keyword
https://read.qxmd.com/read/38497648/using-cleavage-under-targets-and-tagmentation-cut-tag-assay-in-mouse-myoblast-research
#1
JOURNAL ARTICLE
Yuefeng Li, Xiaofen Wu, Ping Hu
This protocol paper aims to provide the new researchers with the full details of using Cleavage Under Targets and Tagmentation (CUT&Tag) to profile the genomic locations of chromatin binding factors, histone marks, and histone variants. CUT&Tag protocols function very well with mouse myoblasts and freshly isolated muscle stem cells (MuSCs). They can easily be applied to many other cell types as long as the cells can be immobilized by Concanavalin-A beads. Compared to CUT&Tag, chromatin immunoprecipitation (ChIP) assays are time-consuming experiments...
March 1, 2024: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/38495916/from-static-to-dynamic-the-influence-of-mechanotransduction-on-skin-equivalents-analyzed-by-bioimaging-and-rnaseq
#2
JOURNAL ARTICLE
Katharina Kaiser, Sofie M Bendixen, Jens Ahm Sørensen, Jonathan R Brewer
In this study, we explore the impact of mechanical stimuli on skin models using an innovative skin-on-a-chip platform, addressing the limitations of conventional transwell-cultured skin equivalents. This platform facilitates cyclic mechanical stimulation through compression and stretching, combined with automated media perfusion. Our findings, using bioimaging and bulk RNA sequencing, reveal increased expression of Keratin 10 and Keratin 14, indicating enhanced skin differentiation and mechanical integrity...
April 2024: Materials today. Bio
https://read.qxmd.com/read/38495565/machine-and-deep-learning-methods-for-predicting-3d-genome-organization
#3
Brydon P G Wall, My Nguyen, J Chuck Harrell, Mikhail G Dozmorov
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution...
March 4, 2024: ArXiv
https://read.qxmd.com/read/38495529/programmable-control-of-nanoliter-droplet-arrays-using-membrane-displacement-traps
#4
JOURNAL ARTICLE
Jason Harriot, Michael Yeh, Mani Pabba, Don L DeVoe
A unique droplet microfluidic technology enabling programmable deterministic control over complex droplet operations is presented. The platform provides software control over user-defined combinations of droplet generation, capture, ejection, sorting, splitting, and merging sequences to enable the design of flexible assays employing nanoliter-scale fluid volumes. The system integrates a computer vision system with an array of membrane displacement traps capable of performing selected unit operations with automated feedback control...
November 10, 2023: Advanced Materials Technologies
https://read.qxmd.com/read/38490999/local-prediction-learning-in-high-dimensional-spaces-enables-neural-networks-to-plan
#5
JOURNAL ARTICLE
Christoph Stöckl, Yukun Yang, Wolfgang Maass
Planning and problem solving are cornerstones of higher brain function. But we do not know how the brain does that. We show that learning of a suitable cognitive map of the problem space suffices. Furthermore, this can be reduced to learning to predict the next observation through local synaptic plasticity. Importantly, the resulting cognitive map encodes relations between actions and observations, and its emergent high-dimensional geometry provides a sense of direction for reaching distant goals. This quasi-Euclidean sense of direction provides a simple heuristic for online planning that works almost as well as the best offline planning algorithms from AI...
March 15, 2024: Nature Communications
https://read.qxmd.com/read/38487805/a-weighted-two-stage-sequence-alignment-framework-to-identify-motifs-from-chip-exo-data
#6
JOURNAL ARTICLE
Yang Li, Yizhong Wang, Cankun Wang, Anjun Ma, Qin Ma, Bingqiang Liu
In this study, we introduce TESA (weighted two-stage alignment), an innovative motif prediction tool that refines the identification of DNA-binding protein motifs, essential for deciphering transcriptional regulatory mechanisms. Unlike traditional algorithms that rely solely on sequence data, TESA integrates the high-resolution chromatin immunoprecipitation (ChIP) signal, specifically from ChIP-exonuclease (ChIP-exo), by assigning weights to sequence positions, thereby enhancing motif discovery. TESA employs a nuanced approach combining a binomial distribution model with a graph model, further supported by a "bookend" model, to improve the accuracy of predicting motifs of varying lengths...
March 8, 2024: Patterns
https://read.qxmd.com/read/38484151/g-quadruplex-landscape-and-its-regulation-revealed-by-a-new-antibody-capture-method
#7
JOURNAL ARTICLE
Subhamoy Datta, Manthan Patel, Chakkarai Sathyaseelan, Chandrama Ghosh, Akanksha Mudgal, Divyesh Patel, Thenmalarchelvi Rathinavelan, Umashankar Singh
Our understanding of DNA G-quadruplexes (G4s) from in vitro studies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s...
March 14, 2024: Oncotarget
https://read.qxmd.com/read/38479789/primary-osteoarthritis-chondrocyte-map-of-chromatin-conformation-reveals-novel-candidate-effector-genes
#8
JOURNAL ARTICLE
Norbert Bittner, Chenfu Shi, Danyun Zhao, James Ding, Lorraine Southam, Diane Swift, Peter Kreitmaier, Mauro Tutino, Odysseas Stergiou, Jackson T S Cheung, Georgia Katsoula, Jenny Hankinson, Jeremy Mark Wilkinson, Gisela Orozco, Eleftheria Zeggini
OBJECTIVES: Osteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organisation in three-dimensional (3D) space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner...
March 13, 2024: Annals of the Rheumatic Diseases
https://read.qxmd.com/read/38475709/shared-and-distinct-interactions-of-type-1-and-type-2-epstein-barr-nuclear-antigen-2-with-the-human-genome
#9
JOURNAL ARTICLE
Kenyatta C M F Viel, Sreeja Parameswaran, Omer A Donmez, Carmy R Forney, Matthew R Hass, Cailing Yin, Sydney H Jones, Hayley K Prosser, Arame A Diouf, Olivia E Gittens, Lee E Edsall, Xiaoting Chen, Hope Rowden, Katelyn A Dunn, Rui Guo, Andrew VonHandorf, Merrin Man Long Leong, Kevin Ernst, Kenneth M Kaufman, Lucinda P Lawson, Ben Gewurz, Bo Zhao, Leah C Kottyan, Matthew T Weirauch
BACKGROUND: There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions...
March 12, 2024: BMC Genomics
https://read.qxmd.com/read/38473942/joint-gwas-linkage-mapping-and-transcriptome-analysis-to-reveal-the-genetic-basis-of-plant-architecture-related-traits-in-maize
#10
JOURNAL ARTICLE
Xuefeng Lu, Pengfei Liu, Liang Tu, Xiangyang Guo, Angui Wang, Yunfang Zhu, Yulin Jiang, Chunlan Zhang, Yan Xu, Zehui Chen, Xun Wu
Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments...
February 26, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38470216/impact-of-clonal-hematopoiesis-of-indeterminate-potential-on-hepatocellular-carcinoma-in-individuals-with-steatotic-liver-disease
#11
JOURNAL ARTICLE
Alfredo Marchetti, Serena Pelusi, Alessio Marella, Francesco Malvestiti, Antony Ricchiuti, Luisa Ronzoni, Marta Lionetti, Vittoria Moretti, Elisabetta Bugianesi, Luca Miele, Umberto Vespasiani-Gentilucci, Paola Dongiovanni, Alessandro Federico, Giorgio Soardo, Roberta D'Ambrosio, Misti V McCain, Helen L Reeves, Vincenzo La Mura, Daniele Prati, Niccolò Bolli, Luca Valenti
BACKGROUND AIMS: Metabolic dysfunction associated steatotic liver disease (MASLD) is a global epidemic and is the most rapidly rising cause of hepatocellular carcinoma (HCC). Clonal hematopoiesis of indeterminate potential (CHIP) contributes to neoplastic and cardiometabolic disorders and is considered a harbinger of tissue inflammation. CHIP was recently associated with increased risk of liver disease. The aim of this study was to examine whether CHIP is associated with HCC development in patients with SLD...
March 11, 2024: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://read.qxmd.com/read/38468745/molecular-detection-of-multidrug-resistance-and-characterizations-of-mutations-in-mycobacterium-tuberculosis-using-polycarbonate-track-etched-membrane-based-dna-bio-chip
#12
JOURNAL ARTICLE
Bharti Jain, Savita Kulkarni
With the widespread use of rifampicin (RMP) and isoniazid (INH), multidrug resistance (MDR) in Mycobacterium tuberculosis (M.tb) poses a threat to the success of tuberculosis (TB) control programs. We have developed a new polycarbonate track-etched membranes (PC-TEM) based DNA bio-chip designed for rapid detection of mutations conferring MDR in  M.tb  culture isolates. Bio-chips were designed to contain 14 specific probes for wild type and mutated allele of selected codons within 80 bp rifampicin resistance determining region of rpoB gene, katG  gene and  mabA-inhA  regulatory region...
March 2024: Indian Journal of Microbiology
https://read.qxmd.com/read/38468288/uchl1-contributes-to-insensitivity-to-endocrine-therapy-in-triple-negative-breast-cancer-by-deubiquitinating-and-stabilizing-klf5
#13
JOURNAL ARTICLE
Juan Li, Yu Liang, Shijie Zhou, Jie Chen, Chihua Wu
BACKGROUND: Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is a deubiquitinating enzyme that regulates ERα expression in triple-negative cancer (TNBC). This study aimed to explore the deubiquitination substrates of UCHL1 related to endocrine therapeutic responses and the mechanisms of UCHL1 dysregulation in TNBC. METHODS: Bioinformatics analysis was conducted using online open databases. TNBC representative MDA-MB-468 and SUM149 cells were used for in vitro and in-vivo studies...
March 11, 2024: Breast Cancer Research: BCR
https://read.qxmd.com/read/38467101/rapid-and-accurate-sers-assay-of-disease-related-nucleic-acids-based-on-isothermal-cascade-signal-amplifications-of-crispr-cas13a-system-and-catalytic-hairpin-assembly
#14
JOURNAL ARTICLE
Jingjing Zhang, Zhilong Chen, Huiming Lv, Jing Liang, Chenlong Yan, Chunyuan Song, Lianhui Wang
Developing rapid, accurate and convenient nucleic acid diagnostic techniques is essential for the prevention and control of contagious diseases that are prone to gene mutations and may have homologous sequences, especially emerging infectious diseases such as the SARS-CoV-2 pandemic. Herein, a one-pot SERS assay integrating isothermal cascade signal amplification strategy (i.e., CRISPR/Cas13a system (Cas13a) and catalytic hairpin assembly (CHA), Cas13a-CHA) and SERS-active silver nanorods (AgNRs) sensing chips was proposed for rapid and accurate detection of disease-related nucleic acids...
March 6, 2024: Biosensors & Bioelectronics
https://read.qxmd.com/read/38465708/nrf2-pre-recruitment-at-enhancer-2-is-a-hallmark-of-h-2-o-2-induced-epigenetic-transcriptional-memory-in-the-hmox1-gene-in-human-umbilical-artery-endothelial-cells
#15
JOURNAL ARTICLE
Ivo Carrasco-Wong, Gernot Längst, Luis Sobrevia, Paola Casanello
Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in arterial endothelium. However, specific mechanisms by which the pro-oxidant fetal environment in MO could modulate the vascular gene expression and function during the offspring's postnatal life are elusive. We tested if oxidative stress could reprogram the antioxidant-coding gene's response to a pro-oxidant challenge through an epigenetic transcriptional memory (ETM) mechanism...
March 11, 2024: Journal of Cellular Physiology
https://read.qxmd.com/read/38464314/complete-chromosome-21-centromere-sequences-from-a-down-syndrome-family-reveal-size-asymmetry-and-differences-in-kinetochore-attachment
#16
F Kumara Mastrorosa, Allison N Rozanski, William T Harvey, Jordan Knuth, Gage Garcia, Katherine M Munson, Kendra Hoekzema, Glennis A Logsdon, Evan E Eichler
Down syndrome is the most common form of human intellectual disability caused by precocious segregation and nondisjunction of chromosome 21. Differences in centromere structure have been hypothesized to play a potential role in this process in addition to the well-established risk of advancing maternal age. Using long-read sequencing, we completely sequenced and assembled the centromeres from a parent-child trio where Trisomy 21 arose in the child as a result of a meiosis I error. The proband carries three distinct chromosome 21 centromere haplotypes that vary by 11-fold in length--both the largest (H1) and smallest (H2) originating from the mother...
February 26, 2024: bioRxiv
https://read.qxmd.com/read/38462366/-pathogenetic-analysis-of-transfusion-related-acute-lung-injury-caused-by-human-leukocytes-antigen-antibody-against-human-leukocyte-antigen
#17
JOURNAL ARTICLE
J Deng, X Z Xu, X Ye, Y K Chen, H Q Ding, J Liu, W J Xia, D W Chen, Y R Xu
From September 2019 to October 2020, pathogenetic analysis of three patients clinically diagnosed as transfusion-related acute lung injury (TRALI) caused by human leukocyte antibodies was conducted by Guangzhou Blood Centre, including 2 males and 1 female, aged 56, 50 and 20 years old, respectively. Solid phase agglutination, anti-human globulin test and flow cytometry method were used to detect the presence of antibodies against patients. Sequencing-based human leukocyte antigen (HLA-SBT) typing technique was used to detect the human leukocyte antigen (HLA) genotypes of patients...
March 19, 2024: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://read.qxmd.com/read/38462363/-analysis-of-transfusion-effect-of-different-platelet-matching-schemes-in-patients-with-platelet-transfusion-refractoriness
#18
JOURNAL ARTICLE
Y J Liang, H Wang, P Z Zhao, F Wang, Q Li, Y Xu, Y X Wu, D M Zhang, X H He
Objective: To analyze the transfusion effect of different platelet matching schemes in patients with platelet transfusion refractoriness (PTR). Methods: A total of 94 patients with PTR received by Taiyuan Blood Center from January to December 2021 were retrospectively analyzed, including 26 males and 68 females, aged 53(34,66) years. Platelet antibody screening was performed by enzyme-linked immunosorbent assay (ELISA). For patients with positive human leukocyte antigen (HLA) class Ⅰ antibodies, Luminex platform liquid chip assay was used to identify the specificity of antibodies, and platelets with missing allelic expression antigen corresponding to their specific antibodies were found in the platelet donor gene database established in our laboratory...
March 19, 2024: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://read.qxmd.com/read/38461471/how-diverse-a-monocentric-chromosome-can-be-repeatome-and-centromeric-organization-of-juncus-effusus-juncaceae
#19
JOURNAL ARTICLE
Yhanndra Dias, Yennifer Mata-Sucre, Gokilavani Thangavel, Lucas Costa, Mariana Báez, Andreas Houben, André Marques, Andrea Pedrosa-Harand
Juncus is the largest genus of Juncaceae and was considered holocentric for a long time. Recent findings, however, indicated that 11 species from different clades of the genus have monocentric chromosomes. Thus, the Juncus centromere organization and evolution need to be reassessed. We aimed to investigate the major repetitive DNA sequences of two accessions of Juncus effusus and its centromeric structure by employing whole-genome analyses, fluorescent in situ hybridization, CENH3 immunodetection, and chromatin immunoprecipitation sequencing...
March 10, 2024: Plant Journal
https://read.qxmd.com/read/38461243/mal-expression-downregulation-through-suppressive-h3k27me3-marks-at-the-promoter-in-hpv16-related-cervical-cancers-is-prognostically-relevant-and-manifested-by-the-interplay-of-novel-mal-antisense-long-noncoding-rna-ac103563-8-e7-oncoprotein-and-ezh2
#20
JOURNAL ARTICLE
Abarna Sinha, Abhisikta Ghosh, Arnab Ghosh, Sonia Mathai, Jaydip Bhaumik, Asima Mukhopadhyay, Arindam Maitra, Nidhan K Biswas, Sharmila Sengupta
BACKGROUND: MAL (T-lymphocyte maturation-associated protein) is highly downregulated in most cancers, including cervical cancer (CaCx), attributable to promoter hypermethylation. Long noncoding RNA genes (lncGs) play pivotal roles in CaCx pathogenesis, by interacting with human papillomavirus (HPV)-encoded oncoproteins, and epigenetically regulating coding gene expression. Hence, we attempted to decipher the impact and underlying mechanisms of MAL downregulation in HPV16-related CaCx pathogenesis, by interrogating the interactive roles of MAL antisense lncRNA AC103563...
March 10, 2024: Clinical Epigenetics
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