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Mutational profile evaluates metastatic capacity of Chinese colorectal cancer patients, revealed by whole-exome sequencing Genomics (IF 4.4) Pub Date : 2024-03-16 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
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Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection Genomics (IF 4.4) Pub Date : 2024-03-14 Huifen Zhang, Zhengwen Liu, Ruimei Geng, Min Ren, Lirui Cheng, Dan Liu, Caihong Jiang, Liuying Wen, Zhiliang Xiao, Aiguo Yang
The 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 infection were performed. A total of 33 genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response
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A comprehensive analysis integrating phenotypic assessment uncovering thornless cultivar lineages in Aralia elata Genomics (IF 4.4) Pub Date : 2024-03-12 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
is an woody plant species found in Northeastern Asia. To understand how genetic pools are distributed for clones, we were to analyze the population structure of cultivars and identify how these are correlated with thorn-related phenotype which determines the utility of . We found that the assembled genome of ‘Yeongchun’ shared major genomic compartments with the public genome assembled from the wild-type
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Physiology and transcriptome of Sapindus mukorossi seeds at different germination stages Genomics (IF 4.4) Pub Date : 2024-03-11 Jia Liu, Sumei Qiu, Tingting Xue, Yingdan Yuan
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
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Comprehensive multi-omics analysis and experimental verification reveal PFDN5 is a novel prognostic and therapeutic biomarker for gastric cancer Genomics (IF 4.4) Pub Date : 2024-03-04 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
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miR-210 promotes immune- and suppresses oocyte meiosis-related genes in the zebrafish ovarian cells Genomics (IF 4.4) Pub Date : 2024-03-02 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
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Differential mRNA profiles reveal the potential roles of genes involved in lactate stimulation in mouse macrophages Genomics (IF 4.4) Pub Date : 2024-03-02 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
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Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function Genomics (IF 4.4) Pub Date : 2024-03-01 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)
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From sequences to therapeutics: Using machine learning to predict chemically modified siRNA activity Genomics (IF 4.4) Pub Date : 2024-03-01 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
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The oral microbiome of newly diagnosed tuberculosis patients; a pilot study Genomics (IF 4.4) Pub Date : 2024-02-29 Muhammad Shahzad, Muhammad Saeed, Humaira Amin, Nada Binmadi, Zafar Ullah, Sana Bibi, Simon C. Andrew
Changes in oral microbiota composition (dysbiosis) have 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. This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment
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Screening of hair follicle telogen-associated circRNAs in sheep and construction of their ceRNA network Genomics (IF 4.4) Pub Date : 2024-02-29 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
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Arginine (315) is required for the PLIN2-CGI-58 interface and plays a functional role in regulating nascent LDs formation in bovine adipocytes Genomics (IF 4.4) Pub Date : 2024-02-29 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
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Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. ‘Cabernet Franc’) skin coloration Genomics (IF 4.4) Pub Date : 2024-02-23 Ao Li, Fengxia Wang, Tingting Ding, Ke Li, Huiping Liu, Qingtian Zhang, Qian Mu, Hongjun Zhao, Shouming Shan, Pengfei Wang
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. ‘Cabernet Franc’) skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green
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Discovery of a novel miRNA involved in the regulation of male infertility in zebrafish Genomics (IF 4.4) Pub Date : 2024-02-23 Wen Fu, Feng Liu, Yingying Wang, Ze Li, Wenpei Deng, Wenbin Liu, Jinhui Liu, Liangyue Peng, Yamei Xiao
Azoospermia and asthenospermia are common manifestations of male infertility, but it needs further studies to understand the intrinsic regulation mechanism. As a popular model organism, zebrafish is often used to assess reproductive complications. In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification
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Amino acid metabolism and MAP kinase signaling pathway play opposite roles in the regulation of ethanol production during fermentation of sugarcane molasses in budding yeast Genomics (IF 4.4) Pub Date : 2024-02-21 Linghuo Jiang, Yuzhi Shen, Yongqiang Jiang, Weiping Mei, Liudan Wei, Jinrong Feng, Chunyu Wei, Xiufan Liao, Yiping Mo, Lingxin Pan, Min Wei, Yiying Gu, Jiashi Zheng
Sugarcane molasses is one of the main raw materials for bioethanol production, and is the major biofuel-producing organism. In this study, a batch fermentation model has been used to examine ethanol titers of deletion mutants for all yeast nonessential genes in this yeast genome. A total of 42 genes are identified to be involved in ethanol production during fermentation of sugarcane molasses. Deletion
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WITHDRAWN: Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding Genomics (IF 4.4) Pub Date : 2024-02-21 Hui Li, Abdullah, Hongxia Yang, Hua Guo, Ye Yuan, Ibrar Ahmed, Guohui Li, Yu Wang, Yanxu Chang, Peter Poczai, Xiaoxuan Tian
After consultation with external experts, the authors acknowledged discrepancies in the classification of certain Berberis samples discussed in the article. Berberis is one of the most complex plant genera, and identifications are very hard, limited to only a handful of experts due to rampant hybridizations and other issues of reticulate evolution. This article has therefore been withdrawn at the request
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Clinical value of FAT1 mutations to indicate the immune response in colorectal cancer patients Genomics (IF 4.4) Pub Date : 2024-02-15 Wei Zhu, Lan Yang, Yu Gao, Yi Zhou, Yuqian Shi, Kaihua Liu, Ruoying Yu, Yang Shao, Wentong Zhang, Guosheng Wu, Junjun He
Immunotherapy is currently approved for CRC whose tumors have high MSI-H. To find additional biomarkers for immunotherapy in CRC, targeted sequencing was performed on tumor tissues from a discovery cohort of 161 CRC patients. Validation cohorts from the cBioPortal were also used for survival and tumor cell infiltration analyses. The -mutated CRC group often co-occurred with MSI events and displayed
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Integrated gene co-expression network analysis and experimental validation revealed potential targets of human urine extract CDA-II in treating chronic myeloid leukemia Genomics (IF 4.4) Pub Date : 2024-02-06 Lei Jiang, Haoyuan Hong, Shulin Xiang, Han Li, Jianyu Ji, Mei Lan, Bin Luo
Cell differentiation agent II (CDA-II) exhibits potent anti-proliferative and apoptosis-inducing properties against a variety of cancer cells. However, its mechanism of action in chronic myeloid leukemia (CML) remains unclear. Cell counting Kit 8 (CCK-8) and flow cytometry were used to investigate the effects of CDA-II on the biological characteristics of K562 cells. Gene (mRNA and lncRNA) expression
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The SOC1 gene plays an important role in regulating litchi flowering time Genomics (IF 4.4) Pub Date : 2024-02-01 Yuyu Shi, Shuwei Zhang, Qiulin Gui, Haowei Qing, Ming Li, Chenxin Yi, Huiqin Guo, Houbin Chen, Jiongzhi Xu, Feng Ding
Litchi ( Sonn.) is a valuable subtropical fruit tree with high-quality fruit. However, its economic benefits and sustainable development are restrained by a number of challenges. One major challenge is the lack of extremely early and late maturing high-quality varieties due to limited availability of varieties suitable for commercial cultivation and outdated breeding methods, resulting in an imbalanced
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Intestinal epithelial adaptations to vertical sleeve gastrectomy defined at single-cell resolution Genomics (IF 4.4) Pub Date : 2024-02-01 Kieran Koch-Laskowski, Ki-Suk Kim, Maigen Bethea, Kelly N.Z. Fuller, Darleen A. Sandoval, Praveen Sethupathy
The gut plays a key role in regulating metabolic health. Dietary factors disrupt intestinal physiology and contribute to obesity and diabetes, whereas bariatric procedures such as vertical sleeve gastrectomy (VSG) cause gut adaptations that induce robust metabolic improvements. However, our understanding of these adaptations at the cellular and molecular levels remains limited. In a validated murine
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Transcriptome-wide N6-methyladenosine (m6A) methylation profiling of long non-coding RNAs in ovarian endometriosis Genomics (IF 4.4) Pub Date : 2024-01-28 Hengwei Liu, Jiaxin Liang, Xin Dai, Yuan Peng, Wenqian Xiong, Ling Zhang, Xiaoou Li, Wenyuan Li, Keyi Liu, Siyi Bi, Xiwen Wang, Wei Zhang, Yi Liu
N6-methyladenosine (m6A) methylation is the most prevalent internal epigenetic posttranscriptional mechanism for regulating mammalian RNA. Despite recent advances in determining the biological functions of m6A methylation, its association with the pathology of ovarian endometriosis remains uncertain. Herein, we performed m6A transcriptome-wide profiling to identify key lncRNAs with m6A modification
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Identification of STAT3 as a biomarker for cellular senescence in liver fibrosis: A bioinformatics and experimental validation study Genomics (IF 4.4) Pub Date : 2024-01-28 Xue Pang, Shang Gao, Tao Liu, Feng Xia Xu, Chang Fan, Jia Fu Zhang, Hui Jiang
Cellular senescence is associated with a dysregulated inflammatory response, which is an important driver of the development of liver fibrosis (LF). This study aimed to investigate the effect of cellular senescence on LF and identify potential key biomarkers through bioinformatics analysis combined with validation experiments in vivo and in vitro. The Gene Expression Omnibus (GEO) database and GeneCards
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EPHB2 as a key mediator of glioma progression: Insights from microenvironmental receptor ligand-related prognostic gene signature Genomics (IF 4.4) Pub Date : 2024-01-28 Liming Tan, Jingyuan Zhou, Zhenyu Nie, Ding Li, Bing Wang
Malignant gliomas, characterized by pronounced heterogeneity, a complex microenvironment, and a propensity for relapse and drug resistaniguree, pose significant challenges in oncology. 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
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Stress adaptation in Tibetan cashmere goats is governed by inherent metabolic differences and manifested through variable cashmere phenotypes Genomics (IF 4.4) Pub Date : 2024-01-28 Bingru Zhao, Langda Suo, Yujiang Wu, Tong Chen, Hanikezi Tulafu, Qingwei Lu, Wenna Liu, Abdul Sammad, Cuiling Wu, Xuefeng Fu
Tibetan cashmere goats are not only served as a valuable model for studying adaptation to hypoxia and high-altitude conditions but also playing a pivotal role in bolstering local economies through the provision of premium quality cashmere yarn. In this study, we performed an integration and network analysis of metabolomic, transcriptomic and proteomic to elucidate the role of differentially expressed
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A comprehensive coding and microRNA transcriptome of vertebral bone in postlarvae and juveniles of Senegalese sole (Solea senegalensis) Genomics (IF 4.4) Pub Date : 2024-01-28 Carmen Bouza, Ana P. Losada, Carlos Fernández, José A. Álvarez-Dios, Ana Manuela de Azevedo, Andrés Barreiro, Damián Costas, María Isabel Quiroga, Paulino Martínez, Sonia Vázquez
Understanding vertebral bone development is essential to prevent skeletal malformations in farmed fish related to genetic and environmental factors. This is an important issue in , with special impact of spinal anomalies in postlarval and juvenile stages. Vertebral bone transcriptomics in farmed fish mainly comes from coding genes, and barely on miRNA expression. Here, we used RNA-seq of spinal samples
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Overexpression and nonsynonymous mutations of UDP-glycosyltransferases are potentially associated with pyrethroid resistance in Anopheles funestus Genomics (IF 4.4) Pub Date : 2024-01-23 Talal Al-Yazeedi, Abdullahi Muhammad, Helen Irving, Seung-Joon Ahn, Jack Hearn, Charles S. Wondji
UDP-glycosyltransferases (UGTs) enzymes are pivotal in insecticide resistance by transforming hydrophobic substrates into more hydrophilic forms for efficient cell elimination. This study provides the first comprehensive investigation of UGT genes, their evolution, and their association with pyrethroid resistance. We employed a genome-wide association study using pooled sequencing (GWAS-PoolSeq) and
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Identification and validation of CRLF1 and NRG1 as immune-related signatures in hypertrophic scar Genomics (IF 4.4) Pub Date : 2024-01-21 Boya Yu, Yalei Cao, Shiyi Li, Ruiqi Bai, Guiwen Zhou, Qiang Fu, Liming Liang, Weijie Gu, Lixia Zhang, Minliang Chen
Hypertrophic scar (HTS) is a prevalent chronic inflammatory skin disorder characterized by abnormal proliferation and extracellular matrix deposition and the precise mechanisms underlying HTS remain elusive. This study aimed to identify and validate potential immune-related genes associated with hypertrophic scar formation. Skin samples from normal ( = 12) and hypertrophic scar tissues (n = 12) were
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Effectiveness of a novel rat model of off-target PLA2R1 knockout to renal impairment Genomics (IF 4.4) Pub Date : 2024-01-16 Bo Huang, Zitong Zhang, Wendong Sui, Lu Zhao, Yinyin Li, Li Feng, Daihe Yang, Yun Zhou
Phospholipase A2 receptor 1 (PLA2R1) plays a crucial role in various diseases, including membranous nephropathy. However, the precise implications of PLA2R1 deficiency remain poorly understood. 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
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Unraveling a novel hippo-associated immunological prognostic signature: The contribution of SERPINE1 in facilitating colorectal cancer progression via the notch signaling pathway Genomics (IF 4.4) Pub Date : 2024-01-14 Xingyao Su, Xiaofeng Wang, Jie Lai, Shengxun Mao, Huizi Li
Accumulating evidence demonstrated that Hippo signaling pathway is implicated in tumor initiation and progression. However, there have been limited studies on establishing signatures utilizing genes related to the Hippo pathway to evaluate prognosis and clinical efficacy in colorectal cancer (CRC) patients. Hippo pathway-associated genes with prognostic significance were identified in the TCGA database
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A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq Genomics (IF 4.4) Pub Date : 2024-01-14 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, Genevieve Dall, Clare L. Scott, Zachery Moore, James R. Whittle, Saskia Freytag, Sarah A. Best, Anthony T. Papenfuss, Sam W.Z. Olechnowicz
Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of sample multiplexing reagents can impact data quality and experimental outcomes. 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
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HSCs-derived exosomes regulate the levels of inflammatory cytokines in HIBECs through miR-122-5p mediated p38 MAPK signaling pathway Genomics (IF 4.4) Pub Date : 2024-01-14 Yaqin Zhang, Xiangzhi Zhang, Ruofei Chen, Ziying Jiao, Bing Shen, Zongwen Shuai
PBC is an autoimmune-mediated liver disease, and intrahepatic biliary epithelial cells (IBECs) are the target cells of early damage. Previous studies found that miRNAs and inflammation is closely related to PBC. 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
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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 (IF 4.4) Pub Date : 2024-01-11 Jianhong Yu, Xiuping Wu, Jianchao Ni, Jianhai Zhang
Abstract not available
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Comparative proteomic analysis across the developmental stages of the Eimeria tenella Genomics (IF 4.4) Pub Date : 2024-01-10 Xueting Ma, Baohong Liu, Zhenxing Gong, Jing Wang, Zigang Qu, Jianping Cai
is the main pathogen responsible for coccidiosis in chickens. The life cycle of is, arguably, the least complex of all Coccidia, with only one host. However, it presents different developmental stages, either in the environment or in the host and either intracellular or extracellular. Its signaling and metabolic pathways change with its different developmental stages. Until now, little is known about
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Cell specification and functional interactions in the pig blastocyst inferred from single-cell transcriptomics and uterine fluids proteomics Genomics (IF 4.4) Pub Date : 2024-01-09 Adrien Dufour, Cyril Kurylo, Jan B. Stöckl, Denis Laloë, Yoann Bailly, Patrick Manceau, Frédéric Martins, Ali G. Turhan, Stéphane Ferchaud, Bertrand Pain, Thomas Fröhlich, Sylvain Foissac, Jérôme Artus, Hervé Acloque
The 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
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Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco Genomics (IF 4.4) Pub Date : 2024-01-09 Zhiliang Xiao, Zhengwen Liu, Huifen Zhang, Aiguo Yang, Lirui Cheng, Dan Liu, Caihong Jiang, Shizhou Yu, Zhixiao Yang, Min Ren, Ruimei Geng
Bacterial wilt (BW) caused by is a globally prevalent bacterial soil-borne disease. In this study, transcriptome sequencing were subjected to roots after infection with the in the resistant and susceptible tobacco variety. DEGs that responded to infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction
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Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs Genomics (IF 4.4) Pub Date : 2024-01-03 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
Nile 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
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Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity Genomics (IF 4.4) Pub Date : 2024-01-03 Heng Du, Chenguang Diao, Yue Zhuo, Xianrui Zheng, Zhengzheng Hu, Shiyu Lu, Wenjiao Jin, Lei Zhou, Jian-Feng Liu
There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the
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Identification of rat Vstm1 with conservative anti-inflammatory effect between rat and human homologs Genomics (IF 4.4) Pub Date : 2023-12-30 Yuzhe Hu, Yingzhe Sun, Ting Li, Wenling Han, Pingzhang Wang
Human VSTM1 (also known as SIRL1) is an inhibitory immune checkpoint receptor involved in leukocyte activation. Identification of the homologous genes in other species, such as mice and rats, will undoubtedly contribute to functional studies and clinical applications. Here, we successfully cloned the Vstm1 gene in rats, as supported by high-throughput sequencing data. However, Vstm1 is degenerated
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Multiple omics analysis reveals the regulation of SIRT5 on mitochondrial function and lipid metabolism during the differentiation of bovine preadipocytes Genomics (IF 4.4) Pub Date : 2023-12-27 Jieyun Hong, Sayed Haidar Abbas Raza, Hongming Ma, Weina Cao, Yuqing Chong, Jiao Wu, Dongmei Xi, Weidong Deng
Preadipocyte differentiation represents a critical stage in adipogenesis, with mitochondria playing an undeniable pivotal role. Given the intricate interplay between transcription and metabolic signaling during adipogenesis, the regulation of sirtuin 5 (SIRT5) on mitochondrial function and lipid metabolism was revealed via multiple omics analysis. The findings suggest that SIRT5 plays a crucial role
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Transcriptomic analysis of the longissimus thoracis muscle in pigs has identified molecular regulatory patterns associated with meat quality Genomics (IF 4.4) Pub Date : 2023-12-31 Qiangqiang Chen, Zhirong Chen, Qian Sun, Wei Zhang, Fen Wu, Guoliang Liu, Tenghao Wang, Zhen Wang, Qishan Wang, Jinzhi Zhang
Meat quality is a critical aspect of pig breeding. In addition to genetics, meat quality is also influenced by nutritional and environmental factors. In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular
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Necroptosis-related genes allow novel insights into predicting graft loss and diagnosing delayed graft function in renal transplantation Genomics (IF 4.4) Pub Date : 2023-12-30 Jiale Wang, Cuinan Lu, Jingwen Wang, Ying Wang, Huanjing Bi, Jin Zheng, Xiaoming Ding
Ischemia–reperfusion injury (IRI) is an inevitable pathophysiological phenomenon in kidney transplantation. Necroptosis is an undoubtedly important contributing mechanism in renal IRI. We first screened differentially expressed necroptosis-related genes (DENRGs) from public databases. Eight DENRGs were validated by independent datasets and verified by qRT-PCR in a rat IRI model. We used univariate
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Transcriptional and functional analysis of plasma exosomal microRNAs in acute viral myocarditis Genomics (IF 4.4) Pub Date : 2023-12-30 Qinchao Wu, Chao Huang, Ruolan Chen, Daisong Li, Guoliang Zhang, Haichu Yu, Yonghong Li, Bingxue Song, Ning Zhang, Bing Li, Xianming Chu
Aim To assess the differential expression profiles of exosome-derived microRNA (miRNA) and reveal their potential functions in patients with acute viral myocarditis (AVMC). Materials & methods Peripheral blood samples were collected from 9 patients diagnosed with AVMC and 9 healthy controls (HC) in the Affiliated Hospital of Qingdao University from July 2021 to September 2022. The exosomal miRNA expression
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Expression of accessory genes in Salmonella requires the presence of the Gre factors Genomics (IF 4.4) Pub Date : 2023-12-30 Tania Gaviria-Cantin, Llorenç Fernández-Coll, Andrés Felipe Vargas, Carlos Jonay Jiménez, Cristina Madrid, Carlos Balsalobre
Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription
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Identification of circular RNA-Dcaf6 as a therapeutic target for optic nerve crush-induced RGC degeneration Genomics (IF 4.4) Pub Date : 2023-12-30 Yuke Ji, Jing Li, Sha Liu, Junya Zhu, Jin Yao, Ke-ran Li, Biao Yan
The death of retinal ganglion cells (RGCs) can cause irreversible injury in visual function. Clarifying the mechanism of RGC degeneration is critical for the development of therapeutic strategies. Circular RNAs (circRNAs) are important regulators in many biological and pathological processes. Herein, we performed circRNA microarrays to identify dysregulated circRNAs following optic nerve crush (ONC)
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Genome-wide transcriptomic and biochemical profiling of major depressive disorder: Unravelling association with susceptibility, severity, and antidepressant response Genomics (IF 4.4) Pub Date : 2023-12-27 Priyanka Singh, Ankit Srivastava, Lini Philip, Simranpreet Kaur Ahuja, , Chitra Rawat, Rintu Kutum, Jyoti Yadav, Mamta Sood, Rakesh Kumar Chadda, Debasis Dash, Divya Vohora, Ritushree Kukreti
Identifying biomarkers for diagnosing Major Depressive Disorder (MDD), assessing its severity, and guiding treatment is crucial. We conducted whole genome transcriptomic study in North Indian population, and analyzed biochemical parameters. Our longitudinal study investigated gene-expression profiles from 72 drug-free MDD patients and 50 healthy controls(HCs) at baseline and 24 patients after 12-weeks
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Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs Genomics (IF 4.4) Pub Date : 2023-12-20 Weiwei Wang, Yan Sun, Pengfei Xu, Hao Liang, Yue Wang, Dadong Deng, Jianhua Cao, Mei Yu
The myometrium, composed of the inner circular muscle (CM) and outer longitudinal muscle (LM), is crucial in establishing and maintaining early pregnancy. However, the molecular mechanisms involved are not well understood. In this study, we identified the transcriptomic features of the CM and LM collected from the mesometrial (M) and anti-mesometrial (AM) sides of the pig uterus on day 18 of pregnancy
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A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae Genomics (IF 4.4) Pub Date : 2023-12-24 Jessica C. Winn, Simo N. Maduna, Aletta E. Bester-van der Merwe
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly
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A comprehensive exploration of the heterogeneity of immune cells in Han and Zang systemic lupus erythematosus patients via single-cell RNA sequencing Genomics (IF 4.4) Pub Date : 2023-12-20 Yongzhuo Wu, Chongjun Weng, Yali Zhou, Qinghuan Zhu, Yingying Liu, Junjuan Zheng, Binbin Yang, Wenting Cao, Limei Yuan, Meng Yang, Danqi Deng
Systemic Lupus Erythematosus (SLE) is an autoimmune sickness with unclear pathogenesis. The goal of this research was to reveal the heterogeneity of immune cells in SLE patients of Han and Zang nationality by single-cell RNA sequencing (scRNA-seq) and bioinformatics profiling. Methods A total of 94,102 peripheral blood mononuclear cells (PBMCs) from six volunteers with SLE (3 Zang, 3 Han) and six healthy
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Genome analysis of the mpox (formerly monkeypox) virus and characterization of core/variable regions Genomics (IF 4.4) Pub Date : 2023-12-16 Zehui Yu, Xiaoxia Zou, Zhaobin Deng, Mingde Zhao, Congwei Gu, Lu Fu, Wudian Xiao, Manli He, Lvqin He, Qian Yang, Sicheng Liang, Chengli Wen, Muhan Lü
Since smallpox was eradicated in 1980, the monkeypox virus (MPXV) has emerged as the most threatening orthopoxvirus in the world. In this study, we conducted a comprehensive analysis of the currently published complete genome sequences of the monkeypox virus. The core/variable regions were identified through core-pan analysis of MPXV. Besides single-nucleotide polymorphisms, our study also revealed
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CircPHKB decreases the sensitivity of liver cancer cells to sorafenib via miR-1234-3p/CYP2W1 axis Genomics (IF 4.4) Pub Date : 2023-12-17 Lingxi Chen, Hanxi Xiao, Yaran Wu, Dongjing Yan, Meihua Shan, Liangbo Sun, Xiaojing Yan, Dong Liu, Tao Li, Yang Zhang, Li Xiang, An Chen, Shuhui Li, Wei Xiang, Zhenhong Ni, Fengtian He, Mingzhen Yang, Jiqin Lian
Sorafenib is currently the first-line treatment for patients with advanced liver cancer, but its therapeutic efficacy declines significantly after a few months of treatment. Therefore, it is of great importance to investigate the regulatory mechanisms of sorafenib sensitivity in liver cancer cells. In this study, we provided initial evidence demonstrating that circPHKB, a novel circRNA markedly overexpressed
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Comprehensive genomic profiling of small bowel adenocarcinoma by tissue and plasma biopsy Genomics (IF 4.4) Pub Date : 2023-12-21 Dan Yu, Jianzheng Wang, Bo Zheng, Mingming Yuan, Dejian Gu, Rongrong Chen, Xiaobing Chen
Small bowel adenocarcinoma (SBA) is a rare and aggressive malignancy with limited treatment options and poor prognosis. The molecular landscape and immunological characteristics of SBA are poorly understood. Here, we performed comprehensive mutation profiling of tissue and plasma biopsies from 143 and 42 patients with SBA. Analysis showed that SBA had a distinct mutation spectrum from left- and right-sided
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Systems genetics and bioinformatics analyses using ESR1-correlated genes identify potential candidates underlying female bone development Genomics (IF 4.4) Pub Date : 2023-12-21 Akhilesh K. Bajpai, Qingqing Gu, Yan Jiao, Athena Starlard-Davenport, Weikuan Gu, Leigh Darryl Quarles, Zhousheng Xiao, Lu Lu
Estrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed
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Integrative analysis of transcriptome and proteome in primary Sjögren syndrome Genomics (IF 4.4) Pub Date : 2023-12-20 Xiaoting Qiu, Beijia Wang, Hongxiao Gong, Su Bu, Pingping Li, Runzhi Zhao, Mingde Li, Ling Zhu, Xingxing Huo
Objective Primary Sjögren's syndrome (pSS) is a intricate autoimmune disease mainly characterized of immune-mediated destruction of exocrine tissues, such as salivary and lacrimal glands, occurring dry mouth and eyes. Although some breakthroughs in understanding pSS have been uncovered, many questions remain about its pathogenesis, especially the internal relations between exocrine glands and secretions
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Pan-cancer analysis of the tumorigenic role of Fanconi anemia complementation group D2 (FANCD2) in human tumors Genomics (IF 4.4) Pub Date : 2023-12-15 Xiaozhou Xie, Yulong Zhao, Fengying Du, Baoshan Cai, Zhen Fang, Yuan Liu, Yaodong Sang, Chenghao Ma, Zhaodong Liu, Xinshuai Yu, Chi Zhang, Jiayu Jiang, Zi Gao, Yan Liu, Xiaoyan Lin, Haiyan Jing, Xiuming Zhong, Lei Cong, Honghai Dai, Dan Sha, Liang Shang
Monoubiquitination of FANCD2 is a central step in the activation of the Fanconi anemia (FA) pathway after DNA damage. Defects in the FA pathway centered around FANCD2 not only lead to genomic instability but also induce tumorigenesis. At present, few studies have investigated FANCD2 in tumors, and no pan-cancer research on FANCD2 has been conducted. We conducted a comprehensive analysis of the role
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Corrigendum to “Liver transcriptomic and proteomic analyses provide new insight into the pathogenesis of liver fibrosis in mice” [Genomics, Volume 115, Issue 6, November 2023, 110738] Genomics (IF 4.4) Pub Date : 2023-12-15 Lili Zhang, Qiumei Zhou, Jiafu Zhang, Kefeng Cao, Chang Fan, Sen Chen, Hui Jiang, Furong Wu
Abstract not available
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Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma Genomics (IF 4.4) Pub Date : 2023-12-17 Feiling Feng, Xianglei Xing, Guojuan Jiang, Xiaoya Xu, Bin Li, Zhizhen Li, Zhenghua Xie, Yue Wu, Xiaofang Li, Qingxiang Gao, Dongyu Liu, Yang Shen, Jianyang Ao, Dadong Zhang, Yanxin Chang, Xiaoqing Jiang
Cholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed
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A novel link between circPDE3B and ferroptosis in esophageal squamous cell carcinoma progression Genomics (IF 4.4) Pub Date : 2023-12-11 Pengli Zhou, Zhengyang Wu, Qinghui Zhang, Ling Wang, Wenguang Zhang, Xinwei Han
Aim To unravel whether ferroptosis involves with the actions by circPDE3B-mediated facilitation of esophageal squamous cell carcinoma (ESCC) progression. Methods Human ESCC tissues and cell lines were prepared for the evaluation of ferroptosis. Cellular iron, ROS, GSH, and MDA levels were measured to assess ferroptosis. Flow cytometry was employed to analyze apoptosis and cell cycle. Subcellular fractionation
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DOT1L decelerates the development of osteoporosis by inhibiting SRSF1 transcriptional activity via microRNA-181-mediated KAT2B inhibition Genomics (IF 4.4) Pub Date : 2023-12-10 Changsheng Wang, Rongsheng Chen, Xitian Zhu, Xiaobo Zhang, Nancheng Lian
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Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura Genomics (IF 4.4) Pub Date : 2023-12-07 Yaqing Chen, Yu Chen, Xiao-qiang Yu, Qili Feng, Xiaoyun Wang, Lin Liu
Testicular fusion of Spodoptera litura occures during metamorphosis, which benefits sperms development. Previous research identified involvement of ECM-integrin interaction pathways, MMPs in testicular fusion, but the regulatory mechanism remains unclear. RNA-seq was performed to analyze long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in testes, aiming to uncover potential regulatory mechanisms