EPHB2 as a key mediator of glioma progression: Insights from microenvironmental receptor ligand-related prognostic gene signature
This study aimed to investigate the prognostic value of Ligand and Receptor related genes (LRRGs) within the glioma microenvironment. An intersection of 71 ligand-related genes (LRGs) and 2628 receptor-related genes (RRGs) yielded a total of 69 LRRGs. Utilizing the least absolute shrinkage and selection operator (LASSO) regression analysis, a prognostic RiskScore model comprising 28 LRRGs was constructed. The model demonstrated robust prognostic value, further validated in the TCGA-GBMLGG dataset. Subsequent analyses included differential gene expression, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), ...
Source: Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Liming Tan Jingyuan Zhou Zhenyu Nie Ding Li Bing Wang Source Type: research
Identification of STAT3 as a biomarker for cellular senescence in liver fibrosis: A bioinformatics and experimental validation study
CONCLUSIONS: STAT3 may be involved in HCs senescence and promote HSCs activation, which in turn leads to the development of LF. Our findings suggest that STAT3 could be a potential biomarker for LF.PMID:38286349 | DOI:10.1016/j.ygeno.2024.110800 (Source: Genomics)
Source: Genomics - January 29, 2024 Category: Genetics & Stem Cells Authors: Xue Pang Shang Gao Tao Liu Feng Xia Xu Chang Fan Jia Fu Zhang Hui Jiang Source Type: research
Overexpression and nonsynonymous mutations of UDP-glycosyltransferases are potentially associated with pyrethroid resistance in Anopheles funestus
This study provides the first comprehensive investigation of Anopheles funestus UGT genes, their evolution, and their association with pyrethroid resistance. We employed a genome-wide association study using pooled sequencing (GWAS-PoolSeq) and transcriptomics on pyrethroid-resistant An. funestus, along with deep-targeted sequencing of UGTs in 80 mosquitoes Africa-wide. UGT310B2 was consistently overexpressed Africa-wide and significant gene-wise Fst differentiation was observed between resistant and susceptible populations: UGT301C2 and UGT302A3 in Malawi, and UGT306C2 in Uganda. Additionally, nonsynonymous mutations in U...
Source: Genomics - January 24, 2024 Category: Genetics & Stem Cells Authors: Talal Al-Yazeedi Abdullahi Muhammad Helen Irving Seung-Joon Ahn Jack Hearn Charles S Wondji Source Type: research
Identification and validation of CRLF1 and NRG1 as immune-related signatures in hypertrophic scar
CONCLUSION: In this study, two key immune-related genes (CRLF1 and NRG1) were identified as characteristic genes associated with HTS. These findings provide valuable insights into the immune-related mechanisms underlying hypertrophic scar formation.PMID:38262564 | DOI:10.1016/j.ygeno.2024.110797 (Source: Genomics)
Source: Genomics - January 23, 2024 Category: Genetics & Stem Cells Authors: Boya Yu Yalei Cao Shiyi Li Ruiqi Bai Guiwen Zhou Qiang Fu Liming Liang Weijie Gu Lixia Zhang Minliang Chen Source Type: research
Effectiveness of a novel rat model of off-target PLA2R1 knockout to renal impairment
In this study, we created PLA2R1 knockout rats to explore potential consequences resulting from the loss of the PLA2R1 gene. Unexpectedly, our PLA2R1 knockout rats exhibited symptoms resembling those of chronic kidney disease after an 8-week observation period. Notably, several rats developed persistent proteinuria, a hallmark of renal dysfunction. Immunohistochemical and immunofluorescence analyses revealed insignificant glomerular fibrosis, reduced podocyte count, and augmented glomerular expression of complement C3 (C3) compared to immunoglobin A (IgA) and immunoglobin G(IgG) in the rat model. These findings suggest tha...
Source: Genomics - January 18, 2024 Category: Genetics & Stem Cells Authors: Bo Huang Zitong Zhang Wendong Sui Lu Zhao Yinyin Li Li Feng Daihe Yang Yun Zhou Source Type: research
HSCs-derived exosomes regulate the levels of inflammatory cytokines in HIBECs through miR-122-5p mediated p38 MAPK signaling pathway
In this study, we extracted exosomes from serum and human IBECs supernatant, and RNA-sequence analyzed the expression profiles of miRNAs. Elisa measured the levels of inflammatory cytokines. RT- qPCR and western blot detected the levels of miR-122-5p, p38 and p-p38. The results showed that 263 differentially expressed (DE) miRNAs were identified in serum exosomes of PBC patients. The levels of IL-1β, IL-6, IL-12, IL-17 A, IFN-γ, TNF-α and TGF-β1 in peripheral blood of PBC patients were higher than those of normal controls. According to the validation results and previous literature, exosomal miR-122-5p was finally sele...
Source: Genomics - January 16, 2024 Category: Genetics & Stem Cells Authors: Yaqin Zhang Xiangzhi Zhang Ruofei Chen Ziying Jiao Bing Shen Zongwen Shuai Source Type: research
Unraveling a novel hippo-associated immunological prognostic signature: The contribution of SERPINE1 in facilitating colorectal cancer progression via the notch signaling pathway
CONCLUSIONS: To sum up, we established a novel immunological prognostic signature utilizing genes associated with the Hippo pathway. This signature offers accurate prognostic prediction and can guide individualized therapy for patients with CRC.PMID:38224823 | DOI:10.1016/j.ygeno.2024.110794 (Source: Genomics)
Source: Genomics - January 15, 2024 Category: Genetics & Stem Cells Authors: Xingyao Su Xiaofeng Wang Jie Lai Shengxun Mao Huizi Li Source Type: research
A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq
In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across diverse sample types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are ...
Source: Genomics - January 14, 2024 Category: Genetics & Stem Cells Authors: Daniel V Brown Casey J A Anttila Ling Ling Patrick Grave Tracey M Baldwin Ryan Munnings Anthony J Farchione Vanessa L Bryant Amelia Dunstone Christine Biben Samir Taoudi Tom S Weber Shalin H Naik Anthony Hadla Holly E Barker Cassandra J Vandenberg Genevie Source Type: research
Comparative proteomic analysis across the developmental stages of the Eimeria tenella
In this study, protein profiles from the five developmental stages, including unsporulated oocysts (USO), partially sporulated (7 h) oocysts (SO7h), sporulated oocysts (SO), sporozoites (S) and second-generation merozoites (M2), were harvested using the label-free quantitative proteomics approach. Then the differentially expressed proteins (DEPs) for these stages were identified. A total of 314, 432, 689, and 665 DEPs were identified from the comparison of SO7h vs USO, SO vs SO7h, S vs SO, and M2 vs S, respectively. By conducting weighted gene coexpression network analysis (WGCNA), six modules were dissected. Proteins in b...
Source: Genomics - January 12, 2024 Category: Genetics & Stem Cells Authors: Xueting Ma Baohong Liu Zhenxing Gong Jing Wang Zigang Qu Jianping Cai Source Type: research
Cell specification and functional interactions in the pig blastocyst inferred from single-cell transcriptomics and uterine fluids proteomics
Genomics. 2024 Jan 9;116(2):110780. doi: 10.1016/j.ygeno.2023.110780. Online ahead of print.ABSTRACTThe embryonic development of the pig comprises a long in utero pre- and peri-implantation development, which dramatically differs from mice and humans. During this peri-implantation period, a complex series of paracrine signals establishes an intimate dialogue between the embryo and the uterus. To better understand the biology of the pig blastocyst during this period, we generated a large dataset of single-cell RNAseq from early and hatched blastocysts, spheroid and ovoid conceptus and proteomic datasets from corresponding u...
Source: Genomics - January 11, 2024 Category: Genetics & Stem Cells Authors: Adrien Dufour Cyril Kurylo Jan B St öckl Denis Lalo ë Yoann Bailly Patrick Manceau Fr édéric Martins Ali G Turhan St éphane Ferchaud Bertrand Pain Thomas Fr öhlich Sylvain Foissac J érôme Artus Herv é Acloque Source Type: research
Retraction notice to "Relationship between common eNOS gene polymorphisms and predisposition to coronary artery disease: Evidence from a meta-analysis of 155 published association studies" [Genomics, 112/3 (2020) 2452-2458]
Genomics. 2024 Jan 10:110783. doi: 10.1016/j.ygeno.2024.110783. Online ahead of print.NO ABSTRACTPMID:38212241 | DOI:10.1016/j.ygeno.2024.110783 (Source: Genomics)
Source: Genomics - January 11, 2024 Category: Genetics & Stem Cells Authors: Jianhong Yu Xiuping Wu Jianchao Ni Jianhai Zhang Source Type: research
Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco
In this study, transcriptome sequencing were subjected to roots after infection with the R. solanacearum in the resistant and susceptible tobacco variety. DEGs that responded to R. solanacearum infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction, signal transduction and MAPK signalling pathway KEGG terms. Core DEGs in the resistant tobacco response to R. solanacearum infection were enriched in cell wall, membrane, abscisic acid and ethylene terms. qRT-PCR indicated that Nitab4.5_0004899g0110, Nitab4.5_0004234g0080 and...
Source: Genomics - January 10, 2024 Category: Genetics & Stem Cells Authors: Zhiliang Xiao Zhengwen Liu Huifen Zhang Aiguo Yang Lirui Cheng Dan Liu Caihong Jiang Shizhou Yu Zhixiao Yang Min Ren Ruimei Geng Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Epub 2024 Jan 3.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, y...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan 3;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Online ahead of print.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in A...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan 3;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Online ahead of print.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in A...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
