journal
https://read.qxmd.com/read/38537809/discovery-and-characterization-of-sgrna-sequence-independent-dna-cleavage-from-crispr-cas9-in-mouse-embryos
#1
JOURNAL ARTICLE
Liyun Yang, Lijiao Chen, Yang Zheng, Li Deng, Raoxian Bai, Ting Zhang, Zhengbo Wang, Shangang Li
The CRISPR/Cas9 system can induce off-target effects in programmed gene editing, but there have been few reports on cleavage detection and their affection in embryo development. To study these events, sgRNAs with different off-target rates were designed and compared after micro-injected into mouse zygotes, and γH2AX was used for DNA cleavage sites analysis by immunostaining and CUT&Tag. Although the low off-target sgRNA were usually selected for production gene editing animals, γH2AX immunofluorescence indicated that there was a relative DSB peak at 15 h after Cas9 system injection, and the number of γH2AX foci at the peak was significantly higher in the low off-target sgRNA-injected group than in the control group...
March 25, 2024: Genomics
https://read.qxmd.com/read/38537808/study-on-the-interaction-protein-of-transcription-factor-smad3-based-on-turboid-proximity-labeling-technology
#2
JOURNAL ARTICLE
Biao Yan, Ting Zeng, Xiaoshan Liu, Yuanyuan Guo, Hongguang Chen, Shuang Guo, Wu Liu
TurboID is a highly efficient biotin-labelling enzyme, which can be used to explore a number of new intercalating proteins due to the very transient binding and catalytic functions of many proteins. TGF-β/Smad3 signaling pathway is involved in many diseases, especially in diabetic nephropathy and inflammation. In this paper, a stably cell line transfected with Smad3 were constructed by using lentiviral infection. To further investigate the function of TGF-β/Smad3, the protein labeling experiment was conducted to find the interacting protein with Smad3 gene...
March 25, 2024: Genomics
https://read.qxmd.com/read/38537807/hypoxic-environment-promotes-angiogenesis-and-bone-bridge-formation-by-activating-notch-rbpj-signaling-pathway-in-huvecs
#3
JOURNAL ARTICLE
Wendong Liu, Mincheng Zou, Mimi Chen, Zheng Zhang, Yunpeng Mao, Yuhao Yang, Ya Liu, Qin Shi, Xiaodong Wang, Fuyong Zhang
After epiphyseal fracture, the epiphyseal plate is prone to ischemia and hypoxia, leading to the formation of bone bridge and deformity. However, the exact mechanism controlling the bone bridge formation remains unclear. Notch/RBPJ signaling axis has been indicated to regulate angiogenesis and osteogenic differentiation. Our study aims to investigate the mechanism of bone bridge formation after epiphyseal plate injury, and to provide a theoretical basis for new therapeutic approaches to prevent the bone bridge formation...
March 25, 2024: Genomics
https://read.qxmd.com/read/38527595/boosting-edger-robust-by-dealing-with-missing-observations-and-gene-specific-outliers-in-rna-seq-profiles-and-its-application-to-explore-biomarker-genes-for-diagnosis-and-therapies-of-ovarian-cancer
#4
JOURNAL ARTICLE
Bandhan Sarker, Md Matiur Rahaman, Muhammad Habibulla Alamin, Md Ariful Islam, Md Nurul Haque Mollah
The edgeR (Robust) is a popular approach for identifying differentially expressed genes (DEGs) from RNA-Seq profiles. However, it shows weak performance against gene-specific outliers and is unable to handle missing observations. To address these issues, we proposed a pre-processing approach of RNA-Seq count data by combining the iLOO-based outlier detection and random forest-based missing imputation approach for boosting the performance of edgeR (Robust). Both simulation and real RNA-Seq count data analysis results showed that the proposed edgeR (Robust) outperformed the conventional edgeR (Robust)...
March 23, 2024: Genomics
https://read.qxmd.com/read/38521201/identification-of-candidate-genes-associated-with-peanut-pod-length-by-combined-analysis-of-qtl-seq-and-rna-seq
#5
JOURNAL ARTICLE
Zhenghao Lv, Guohu Lan, Baiyi Bai, Penghao Yu, Chuantang Wang, He Zhang, Chao Zhong, Xinhua Zhao, Haiqiu Yu
Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265...
March 21, 2024: Genomics
https://read.qxmd.com/read/38518899/effects-of-crispr-cas9-targeting-of-the-myo-inositol-biosynthesis-pathway-on-hyper-osmotic-tolerance-of-tilapia-cells
#6
JOURNAL ARTICLE
Jens Hamar, Avner Cnaani, Dietmar Kültz
Myo-inositol is an important compatible osmolyte in vertebrates. This osmolyte is produced by the myo-inositol biosynthesis (MIB) pathway composed of myo-inositol phosphate synthase and inositol monophosphatase . These enzymes are among the highest upregulated proteins in tissues and cell cultures from teleost fish exposed to hyperosmotic conditions indicating high importance of this pathway for tolerating this type of stress. CRISPR/Cas9 gene editing of tilapia cells produced knockout lines of MIB enzymes and control genes...
March 20, 2024: Genomics
https://read.qxmd.com/read/38518898/gcn2-eif2%C3%AE-signaling-pathway-negatively-regulates-the-growth-of-triploid-crucian-carp
#7
JOURNAL ARTICLE
Xuejing Wang, Fangyuan Peng, Shuli Yuan, Zhen Huang, Lingwei Tang, Song Chen, Jinhui Liu, Wen Fu, Liangyue Peng, Wenbin Liu, Yamei Xiao
GCN2-eIF2α signaling pathway plays crucial roles in cell growth,development, and protein synthesis. However, in polyploid fish, the function of this pathway is rarely understood. In this study, genes associated with the GCN2-eIF2α pathway (pkr, pek, gcn2, eif2α) are founded lower expression levels in the triploid crucian carp (3nCC) muscle compared to that of the red crucian carp (RCC). In muscle effect stage embryos of the 3nCC, the mRNA levels of this pathway genes are generally lower than those of RCC, excluding hri and fgf21...
March 20, 2024: Genomics
https://read.qxmd.com/read/38513875/a-comprehensive-comparison-of-molecular-and-phenotypic-profiles-between-hepatitis-b-virus-hbv-infected-and-non-hbv-infected-hepatocellular-carcinoma-by-multi-omics-analysis
#8
JOURNAL ARTICLE
Zijie Wu, Zehua Dong, Jiangti Luo, Weiwei Hu, Yue Tong, Xiangdong Gao, Wenbing Yao, Hong Tian, Xiaosheng Wang
Hepatitis B virus (HBV) infection is a major etiology of hepatocellular carcinoma (HCC). An interesting question is how different are the molecular and phenotypic profiles between HBV-infected (HBV+) and non-HBV-infected (HBV-) HCCs? Based on the publicly available multi-omics data for HCC, including bulk and single-cell data, and the data we collected and sequenced, we performed a comprehensive comparison of molecular and phenotypic features between HBV+ and HBV- HCCs. Our analysis showed that compared to HBV- HCCs, HBV+ HCCs had significantly better clinical outcomes, higher degree of genomic instability, higher enrichment of DNA repair and immune-related pathways, lower enrichment of stromal and oncogenic signaling pathways, and better response to immunotherapy...
March 19, 2024: Genomics
https://read.qxmd.com/read/38492821/mutational-profile-evaluates-metastatic-capacity-of-chinese-colorectal-cancer-patients-revealed-by-whole-exome-sequencing
#9
JOURNAL ARTICLE
Yian Yang, Jiawei Chen, Honghua Peng, Zhigang Xiao, Wei Xu, Mingchuan Zheng, Zheng Li, Peiguo Cao
Colorectal cancer (CRC) is the third most common cancer and the prevalence rate of CRC is increasing in the China. In this study, whole-exome sequencing (WES) was performed on primary tissues of 47 CRC Chinese patients including 22 metastatic and 25 non-metastatic patients. By comparison with data from western colorectal cancer patients in the Cancer Genome Atlas (TCGA), we identified a number of genes that are more likely to be mutated in Chinese colorectal cancer patients, such as MUC12, MUC12, MUC2, MUC4, HYDIN and KMT2C...
March 14, 2024: Genomics
https://read.qxmd.com/read/38492820/genome-wide-identification-of-the-tify-gene-family-in-tobacco-and-expression-analysis-in-response-to-ralstonia-solanacearum-infection
#10
JOURNAL ARTICLE
Huifen Zhang, Zhengwen Liu, Ruimei Geng, Min Ren, Lirui Cheng, Dan Liu, Caihong Jiang, Liuying Wen, Zhiliang Xiao, Aiguo Yang
The TIFY gene family plays an essential role in plant development and abiotic and biotic stress responses. In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions...
March 14, 2024: Genomics
https://read.qxmd.com/read/38485062/a-comprehensive-analysis-integrating-phenotypic-assessment-uncovering-thornless-cultivar-lineages-in-aralia-elata
#11
JOURNAL ARTICLE
Jaewook Kim, Yunmi Park, Suyun Moon, Ji-Ae Seo, Jisook Moon, Hyeonseon Park, Bae Young Choi, Sebastin Raveendar, Cheol-Woo Kim, Jong-Wook Chung, Donghwan Shim
Aralia elata is an Araliaceae woody plant species found in Northeastern Asia. To understand how genetic pools are distributed for A.elata clones, we were to analyze the population structure of A.elata cultivars and identify how these are correlated with thorn-related phenotype which determines the utility of A.elata. We found that the de novo assembled genome of 'Yeongchun' shared major genomic compartments with the public A.elata genome assembled from the wild-type from China. To identify the population structure of the 32 Korean and Japanese cultivars, we identified 44 SSR markers and revealed three main sub-clusters using ΔK analysis with one isolated cultivar...
March 12, 2024: Genomics
https://read.qxmd.com/read/38471577/physiology-and-transcriptome-of-sapindus-mukorossi-seeds-at-different-germination-stages
#12
JOURNAL ARTICLE
Jia Liu, Sumei Qiu, Tingting Xue, Yingdan Yuan
Sapindus mukorossi has a wide distribution range, high application value, and broad developmental potential. Previous studies have mostly focused on the medicinal and economic value of soapberry; however, few studies have been conducted on its seed germination. This study measured the physiological indicators and hormone content of soapberry seeds at different germination stages and preliminarily determined that abscisic acid (ABA) and indole- 3-acetic acid (IAA) are the key hormones that affect the germination of soapberry seeds...
March 10, 2024: Genomics
https://read.qxmd.com/read/38447684/comprehensive-multi-omics-analysis-and-experimental-verification-reveal-pfdn5-is-a-novel-prognostic-and-therapeutic-biomarker-for-gastric-cancer
#13
JOURNAL ARTICLE
Yanfei Shao, Galiya Yesseyeva, Yihao Zhi, Jiajie Zhou, Jiasheng Zong, Xueliang Zhou, Xiaodong Fan, Shuchun Li, Ling Huang, Sen Zhang, Feng Dong, Xiao Yang, Minhua Zheng, Jing Sun, Junjun Ma
Prefoldin Subunit 5 (PFDN5) plays a critical role as a member of the prefoldins (PFDNs) in maintaining a finely tuned equilibrium between protein production and degradation. However, there has been no comprehensive analysis specifically focused on PFDN5 thus far. Here, a comprehensive multi-omics (transcriptomics, genomics, and proteomics) analysis, systematic molecular biology experiments (in vitro and in vivo), transcriptome sequencing and PCR Array were performed for identifying the value of PFDN5 in pan-cancer, especially in Gastric Cancer (GC)...
March 4, 2024: Genomics
https://read.qxmd.com/read/38437972/mir-210-promotes-immune-and-suppresses-oocyte-meiosis-related-genes-in-the-zebrafish-ovarian-cells
#14
JOURNAL ARTICLE
Tosca A van Gelderen, Laia Ribas
microRNA-210 (miRNA), a well-documented miRNA, has been implicated in a myriad of biological processes, including responses to hypoxia, angiogenesis, cell proliferation, and male infertility in humans. However, a comprehensive understanding of its functions in fish requires further investigation. This study pursued to elucidate the downstream effect of dre-miR-210-5p on primary ovarian cell culture in zebrafish (Danio rerio), an animal model. A protocol was settled down by incubations with either an miR-210 mimic or a scrambled miRNA in the isolated ovaries...
March 2, 2024: Genomics
https://read.qxmd.com/read/38432499/differential-mrna-profiles-reveal-the-potential-roles-of-genes-involved-in-lactate-stimulation-in-mouse-macrophages
#15
JOURNAL ARTICLE
Limian Cao, Chencheng Feng, Haoming Ye, Heng Zhao, Zhimin Shi, Jun Li, Yayun Wu, Ruojue Wang, Qianru Li, Jinquan Liang, Qiang Ji, Hao Gu, Min Shao
Lactate is a glycolysis end product, and its levels are markedly associated with disease severity, morbidity, and mortality in sepsis. It modulates key functions of immune cells, including macrophages. In this investigation, transcriptomic analysis was performed using lactic acid, sodium lactate, and hydrochloric acid-stimulated mouse bone marrow-derived macrophages (iBMDM), respectively, to identify lactate-associated signaling pathways. After 24 h of stimulation, 896 differentially expressed genes (DEG) indicated were up-regulation, whereas 792 were down-regulated in the lactic acid group, in the sodium lactate group, 128 DEG were up-regulated, and 41 were down-regulated, and in the hydrochloric acid group, 499 DEG were up-regulated, and 285 were down-regulated...
March 1, 2024: Genomics
https://read.qxmd.com/read/38432498/integrated-analysis-of-lncrna-mirna-and-mrna-expression-profiles-reveals-regulatory-pathways-associated-with-pig-testis-function
#16
JOURNAL ARTICLE
Pei Wang, Zhipeng Liu, Xia Zhang, Hailong Huo, Lina Wang, Hongmei Dai, Fuhua Yang, Guiying Zhao, Jinlong Huo
Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds...
March 1, 2024: Genomics
https://read.qxmd.com/read/38431033/from-sequences-to-therapeutics-using-machine-learning-to-predict-chemically-modified-sirna-activity
#17
JOURNAL ARTICLE
Dominic D Martinelli
Small interfering RNAs (siRNAs) exemplify the promise of genetic medicine in the discovery of novel therapeutic modalities. Their ability to selectively suppress gene expression makes them ideal candidates for the development of oligonucleotide pharmaceuticals. Recent advancements in machine learning (ML) have facilitated the design of unmodified siRNA and efficacy prediction. However, a model trained to predict the silencing activity of siRNAs with diverse chemical modification patterns is yet to be published despite the importance of such modifications in designing siRNAs with the potential to reach the level of clinical use...
February 29, 2024: Genomics
https://read.qxmd.com/read/38431032/screening-of-hair-follicle-telogen-associated-circrnas-in-sheep-and-construction-of-their-cerna-network
#18
JOURNAL ARTICLE
Haoran Sun, Xiaochun Yuan, Ningyue Zhang, Zhongze Luo, Liang Zhang, Xinhai Li
Sheep breeds with hair-shedding traits have many advantages over non-shedding sheep breeds, not only because of reduced shearing labor and feeding management costs but also because it reduces in vitro parasites and improves adaptability to summer heat stress. The wool of Dorper sheep naturally sheds in spring due to the periodic growth of hair follicles. CircRNAs primarily regulate the morphogenesis of hair follicles through the ceRNA mechanism. In this study, five 2-year-old Dorper ewes with extreme hair-shedding phenotype (S) and three Dorper ewes with non-shedding (N) phenotype were selected for subsequent analyses...
February 29, 2024: Genomics
https://read.qxmd.com/read/38431031/arginine-315-is-required-for-the-plin2-cgi-58-interface-and-plays-a-functional-role-in-regulating-nascent-lds-formation-in-bovine-adipocytes
#19
JOURNAL ARTICLE
Peiwei Li, Chugang Mei, Sayed Haidar Abbas Raza, Gong Cheng, Yue Ning, Le Zhang, Linsen Zan
Perilipin-2 (PLIN2) can anchor to lipid droplets (LDs) and play a crucial role in regulating nascent LDs formation. Bimolecular fluorescence complementation (BiFC) and flow cytometry were examined to verify the PLIN2-CGI-58 interaction efficiency in bovine adipocytes. GST-Pulldown assay was used to detect the key site arginine315 function in PLIN2-CGI-58 interaction. Experiments were also examined to research these mutations function of PLIN2 in LDs formation during adipocytes differentiation, LDs were measured after staining by BODIPY, lipogenesis-related genes were also detected...
February 29, 2024: Genomics
https://read.qxmd.com/read/38431030/the-oral-microbiome-of-newly-diagnosed-tuberculosis-patients-a-pilot-study
#20
JOURNAL ARTICLE
Muhammad Shahzad, Muhammad Saeed, Humaira Amin, Nada Binmadi, Zafar Ullah, Sana Bibi, Simon C Andrew
BACKGROUND: Changes in oral microbiota composition (dysbiosis) has long been known to play a key role in the pathogenesis of oral and systemic diseases including respiratory diseases. However, till now, no study has assessed changes in oral microbiota following tuberculosis (TB) infection in humans. AIMS: This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment naïve, TB patients. METHODS: Oral swab samples were collected from newly diagnosed TB patients (n = 20) and age, gender and ethnicity matched healthy controls (n = 10)...
February 29, 2024: Genomics
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