Current Genomics最新文献_第8页

Circular RNA Translation in Cardiovascular Diseases 心血管疾病中的环状RNA翻译

4区生物学

Current Genomics Pub Date : 2023-03-01 DOI: 10.2174/1389202924666230911121358

Lijun Wang, Xinxin Cui, Fei Jiang, Yuxue Hu, Wensi Wan, Guoping Li, Yanjuan Lin, Junjie Xiao

引用次数: 0

Mitochondrial Lipid Metabolism Genes as Diagnostic and Prognostic Indicators in Hepatocellular Carcinoma 线粒体脂质代谢基因作为肝细胞癌的诊断和预后指标

4区生物学

Current Genomics Pub Date : 2023-03-01 DOI: 10.2174/1389202924666230914110649

Xuejing Li, Ying Tan, Bihan Liu, Houtian Guo, Yongjian Zhou, Jianhui Yuan, Feng Wang

{"title":"Mitochondrial Lipid Metabolism Genes as Diagnostic and Prognostic Indicators in Hepatocellular Carcinoma","authors":"Xuejing Li, Ying Tan, Bihan Liu, Houtian Guo, Yongjian Zhou, Jianhui Yuan, Feng Wang","doi":"10.2174/1389202924666230914110649","DOIUrl":"https://doi.org/10.2174/1389202924666230914110649","url":null,"abstract":"Background: Due to the heterogeneity of Hepatocellular carcinoma (HCC), there is an urgent need for reliable diagnosis and prognosis. Mitochondria-mediated abnormal lipid metabolism affects the occurrence and progression of HCC. Objective: This study aims to investigate the potential of mitochondrial lipid metabolism (MTLM) genes as diagnostic and independent prognostic biomarkers for HCC. Methods: MTLM genes were screened from the Gene Expression Omnibus (GEO) and Gene Set Enrichment Analysis (GSEA) databases, followed by an evaluation of their diagnostic values in both The Cancer Genome Atlas Program (TCGA) and the Affiliated Cancer Hospital of Guangxi Medical University (GXMU) cohort. The TCGA dataset was utilized to construct a gene signature and investigate the prognostic significance, immune infiltration, and copy number alterations. The validity of the prognostic signature was confirmed through GEO, International Cancer Genome Consortium (ICGC), and GXMU cohorts. Results: The diagnostic receiver operating characteristic (ROC) curve revealed that eight MTLM genes have excellent diagnostic of HCC. A prognostic signature comprising 5 MTLM genes with robust predictive value was constructed using the lasso regression algorithm based on TCGA data. The results of the Stepwise regression model showed that the combination of signature and routine clinical parameters had a higher area under the curve (AUC) compared to a single risk score. Further, a nomogram was constructed to predict the survival probability of HCC, and the calibration curves demonstrated a perfect predictive ability. Finally, the risk score also unveiled the different immune and mutation statuses between the two different risk groups. Conclusion: MTLT-related genes may serve as diagnostic and prognostic biomarkers for HCC as well as novel therapeutic targets, which may be beneficial for facilitating further understanding the molecular pathogenesis and providing potential therapeutic strategies for HCC.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135532118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ACKNOWLEDGEMENTS TO REVIEWERS. 向评审员致谢。

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/138920292306230209163617

引用次数: 0

Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes. 根据年龄，性别和纵向变化的DNA甲基化模式的综合方法

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/1389202924666221207100513

Jeong-An Gim

{"title":"Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes.","authors":"Jeong-An Gim","doi":"10.2174/1389202924666221207100513","DOIUrl":"10.2174/1389202924666221207100513","url":null,"abstract":"Background In humans, age-related DNA methylation has been studied in blood, tissues, buccal swabs, and fibroblasts, and changes in DNA methylation patterns according to age and sex have been detected. To date, approximately 137,000 samples have been analyzed from 14,000 studies, and the information has been uploaded to the NCBI GEO database. Methods A correlation between age and methylation level and longitudinal changes in methylation levels was revealed in both sexes. Here, 20 public datasets derived from whole blood were analyzed using the Illumina BeadChip. Batch effects with respect to the time differences were correlated. The overall change in the pattern was provided as the inverse of the coefficient of variation (COV). Results Of the 20 datasets, nine were from a longitudinal study. All data had age and sex as common variables. Comprehensive details of age-, sex-, and longitudinal change-based DNA methylation levels in the whole blood sample were elucidated in this study. ELOVL2 and FHL2 showed the maximum correlation between age and DNA methylation. The methylation patterns of genes related to mental health differed according to age. Age-correlated genes have been associated with malformations (anteverted nostril, craniofacial abnormalities, and depressed nasal bridge) and drug addiction (drug habituation and smoking). Conclusion Based on 20 public DNA methylation datasets, methylation levels according to age and longitudinal changes by sex were identified and visualized using an integrated approach. The results highlight the molecular mechanisms underlying the association of sex and biological age with changes in DNA methylation, and the importance of optimal genomic information management.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10173416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45797537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome. 新的短RNA基序可能与严重急性呼吸系统综合征冠状病毒2型基因组相关

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/1389202924666230202152351

Miguel Angel Fuertes, Carlos Alonso

{"title":"New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome.","authors":"Miguel Angel Fuertes, Carlos Alonso","doi":"10.2174/1389202924666230202152351","DOIUrl":"10.2174/1389202924666230202152351","url":null,"abstract":"Background: The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention.Objective: The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome.Methods: A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other.Results: We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions.Conclusion: Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10173420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43743054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. 禾本科植物叶绿体基因组测序：近十年的跨越

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/1389202924666221201140603

Yiyu Hu, Yanqing Sun, Qian-Hao Zhu, Longjiang Fan, Jianhua Li

{"title":"Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.","authors":"Yiyu Hu, Yanqing Sun, Qian-Hao Zhu, Longjiang Fan, Jianhua Li","doi":"10.2174/1389202924666221201140603","DOIUrl":"10.2174/1389202924666221201140603","url":null,"abstract":"The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10173419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46645966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long Noncoding RNA and mRNA Expression Profiles in Rats with LPS-induced Myocardial Dysfunction. lps诱导心肌功能障碍大鼠长链非编码RNA和mRNA表达谱

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/1389202924666230119160258

Ye-Chen Han, Zhu-Jun Shen, Ruo-Lan Xiang, Bo Lu, Hao Qian, Jing-Yi Li, Hong-Zhi Xie

{"title":"Long Noncoding RNA and mRNA Expression Profiles in Rats with LPS-induced Myocardial Dysfunction.","authors":"Ye-Chen Han, Zhu-Jun Shen, Ruo-Lan Xiang, Bo Lu, Hao Qian, Jing-Yi Li, Hong-Zhi Xie","doi":"10.2174/1389202924666230119160258","DOIUrl":"10.2174/1389202924666230119160258","url":null,"abstract":"Background: Sepsis is an uncontrolled systemic inflammatory response. Long noncoding RNAs (lncRNAs) are involved in the pathogenesis of sepsis. However, little is known about the roles of lncRNAs in sepsis-induced myocardial dysfunction.Objective: We aimed to determine the regulatory mechanism of lncRNAs in sepsis-induced myocardial dysfunction.Methods: In this study, we analysed the lncRNA and mRNA expression profiles using microarray analysis. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, protein-protein interaction network, and gene set enrichment analysis were used to evaluate the data. We also constructed coding and noncoding coexpression and competing endogenous RNA networks to investigate the mechanisms.Results: In vivo lipopolysaccharide -induced sepsis rat model was established. A total of 387 lncRNAs and 1,952 mRNAs were identified as significantly changed in the left ventricle. Kyoto Encyclopedia of Genes and Genomes analysis of mRNAs showed that the upregulated genes were mainly enriched in the \"complement and coagulation cascade pathway\" and \"immune-related biological processes\" terms. Eight significantly changed lncRNAs detected by RT-qPCR may be responsible for these processes. A competing endogenous RNA network was generated, and the results indicated that eight lncRNAs were related to the \"calcium ion binding\" process.Conclusion: These results demonstrate that crosstalk between lncRNAs and mRNAs may play important roles in the development of sepsis-induced myocardial dysfunction.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10173418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43513765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly and sex-specific differential transcriptome of the white-backed planthopper, Sogatella furcifera 白背飞虱的染色体水平基因组组装和性别特异性差异转录组

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-01-02 DOI: 10.2174/1389202924666230102092822

C. Zhang, Yu-Xuan Ye, Dan-Ting Li, Si-Yu Zhang, Z. Shen

引用次数: 0

Preface 前言

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-01-01 DOI: 10.2174/138920292401230610190952

C. Neri

引用次数: 0

A Deep Clustering-based Novel Approach for Binning of Metagenomics Data. 基于深度聚类的元基因组学数据分选新方法

IF 1.8 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220928150100

Sharanbasappa D Madival, Dwijesh Chandra Mishra, Anu Sharma, Sanjeev Kumar, Arpan Kumar Maji, Neeraj Budhlakoti, Dipro Sinha, Anil Rai

{"title":"A Deep Clustering-based Novel Approach for Binning of Metagenomics Data.","authors":"Sharanbasappa D Madival, Dwijesh Chandra Mishra, Anu Sharma, Sanjeev Kumar, Arpan Kumar Maji, Neeraj Budhlakoti, Dipro Sinha, Anil Rai","doi":"10.2174/1389202923666220928150100","DOIUrl":"10.2174/1389202923666220928150100","url":null,"abstract":"Background: One major challenge in binning Metagenomics data is the limited availability of reference datasets, as only 1% of the total microbial population is yet cultured. This has given rise to the efficacy of unsupervised methods for binning in the absence of any reference datasets.Objective: To develop a deep clustering-based binning approach for Metagenomics data and to evaluate results with suitable measures.Methods: In this study, a deep learning-based approach has been taken for binning the Metagenomics data. The results are validated on different datasets by considering features such as Tetra-nucleotide frequency (TNF), Hexa-nucleotide frequency (HNF) and GC-Content. Convolutional Autoencoder is used for feature extraction and for binning; the K-means clustering method is used.Results: In most cases, it has been found that evaluation parameters such as the Silhouette index and Rand index are more than 0.5 and 0.8, respectively, which indicates that the proposed approach is giving satisfactory results. The performance of the developed approach is compared with current methods and tools using benchmarked low complexity simulated and real metagenomic datasets. It is found better for unsupervised and at par with semi-supervised methods.Conclusion: An unsupervised advanced learning-based approach for binning has been proposed, and the developed method shows promising results for various datasets. This is a novel approach for solving the lack of reference data problem of binning in metagenomics.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/72/5e/CG-23-353.PMC9878855.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0