keyword
https://read.qxmd.com/read/38533916/exosomes-secreted-from-induced-pluripotent-stem-cell-ameliorate-the-lipopolysaccharide-induced-neuroinflammatory-response-via-lncrna-0949
#21
JOURNAL ARTICLE
Lixiu Ma, Ce Xiao, Zhizhe Zhang, Yi-An Zhan
PURPOSE: To study the effect of exosomes derived from the induced pluripotent stem cells (iPSCs) in the neuroinflammatory response of microglia caused by lipopolysaccharide (LPS) and reveal the potential underlying mechanism. METHODS: A permanent microglia cell line HMO6 was activated by LPS. The features of exosomes were analyzed by nano flow cytometry, Western blot and transmission electron microscope. The RNA-seq was used to analyze the difference of noncoding RNA profiles between iPSC-Exos and HMO6 derived exosomes and proved that long no-coding RNA (lncRNA-0949) was highly expressed in the iPSC-Exos...
March 2024: Immunity, Inflammation and Disease
https://read.qxmd.com/read/38533548/integrating-the-analysis-of-human-biopsies-using-post-translational-modifications-proteomics
#22
REVIEW
Sonali Bhardwaj, Mitchell Bulluss, Ana D'Aubeterre, Afshin Derakhshani, Regan Penner, MaryAnn Mahajan, Vinit B Mahajan, Antoine Dufour
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases...
April 2024: Protein Science
https://read.qxmd.com/read/38533111/a-transcriptomic-dataset-for-investigating-the-arabidopsis-unfolded-protein-response-under-chronic-proteotoxic-endoplasmic-reticulum-stress
#23
JOURNAL ARTICLE
Amélie Ducloy, Marianne Azzopardi, Caroline Ivsic, Gwendal Cueff, Delphine Sourdeval, Delphine Charif, Jean-Luc Cacas
The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR ( INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B ) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s...
April 2024: Data in Brief
https://read.qxmd.com/read/38533068/prognostic-prediction-using-a-gene-signature-developed-based-on-exhausted-t-cells-for-liver-cancer-patients
#24
JOURNAL ARTICLE
Yu Zhou, Wanrui Wu, Wei Cai, Dong Zhang, Weiwei Zhang, Yunling Luo, Fujing Cai, Zhenjing Shi
BACKGROUND: Liver hepatocellular carcinoma (LIHC) is a solid primary malignancy with poor prognosis. This study discovered key prognostic genes based on T cell exhaustion and used them to develop a prognostic prediction model for LIHC. METHODS: SingleR's annotations combined with Seurat was used to automatically annotate the single-cell clustering results of the LIHC dataset GSE166635 downloaded from the Gene Expression Omnibus (GEO) database and to identify clusters related to exhausted T cells...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38533057/lrrc59-promotes-the-progression-of-oral-squamous-cell-carcinoma-by-interacting-with-srp-pathway-components-and-enhancing-the-secretion-of-ckap4-containing-exosomes
#25
JOURNAL ARTICLE
Qijun Sun, Lili Jin, Shunli Dong, Ling Zhang
BACKGROUND: As a ribosome receptor, LRRC59 was thought to regulate mRNA translation on the ER membrane. Evidence suggests that LRRC59 is overexpressed in a number of human malignancies and is associated with poor prognoses, but its primary biological function in the development of oral squamous cell carcinoma (OSCC) remains obscure. OBJECTIVE: The purpose of this study is to investigate at the expression changes and functional role of LRRC59 in OSCC. METHODS: LRRC59 gene expression and correlation with prognosis of OSCC patients were first examined using the data from The Cancer Genome Atlas (TCGA) databases...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38533040/comprehensive-single-cell-analysis-reveals-heterogeneity-of-fibroblast-subpopulations-in-ovarian-cancer-tissue-microenvironment
#26
JOURNAL ARTICLE
Bo Ding, Zheng Ye, Han Yin, Xin-Yi Hong, Song-Wei Feng, Jing-Yun Xu, Yang Shen
BACKGROUND: Ovarian cancer, as a highly malignant tumor, features the critical involvement of tumor-associated fibroblasts in the ovarian cancer tissue microenvironment. However, due to the apparent heterogeneity within fibroblast subpopulations, the specific functions of these subpopulations in the ovarian cancer tissue microenvironment remain insufficiently elucidated. METHODS: In this study, we integrated single-cell sequencing data from 32 ovarian cancer samples derived from four distinct cohorts and 3226 bulk RNA-seq data from GEO and TCGA-OV cohorts...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38532459/unveiling-the-functional-heterogeneity-of-cytokine-primed-human-umbilical-cord-mesenchymal-stem-cells-through-single-cell-rna-sequencing
#27
JOURNAL ARTICLE
Zhiwei Hu, Duanduan Li, Shiduo Wu, Ke Pei, Zeqin Fu, Yulin Yang, Yinfu Huang, Jian Yang, Chuntao Liu, Junyuan Hu, Cheguo Cai, Yan Liao
BACKGROUND: Mesenchymal stem cells (MSCs) hold immense promise for use in immunomodulation and regenerative medicine. However, their inherent heterogeneity makes it difficult to achieve optimal therapeutic outcomes for a specific clinical disease. Primed MSCs containing a certain cytokine can enhance their particular functions, thereby increasing their therapeutic potential for related diseases. Therefore, understanding the characteristic changes and underlying mechanisms of MSCs primed by various cytokines is highly important...
March 26, 2024: Cell & Bioscience
https://read.qxmd.com/read/38532383/single-cell-rna-sequencing-reveals-the-immune-features-and-viral-tropism-in-the-central-nervous-system-of-mice-infected-with-japanese-encephalitis-virus
#28
JOURNAL ARTICLE
Ling'en Yang, Junyao Xiong, Yixin Liu, Yinguang Liu, Xugang Wang, Youhui Si, Bibo Zhu, Huanchun Chen, Shengbo Cao, Jing Ye
Japanese encephalitis virus (JEV) is a neurotropic pathogen that causes lethal encephalitis. The high susceptibility and massive proliferation of JEV in neurons lead to extensive neuronal damage and inflammation within the central nervous system. Despite extensive research on JEV pathogenesis, the effect of JEV on the cellular composition and viral tropism towards distinct neuronal subtypes in the brain is still not well comprehended. To address these issues, we performed single-cell RNA sequencing (scRNA-seq) on cells isolated from the JEV-highly infected regions of mouse brain...
March 26, 2024: Journal of Neuroinflammation
https://read.qxmd.com/read/38532351/the-activation-of-iron-deficiency-responses-of-grapevine-rootstocks-is-dependent-to-the-availability-of-the-nitrogen-forms
#29
JOURNAL ARTICLE
Sarhan Khalil, Rebeka Strah, Arianna Lodovici, Petr Vojta, Federica De Berardinis, Jörg Ziegler, Maruša Pompe Novak, Laura Zanin, Nicola Tomasi, Astrid Forneck, Michaela Griesser
BACKGROUND: In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake...
March 26, 2024: BMC Plant Biology
https://read.qxmd.com/read/38532318/whole-transcriptomic-analysis-reveals-overexpression-of-salivary-gland-and-cuticular-proteins-genes-in-insecticide-resistant-anopheles-arabiensis-from-western-kenya
#30
JOURNAL ARTICLE
Diana Omoke, Lucy Mackenzie Impoinvil, Dieunel Derilus, Stephen Okeyo, Helga Saizonou, Nicola Mulder, Nsa Dada, Audrey Lenhart, Luc Djogbénou, Eric Ochomo
BACKGROUND: Effective vector control is key to malaria prevention. However, this is now compromised by increased insecticide resistance due to continued reliance on insecticide-based control interventions. In Kenya, we have observed heterogenous resistance to pyrethroids and organophosphates in Anopheles arabiensis which is one of the most widespread malaria vectors in the country. We investigated the gene expression profiles of insecticide resistant An. arabiensis populations from Migori and Siaya counties in Western Kenya using RNA-Sequencing...
March 27, 2024: BMC Genomics
https://read.qxmd.com/read/38532230/enhancing-oocyte-quality-in-aging-mice-insights-from-mesenchymal-stem-cell-therapy-and-foxo3a-signaling-pathway-activation
#31
JOURNAL ARTICLE
Lingjuan Wang, Yang Liu, Yinhua Song, Qiaojuan Mei, Hongbei Mou, Jiachen Wu, Xinyu Tang, Jihui Ai, Kezhen Li, Houxiu Xiao, Xiaotao Han, Liqun Lv, Huaibiao Li, Ling Zhang, Wenpei Xiang
Ovarian aging reduced the quality of oocytes, resulting in age-related female infertility. It is reported that mesenchymal stem cells (MSCs) therapy can improve age-related ovarian function decline and the success rate of in vitro maturation (IVM) in assisted reproductive therapy. In order to investigate the effectiveness and mechanisms of MSCs to enhance oocyte quality of cumulus oocyte complexes (COCs) in advanced age, this study focus on the respective functional improvement of oocytes and granulosa cells (GCs) from aging mice and further to explore and verify the possible mechanisms...
March 26, 2024: Reproductive Sciences
https://read.qxmd.com/read/38531951/interrogation-of-the-human-cortical-peptidome-uncovers-cell-type-specific-signatures-of-cognitive-resilience-against-alzheimer-s-disease
#32
JOURNAL ARTICLE
G R Morgan, B C Carlyle
Alzheimer's disease (AD) is characterised by age-related cognitive decline. Brain accumulation of amyloid-β plaques and tau tangles is required for a neuropathological AD diagnosis, yet up to one-third of AD-pathology positive community-dwelling elderly adults experience no symptoms of cognitive decline during life. Conversely, some exhibit chronic cognitive impairment in absence of measurable neuropathology, prompting interest into cognitive resilience-retained cognition despite significant neuropathology-and cognitive frailty-impaired cognition despite low neuropathology...
March 26, 2024: Scientific Reports
https://read.qxmd.com/read/38531795/unlocking-the-therapeutic-potential-of-lncrna-blacat1-in-hypopharynx-squamous-cell-carcinoma
#33
JOURNAL ARTICLE
Fan-Li Liu, Zhan-Cheng Zhang, Sheng-Li Zhou, Xu-Liang Liu, Wei Xu
BACKGROUND: Identifying the key molecular targets in hypopharynx squamous cell carcinoma (HSCC) is crucial for understanding this prevalent and highly fatal type of head and neck tumor. The study aims to enhance comprehension of the HSCC process by accurately identifying these key molecular targets. MATERIALS AND METHODS: In this study, we examined 47 clinical tissue samples from individuals diagnosed with HSCC using RNA-seq high-throughput assay. Quantitative real-time PCR (RT-PCR) was used to compare long non-coding RNA (lncRNA) bladder cancer-associated transcript 1 ( BLACAT1 ) expression in HSCC tissues versus adjacent non-tumor tissues...
March 2024: Discovery Medicine
https://read.qxmd.com/read/38531647/chemical-manipulation-of-m-1-a-mediates-its-detection-in-human-trna
#34
JOURNAL ARTICLE
Kinga Pajdzik, Ruitu Lyu, Xiaoyang Dou, Chang Ye, Li-Sheng Zhang, Qing Dai, Chuan He
N 1 -methyl adenosine (m1 A) is a wide-spread RNA modification present in tRNA, rRNA and mRNA. m1 A modification sites in tRNAs are evolutionary conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1 A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1 A can notably modulate RNA structure. It also blocks Watson-Crick-Franklin base pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high throughput sequencing methods have been developed to sequence m1 A...
March 26, 2024: RNA
https://read.qxmd.com/read/38531607/a-roadmap-for-selecting-and-utilizing-optimal-features-in-scrna-sequencing-data-analysis-for-stem-cell-research-a-comprehensive-review
#35
REVIEW
Maath Alani, Hamza Altarturih, Selin Pars, Bahaa Al-Mhanawi, Ernst J Wolvetang, Mohammed R Shaker
Stem cells and the cells they produce are unique because they vary from one cell to another. Traditional methods of studying cells often overlook these differences. However, the development of new technologies for studying individual cells has greatly changed biological research in recent years. Among these innovations, single-cell RNA sequencing (scRNA-seq) stands out. This technique allows scientists to examine the activity of genes in each cell, across thousands or even millions of cells. This makes it possible to understand the diversity of cells, identify new types of cells, and see how cells differ across different tissues, individuals, species, times, and conditions...
March 27, 2024: International Journal of Stem Cells
https://read.qxmd.com/read/38531201/cirp-increases-foxp3-regulatory-t-cells-and-inhibits-development-of-th17-cells-by-enhancing-tlr4-il-2-signaling-in-the-late-phase-of-sepsis
#36
JOURNAL ARTICLE
Zongsheng Wu, Xu Liu, Wei Huang, Jing Chen, Songli Li, Jie Chao, Jianfeng Xie, Ling Liu, Yi Yang, Xiaojing Wu, Haibo Qiu
BACKGROUND: T helper (Th) cell imbalances have been associated with the pathophysiology of sepsis, including the Th1/Th2 and Th17/T regulatory cells (Treg) paradigms. Cold-inducible RNA-binding protein (CIRP), a novel damage-associated molecular pattern (DAMP) was reported that could induce T cell activation, and skew CD4+ T cells towards a Th1 profile. However, the effect and underlying mechanisms of CIRP on Th17/Treg differentiation in sepsis still remains unknown. METHODS: A prospective exploratory study including patients with sepsis was conducted...
March 25, 2024: International Immunopharmacology
https://read.qxmd.com/read/38530845/differential-carbonic-anhydrase-activities-control-ebv-induced-b-cell-transformation-and-lytic-cycle-reactivation
#37
JOURNAL ARTICLE
Samaresh Malik, Joyanta Biswas, Purandar Sarkar, Subhadeep Nag, Chandrima Gain, Shatadru Ghosh Roy, Bireswar Bhattacharya, Dipanjan Ghosh, Abhik Saha
Epstein-Barr virus (EBV) contributes to ~1% of all human cancers including several B-cell neoplasms. A characteristic feature of EBV life cycle is its ability to transform metabolically quiescent B-lymphocytes into hyperproliferating B-cell blasts with the establishment of viral latency, while intermittent lytic cycle induction is necessary for the production of progeny virus. Our RNA-Seq analyses of both latently infected naïve B-lymphocytes and transformed B-lymphocytes upon lytic cycle replication indicate a contrasting expression pattern of a membrane-associated carbonic anhydrase isoform CA9, an essential component for maintaining cell acid-base homeostasis...
March 26, 2024: PLoS Pathogens
https://read.qxmd.com/read/38530808/macrophages-suppress-cardiac-reprogramming-of-fibroblasts-in-vivo-via-ifn-mediated-intercellular-self-stimulating-circuit
#38
JOURNAL ARTICLE
Hao Wang, Junbo Yang, Yihong Cai, Yang Zhao
Direct conversion of cardiac fibroblasts (CFs) to cardiomyocytes (CMs) in vivo to regenerate heart tissue is an attractive approach. After myocardial infarction (MI), heart repair proceeds with an inflammation stage initiated by monocytes infiltration of the infarct zone establishing an immune microenvironment. However, whether and how the MI microenvironment influences the reprogramming of CFs remains unclear. Here, we found that in comparison with cardiac fibroblasts (CFs) cultured in vitro, CFs that transplanted into infarct region of MI mouse models resisted to cardiac reprogramming...
March 26, 2024: Protein & Cell
https://read.qxmd.com/read/38530577/bajitianwan-formula-extract-ameliorates-bone-loss-induced-by-iron-overload-via-activating-rage-pi3k-akt-pathway-based-on-network-pharmacology-and-transcriptomic-analysis
#39
JOURNAL ARTICLE
Weifan Xu, Tao Jiang, Luying Ding, Yiping Jiang, Lichao Zhang, Tianshuang Xia, Hailiang Xin
Osteoporosis (OP) is closely related to iron overload. Bajitianwan (BJTW) is a traditional Chinese medicine formulation used for treating senile diseases such as dementia and osteoporosis. Modern pharmacological researches have found that BJTW has beneficial effect on bone loss and memory impairment in aging rats. This paper aimed to explore the role and mechanism of BJTW in ameliorating iron overload-induced bone loss. Furthermore, BJTW effectively improved the bone micro-structure of the femur in mice, and altered bone metabolism biomarkers alkaline phosphatase (ALP) and osteocalcin (OCN) in serum, as well as oxidative indexes superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR) glutathione (GSH) and malondialdehyde (MDA) in liver...
March 26, 2024: Journal of Natural Medicines
https://read.qxmd.com/read/38530488/isolation-identification-and-transcriptome-analysis-of-triadimefon-degrading-strain-enterobacter-hormaechei-ty18
#40
JOURNAL ARTICLE
Yan Wang, Qi Guan, Wenhui Jiao, Jiangbo Li, Rui Zhao, Xiqian Zhang, Weixin Fan, Chunwei Wang
Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon...
March 26, 2024: Biodegradation
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