dark matter with uncharacterized biodiversity. We developed and applied an algorithm to predict transcripts for Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria) with newly generated ONT direct RNA sequencing data while predicting transcripts for Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria) using publicly available data...
April 2, 2024: bioRxiv
#5
JOURNAL ARTICLE
Sonya Watson, Kathie J Ngo, Hannah A Stevens, Darice Y Wong, Jihye Kim, Yongjun Song, Beomman Han, Seong-In Hyun, Rin Khang, Seung Woo Ryu, Eugene Lee, Gohun Seo, Hane Lee, Clara Lajonchere, Brent L Fogel
BACKGROUND AND OBJECTIVES: Exome sequencing (ES) demonstrates a 20-50 percent diagnostic yield for patients with a suspected monogenic neurologic disease. Despite the proven efficacy in achieving a diagnosis for such patients, multiple barriers for obtaining exome sequencing remain. This study set out to assess the efficacy of ES in patients with primary neurologic phenotypes who were appropriate candidates for testing but had been unable to pursue clinical testing. METHODS: A total of 297 patients were identified from the UCLA Clinical Neurogenomics Research Center Biobank, and ES was performed, including bioinformatic assessment of copy number variation and repeat expansions...
June 2024: Neurology. Genetics
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JOURNAL ARTICLE
Didu S Kariyawasam, Joanne Scarfe, Christian Meagher, Michelle A Farrar, Kaustav Bhattacharya, Stacy M Carter, Ainsley J Newson, Margaret Otlowski, Jo Watson, Nicole Millis, Sarah Norris
BACKGROUND: Newborn bloodspot screening is a well-established population health initiative that detects serious, childhood-onset, treatable conditions to improve health outcomes. With genomic technologies advancing rapidly, many countries are actively discussing the introduction of genomic assays into newborn screening programs. While adding genomic testing to Australia's newborn screening program could improve outcomes for infants and families, it must be considered against potential harms, ethical, legal, equity and social implications, and economic and health system impacts...
2024: PloS One
#7
JOURNAL ARTICLE
Marina Martínez-Álvaro, Jennifer Mattock, Óscar González-Recio, Alejandro Saborío-Montero, Ziqing Weng, Joana Lima, Carol-Anne Duthie, Richard Dewhurst, Matthew A Cleveland, Mick Watson, Rainer Roehe
BACKGROUND: Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage. RESULTS: By analysing longitudinal body weights during the finishing period and genomic and metagenomic data from 359 beef cattle, our study demonstrates that the influence of the host genome on the functional rumen microbiome contributes to the temporal variation in average daily gain (ADG) in different months (ADG1 , ADG2 , ADG3 , ADG4 )...
March 15, 2024: Genetics, Selection, Evolution: GSE
#8
JOURNAL ARTICLE
Laura Chavarría-Pizarro, Kattia Núñez-Montero, Mariela Gutiérrez-Araya, William Watson-Guido, William Rivera-Méndez, Javier Pizarro-Cerdá
Antimicrobial resistance has been considered a public health threat. The World Health Organization has warned about the urgency of detecting new antibiotics from novel sources. Social insects could be crucial in the search for new antibiotic metabolites, as some of them survive in places that favor parasite development. Recent studies have shown the potential of social insects to produce antimicrobial metabolites (e.g. ants, bees, and termites). However, most groups of social wasps remain unstudied. Here, we explored whether Actinobacteria are associated with workers in the Neotropical Social Wasps (Epiponini) of Costa Rica and evaluated their putative inhibitory activity against other bacteria...
2024: FEMS Microbes
#9
JOURNAL ARTICLE
Claire E L Smith, Virginie Laugel-Haushalter, Ummey Hany, Sunayna Best, Rachel L Taylor, James A Poulter, Saskia B Wortmann, Rene G Feichtinger, Johannes A Mayr, Suhaila Al Bahlani, Georgios Nikolopoulos, Alice Rigby, Graeme C Black, Christopher M Watson, Sahar Mansour, Chris F Inglehearn, Alan J Mighell, Agnès Bloch-Zupan
BACKGROUND: Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease. METHODS: Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability...
March 8, 2024: Journal of Medical Genetics
#10
JOURNAL ARTICLE
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function...
February 12, 2024: Nature Microbiology
#11
JOURNAL ARTICLE
Aaron L Phillips, Scott Ferguson, Rachel A Burton, Nathan S Watson-Haigh
Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome...
February 9, 2024: PLoS Computational Biology
#12
JOURNAL ARTICLE
Yantong Cai, Jia Lv, Rui Li, Xiaowen Huang, Shi Wang, Zhenmin Bao, Qifan Zeng
Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study. Deqformer utilizes the oligonucleotides sequence of each probe, drawing inspiration from Watson-Crick base pairing and incorporating two BERT encoders to capture the underlying information from the forward and reverse probe strands, respectively...
January 22, 2024: Briefings in Bioinformatics
#13
JOURNAL ARTICLE
Itidal Reslane, Luke D Handke, Gabrielle F Watson, Dhananjay Shinde, Jong-Sam Ahn, Jennifer L Endres, Fareha Razvi, Emily A Gilbert, Kenneth W Bayles, Vinai C Thomas, McKenzie K Lehman, Paul D Fey
Genome sequencing has demonstrated that Staphylococcus aureus encodes arginine biosynthetic genes argDCJBFGH synthesizing proteins that mediate arginine biosynthesis using glutamate as a substrate. Paradoxically, however, S. aureus does not grow in a defined, glutamate-replete medium lacking arginine and glucose (CDM-R). Studies from our laboratory have found that specific mutations are selected by S. aureus that facilitate growth in CDM-R. However, these selected mutants synthesize arginine utilizing proline as a substrate rather than glutamate...
February 1, 2024: Journal of Bacteriology
#14
JOURNAL ARTICLE
Li-Juan Wang, Qian Liu, Ying-Ying Lu, Le Liang, Chun-Yang Zhang
N 6 -Methyladenine (6mdA) and N 4 -methylcytosine (4mdC) are the two most dominant DNA modifications in both prokaryotes and eukaryotes, but standard hybridization-based techniques cannot be applied for the 6mdA/4mdC assay. Herein, we demonstrate the silver-coordinated Watson-Crick pairing-driven three-dimensional (3D) DNA walker for locus-specific detection of genomic 6mdA/4mdC at the single-molecule level. 6mdA-DNA and 4mdC-DNA can selectively hybridize with the binding probes (BP1 and BP2) to form 6mdA-DNA-BP1 and 4mdC-DNA-BP2 duplexes...
January 28, 2024: Analytical Chemistry
#15
REVIEW
Oneil G Bhalala, Rosie Watson, Nawaf Yassi
Late-onset Alzheimer's disease is the leading cause of dementia worldwide, accounting for a growing burden of morbidity and mortality. Diagnosing Alzheimer's disease before symptoms are established is clinically challenging, but would provide therapeutic windows for disease-modifying interventions. Blood biomarkers, including genetics, proteins and metabolites, are emerging as powerful predictors of Alzheimer's disease at various timepoints within the disease course, including at the preclinical stage. In this review, we discuss recent advances in such blood biomarkers for determining disease risk...
January 19, 2024: International Journal of Molecular Sciences
#16
JOURNAL ARTICLE
Sophie Giguère, Xuesong Wang, Sabrina Huber, Liling Xu, John Warner, Stephanie R Weldon, Jennifer Hu, Quynh Anh Phan, Katie Tumang, Thavaleak Prum, Duanduan Ma, Kathrin H Kirsch, Usha Nair, Peter Dedon, Facundo D Batista
Antibodies are produced at high rates to provide immunoprotection, which puts pressure on the B cell translational machinery. Here, we identified a pattern of codon usage conserved across antibody genes. One feature thereof is the hyperutilization of codons that lack genome-encoded Watson-Crick transfer RNAs (tRNAs), instead relying on the posttranscriptional tRNA modification inosine (I34), which expands the decoding capacity of specific tRNAs through wobbling. Antibody-secreting cells had increased I34 levels and were more reliant on I34 for protein production than naïve B cells...
January 12, 2024: Science
#17
Blake Vuocolo, Roberta Sierra, Dan Brooks, Christopher Holder, Lauren Urbanski, Keila Rodriguez, Jose David Gamez, Surya Narayan Mulukutla, Lori Berry, Ana Hernandez, Alberto Allegre, Humberto Hidalgo, Sarah Rodriguez, Sandy Magallan, Jeremy Gibson, Juan Carlos Bernini, Melanie Watson, Robert Nelson, Lizbeth Mellin-Sanchez, Hongzheng Dai, Claudia Soler-Alfonso, Kent Carter, Brendan Lee, Seema R Lalani
Background The utilization of genomic information to improve health outcomes is progressively becoming more common in clinical practice. Nonetheless, disparities persist in accessing genetic services among ethnic minorities, individuals with low socioeconomic status, and other vulnerable populations. The Rio Grande Valley at the Texas-Mexico border is predominantly Hispanic with a high poverty rate and an increased prevalence of birth defects, with very limited access to genetics services. The cost of a diagnosis is often times out of reach for these underserved families...
December 13, 2023: Research Square
#18
JOURNAL ARTICLE
Shuliang Gao, Huiwen Guan, Hanan Bloomer, Douglas Wich, Donghui Song, Jennifer Khirallah, Zhongfeng Ye, Yu Zhao, Mengting Chen, Chutian Xu, Lihan Liu, Qiaobing Xu
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells...
January 9, 2024: Proceedings of the National Academy of Sciences of the United States of America
#19
JOURNAL ARTICLE
Joshua Nolan, James Buchanan, John Taylor, Joao Almeida, Tina Bedenham, Edward Blair, Suzanne Broadgate, Samantha Butler, Angela Cazeaux, Judith Craft, Treena Cranston, Gillian Crawford, Jamie Forrest, Jessica Gabriel, Elaine George, Donna Gillen, Ash Haeger, Jillian Hastings Ward, Lara Hawkes, Claire Hodgkiss, Jonathan Hoffman, Alan Jones, Fredrik Karpe, Dalia Kasperaviciute, Erika Kovacs, Sarah Leigh, Elizabeth Limb, Anjali Lloyd-Jani, Javier Lopez, Anneke Lucassen, Carlos McFarlane, Anthony W O'Rourke, Emily Pond, Catherine Sherman, Helen Stewart, Ellen Thomas, Simon Thomas, Tessy Thomas, Kate Thomson, Hannah Wakelin, Susan Walker, Melanie Watson, Eleanor Williams, Elizabeth Ormondroyd
PURPOSE: The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolaemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia, von Hippel-Lindau. Here we report disclosure processes, manifestation of AF-related disease, outcomes and costs. METHODS: An observational study in an area representing one-fifth of England...
December 19, 2023: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#20
JOURNAL ARTICLE
Timothy Páez-Watson, Mark C M van Loosdrecht, S Aljoscha Wahl
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs)...
December 17, 2023: Water Research
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