keyword
https://read.qxmd.com/read/38547401/clustering-single-cell-multi-omics-data-via-graph-regularized-multi-view-ensemble-learning
#1
JOURNAL ARTICLE
Fuqun Chen, Guanhua Zou, Yongxian Wu, Le Ou-Yang
MOTIVATION: Single-cell clustering plays a crucial role in distinguishing between cell types, facilitating the analysis of cell heterogeneity mechanisms. While many existing clustering methods rely solely on gene expression data obtained from single-cell RNA sequencing techniques to identify cell clusters, the information contained in mono-omic data is often limited, leading to suboptimal clustering performance. The emergence of single-cell multi-omics sequencing technologies enables the integration of multiple omics data for identifying cell clusters, but how to integrate different omics data effectively remains challenging...
March 28, 2024: Bioinformatics
https://read.qxmd.com/read/38547315/one-shot-single-cell-proteome-and-metabolome-analysis-strategy-for-the-same-single-cell
#2
JOURNAL ARTICLE
Jie Wu, Qin-Qin Xu, Yi-Rong Jiang, Jian-Bo Chen, Wei-Xin Ying, Qian-Xi Fan, Hui-Feng Wang, Yu Wang, Shao-Wen Shi, Jian-Zhang Pan, Qun Fang
Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling...
March 28, 2024: Analytical Chemistry
https://read.qxmd.com/read/38547073/stochastic-modeling-of-a-gene-regulatory-network-driving-b-cell-development-in-germinal-centers
#3
JOURNAL ARTICLE
Alexey Koshkin, Ulysse Herbach, María Rodríguez Martínez, Olivier Gandrillon, Fabien Crauste
Germinal centers (GCs) are the key histological structures of the adaptive immune system, responsible for the development and selection of B cells producing high-affinity antibodies against antigens. Due to their level of complexity, unexpected malfunctioning may lead to a range of pathologies, including various malignant formations. One promising way to improve the understanding of malignant transformation is to study the underlying gene regulatory networks (GRNs) associated with cell development and differentiation...
2024: PloS One
https://read.qxmd.com/read/38547069/correction-for-keum-et-al-heterogeneous-osteoimmune-profiles-via-single-cell-transcriptomics-in-osteoporotic-patients-who-fail-bisphosphonate-treatment
#4
JOURNAL ARTICLE
(no author information available yet)
No abstract text is available yet for this article.
April 2, 2024: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/38546923/vascular-mimicry-in-zebrafish-fin-regeneration-how-macrophages-build-new-blood-vessels
#5
JOURNAL ARTICLE
Anita Senk, Jennifer Fazzari, Valentin Djonov
Vascular mimicry has been thoroughly investigated in tumor angiogenesis. In this study, we demonstrate for the first time that a process closely resembling tumor vascular mimicry is present during physiological blood vessel formation in tissue regeneration using the zebrafish fin regeneration assay. At the fin-regenerating front, vasculature is formed by mosaic blood vessels with endothelial-like cells possessing the morphological phenotype of a macrophage and co-expressing both endothelial and macrophage markers within single cells...
March 28, 2024: Angiogenesis
https://read.qxmd.com/read/38546812/salt-and-heat-stress-enhances-hydrogen-production-in-cyanobacteria
#6
JOURNAL ARTICLE
Panayiotis-Ilias Broussos, George E Romanos, Kostas Stamatakis
Cyanobacteria are among the most suitable organisms for the capture of excessive amounts of CO2 and can be grown in extreme environments. In our research we use the single-celled freshwater cyanobacteria Synechococcus elongatus PCC7942 PAMCOD strain and Synechocystis sp. PCC6714 for the production of carbohydrates and hydrogen. PAMCOD strain and Synechocystis sp. PCC6714 synthesize sucrose when exposed to salinity stress, as their main compatible osmolyte. We examined the cell proliferation rate and the sucrose accumulation in those two different strains of cyanobacteria under salt (0...
March 28, 2024: Photosynthesis Research
https://read.qxmd.com/read/38546806/development-of-a-highly-efficient-solubilization-method-for-mass-spectrometric-analysis-of-phospholipids-in-living-single-cells
#7
JOURNAL ARTICLE
Jo Sakata, Aogu Furusho, Eiji Sugiyama, Iwao Sakane, Kenichiro Todoroki, Hajime Mizuno
Phospholipids are vital constituents of the cell membrane and aid in signal transduction. Phospholipid profiles vary distinctively with the cell type. Notably, specific phospholipid molecules are present in significantly higher or lower concentrations in cancer cells versus normal cells. In this study, live single-cell mass spectrometry (MS) was developed for analyzing phospholipids at the single-cell level. This method facilitates rapid molecular analysis of cells under microscopic observation. For nanoelectrospray ionization, phospholipids were extracted from single cells isolated in a glass capillary through a high-efficiency process...
March 28, 2024: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://read.qxmd.com/read/38546434/intestinal-strictures-in-crohn-s-disease-an-update-from-2023
#8
REVIEW
Zishan Liu, Zhuoyan Huang, Yu Wang, Shanshan Xiong, Sinan Lin, Jinshen He, Jinyu Tan, Caiguang Liu, Xiaomin Wu, Jing Nie, Weidong Huang, Yao Zhang, Longyuan Zhou, Ren Mao
Crohn's disease (CD) is a chronic inflammatory disease that leads to intestinal stricture in nearly 35% of cases within 10 years of initial diagnosis. The unknown pathogenesis, lack of universally accepted criteria, and absence of an effective management approach remain unconquered challenges in structuring CD. The pathogenesis of stricturing CD involves intricate interactions between factors such as immune cell dysbiosis, fibroblast activation, and microecology imbalance. New techniques such as single-cell sequencing provide a fresh perspective...
March 28, 2024: United European Gastroenterology Journal
https://read.qxmd.com/read/38546390/tumor-microenvironment-landscapes-supporting-egfr-mutant-nsclc-are-modulated-at-the-single-cell-interaction-level-by-unesbulin-treatment
#9
JOURNAL ARTICLE
Giorgia Maroni, Indira Krishnan, Roberta Alfieri, Valerie A Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Marla Weetall, Art Branstrom, Giulia Braccini, Eva Cabrera San Millán, Barbara Storti, Ranieri Bizzarri, Olivier Kocher, Daniela S Daniela Sanchez Bassères, Robert S Welner, Maria Cristina Magli, Ivan Merelli, John G Clohessy, Azhar Ali, Daniel G Tenen, Elena Levantini
UNLABELLED: Lung cancer is the leading cause of cancer deaths. Lethal pulmonary adenocarcinomas (ADC) present with frequent mutations in the EGFR. Genetically engineered murine models of lung cancer expedited comprehension of the molecular mechanisms driving tumorigenesis and drug response. Here, we systematically analyzed the evolution of tumor heterogeneity in the context of dynamic interactions occurring with the intermingled tumor microenvironment (TME) by high-resolution transcriptomics...
March 26, 2024: Cancer Res Commun
https://read.qxmd.com/read/38546385/a-novel-risk-signature-based-on-liquid-liquid-phase-separation-related-genes-reveals-prognostic-and-tumour-microenvironmental-features-in-clear-cell-renal-cell-carcinoma
#10
JOURNAL ARTICLE
Qing Lu, Ping Xi, Suling Xu, Zhicheng Zhang, Binbin Gong, Ji Liu, Qiqi Zhu, Ting Sun, Shaoxing Zhu, Ru Chen
BACKGROUND: Clear cell renal cell carcinoma(ccRCC) is one of the most common malignancies. However, there are still many barriers to its underlying causes, early diagnostic techniques and therapeutic approaches. MATERIALS AND METHODS: The Cancer Genome Atlas (TCGA)- Kidney renal clear cell (KIRC) cohort differentially analysed liquid-liquid phase separation (LLPS)-related genes from the DrLLPS website. Univariate and multivariate Cox regression analyses and LASSO regression analyses were used to construct prognostic models...
March 27, 2024: Aging
https://read.qxmd.com/read/38546296/single-cell-based-molecular-classification-in-systematic-treatment-of-hepatocellular-carcinoma-from-in-silico-to-bedside
#11
JOURNAL ARTICLE
Tuo Deng, Gang Chen
No abstract text is available yet for this article.
March 28, 2024: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://read.qxmd.com/read/38546278/mesenchymal-stem-cells-alleviate-mouse-liver-fibrosis-by-inhibiting-pathogenic-function-of-intrahepatic-b-cells
#12
JOURNAL ARTICLE
Xudong Feng, Bing Feng, Jiahang Zhou, Jinfeng Yang, Qiaoling Pan, Jiong Yu, Dandan Shang, Lanjuan Li, Hongcui Cao
BACKGROUND AIMS: The immunomodulatory characteristics of mesenchymal stem cells (MSCs) make them a promising therapeutic approach for liver fibrosis (LF). Here, we postulated that MSCs could potentially suppress the pro-fibrotic activity of intrahepatic B cells, thereby inhibiting LF progression. APPROACH RESULTS: Administration of MSCs significantly ameliorated LF as indicated by reduced myofibroblast activation, collagen deposition, and inflammation. The treatment efficacy of MSCs can be attributed to decreased infiltration, activation, and pro-inflammatory cytokine production of intrahepatic B cells...
March 28, 2024: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://read.qxmd.com/read/38546270/aggregation-enabled-electrochemistry-in-confined-nanopore-capable-of-complementary-faradaic-and-non-faradaic-detection
#13
JOURNAL ARTICLE
Si-Hao Wu, Shuang-Chen Zhang, Yu-Han Kang, Yi-Feng Wang, Zu-Ming Duan, Ming-Jian Jing, Wei-Wei Zhao, Hong-Yuan Chen, Jing-Juan Xu
Electrochemistry that empowers innovative nanoscopic analysis has long been pursued. Here, the concept of aggregation-enabled electrochemistry (AEE) in a confined nanopore is proposed and devised by reactive oxygen species (ROS)-responsive aggregation of CdS quantum dots (QDs) within a functional nanopipette. Complementary Faradaic and non-Faradaic operations of the CdS QDs aggregate could be conducted to simultaneously induce the signal-on of the photocurrents and the signal-off of the ionic signals. Such a rationale permits the cross-checking of the mutually corroborated signals and thus delivers more reliable results for single-cell ROS analysis...
March 28, 2024: Nano Letters
https://read.qxmd.com/read/38545758/tigit-blockade-reshapes-the-tumor-microenvironment-based-on-the-single-cell-rna-sequencing-analysis
#14
JOURNAL ARTICLE
Yanyan Lang, Hao Huang, Hongwei Jiang, Shaoxian Wu, Yaping Chen, Bin Xu, Yingting Liu, Dawei Zhu, Xiao Zheng, Lujun Chen, Jingting Jiang
Immune checkpoint blockade therapy is a pivotal approach in treating malignant tumors. TIGIT has emerged as a focal point of interest among the diverse targets for tumor immunotherapy. Nonetheless, there is still a lack of comprehensive understanding regarding the immune microenvironment alterations following TIGIT blockade treatment. To bridge this knowledge gap, we performed single-cell sequencing on mice both before and after the administration of anti-TIGIT therapy. Our analysis revealed that TIGIT was predominantly expressed on T cells and natural killer (NK) cells...
March 28, 2024: Journal of Immunotherapy
https://read.qxmd.com/read/38545192/predicting-mechanism-of-immune-response-in-microsatellite-instability-colorectal-cancer
#15
JOURNAL ARTICLE
Peng Sun, Yusong Luan, Xuhao Cai, Qi Liu, Peide Ren, Pengpan Xin, Yonggang Yu, Bolun Song, Yangyang Wang, Huijing Chang, Haoyue Ma, Yinggang Chen
Colorectal cancer (CRC), also known as colon cancer, is the third most common cancer and the fourth most cause of cancer-related death in the world. CRC can be classified into two major subtypes, including microsatellite instability (MSI) and microsatellite stability (MSS), which showed different characteristics in immunotherapy. Low sensitivity of diagnostic biomarkers and metastasis are still the principal cause of mortality, especially in MSI. Here, applying computational programs, we identified recurring expression programs based on single cell RNA sequencing (scRNA-Seq) data of CRC cell lines...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38545165/richness-of-yeast-community-associated-with-apple-fruits-in-estonia
#16
JOURNAL ARTICLE
Arnold Kristjuhan, Kersti Kristjuhan, Tiina Tamm
Yeasts are single-celled fungi that are widespread around the globe. They are part of a community of microorganisms that use a wide variety of habitats, including fruit surfaces. This study aimed to characterise the culturable epiphytic yeasts associated with apple fruits. The isolated yeast strains were identified by sequencing the 5.8S-ITS region and D1/D2 region of the large subunit ribosomal RNA gene and maintained for long-term storage. A total of 230 yeast isolates belonging to 33 species were recovered...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38545125/advances-in-single-cell-sequencing-technology-in-microbiome-research
#17
REVIEW
Yinhang Wu, Jing Zhuang, Yifei Song, Xinyi Gao, Jian Chu, Shuwen Han
With the rapid development of histological techniques and the widespread application of single-cell sequencing in eukaryotes, researchers desire to explore individual microbial genotypes and functional expression, which deepens our understanding of microorganisms. In this review, the history of the development of microbial detection technologies was revealed and the difficulties in the application of single-cell sequencing in microorganisms were dissected as well. Moreover, the characteristics of the currently emerging microbial single-cell sequencing (Microbe-seq) technology were summarized, and the prospects of the application of Microbe-seq in microorganisms were distilled based on the current development status...
July 2024: Genes & Diseases
https://read.qxmd.com/read/38545113/the-role-of-dermal-fibroblasts-in-autoimmune-skin-diseases
#18
REVIEW
Zeqi Shi, Zhong Liu, Yujia Wei, Ri Zhang, Yunhua Deng, Dong Li
Fibroblasts are an important subset of mesenchymal cells in maintaining skin homeostasis and resisting harmful stimuli. Meanwhile, fibroblasts modulate immune cell function by secreting cytokines, thereby implicating their involvement in various dermatological conditions such as psoriasis, vitiligo, and atopic dermatitis. Recently, variations in the subtypes of fibroblasts and their expression profiles have been identified in these prevalent autoimmune skin diseases, implying that fibroblasts may exhibit distinct functionalities across different diseases...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38544968/portable-and-autonomous-pedot-modified-flexible-paper-based-methanol-fuel-cell-sensing-platform-applied-to-l1cam-recombinant-protein-detection
#19
JOURNAL ARTICLE
Liliana P T Carneiro, Alexandra M F R Pinto, Dzmitry Ivanou, Adélio M Mendes, M Goreti F Sales
This work describes first a 5-stack direct methanol fuel cell (DMFC) based on poly(3,4-ethylenedioxythiophene)-modified paper (PEDOT/PB-DMFC), which acts as an energy source and biosensor, coupled to an electrochromic cell (EC). It is autonomous and monitors the biosensor response by color change, as appropriate for point-of-care (POC) applications. In detail, DMFC strips were developed from square Whatman paper, and the EC was made on baking paper treated with polydimethylsiloxane (PDMS). The PEDOT/PB-DMFCs operate in a passive mode with a few microliters of diluted methanol...
March 22, 2024: ACS applied polymer materials
https://read.qxmd.com/read/38544605/a-study-on-the-brewing-of-prot-tea-by-blending-spirulina-arthrospira-platensis-with-green-tea
#20
JOURNAL ARTICLE
Rajesh Kanna Gopal, Sruthilakshmi Govindaraj
Introduction Among different blue-green algae, Spirulina ( Arthrospira platensis ) is known for its high protein content and is hence considered a dietary single-cell protein. In recent decades, Spirulina has been one of the nutritive additives in food and beverage products to enhance the nutritional value of food products. The aim of this study was to brew a "Prot-Tea" enriched with antioxidants and protein for nutrition care. Materials and methods In combination, both the Spirulina and green tea were brewed together in three different formulations: formulation A: 0...
February 2024: Curēus
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