Current Genomics最新文献_第7页

Decoding the Link between Periodontitis and Neuroinflammation: The Journey of Bacterial Extracellular Vesicles 破解牙周炎和神经炎症之间的联系:细菌细胞外囊泡的旅程

4区生物学

Current Genomics Pub Date : 2023-10-15 DOI: 10.2174/0113892029258657231010065320

Heon-Jin Lee, Youngkyun Lee, Su-Hyung Hong, Jin-Woo Park

引用次数: 0

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement. 植物育种的时代:传统育种到基因组学辅助育种的作物改良

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-06-23 DOI: 10.2174/1389202924666230517115912

Thumadath Palayullaparambil Ajeesh Krishna, Duraipandiyan Veeramuthu, Theivanayagam Maharajan, Mariapackiam Soosaimanickam

{"title":"The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement.","authors":"Thumadath Palayullaparambil Ajeesh Krishna, Duraipandiyan Veeramuthu, Theivanayagam Maharajan, Mariapackiam Soosaimanickam","doi":"10.2174/1389202924666230517115912","DOIUrl":"10.2174/1389202924666230517115912","url":null,"abstract":"Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"1 1","pages":"24-35"},"PeriodicalIF":2.6,"publicationDate":"2023-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10334699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41425964","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

Insights into Metabolic Engineering of Bioactive Molecules in Tetrastigma Hemsleyanum Diels & Gilg: A Traditional Medicinal Herb 赤柱藻生物活性分子代谢工程研究进展吉尔:一种传统的草药

4区生物学

Current Genomics Pub Date : 2023-03-01 DOI: 10.2174/0113892029251472230921053135

Ajeesh Krishna TP, Maharajan Theivanayagam, Adarsh Krishna, Antony Ceasar Stanislaus

{"title":"Insights into Metabolic Engineering of Bioactive Molecules in Tetrastigma Hemsleyanum Diels & Gilg: A Traditional Medicinal Herb","authors":"Ajeesh Krishna TP, Maharajan Theivanayagam, Adarsh Krishna, Antony Ceasar Stanislaus","doi":"10.2174/0113892029251472230921053135","DOIUrl":"https://doi.org/10.2174/0113892029251472230921053135","url":null,"abstract":"Abstract: Plants are a vital source of bioactive molecules for various drug development processes. Tetrastigma hemsleyanum is one of the endangered medicinal plant species well known to the world due to its wide range of therapeutic effects. Many bioactive molecules have been identified from this plant, including many classes of secondary metabolites such as flavonoids, phenols, terpenoids, steroids, alkaloids, etc. Due to its slow growth, it usually takes 3-5 years to meet commercial medicinal materials for this plant. Also, T. hemsleyanum contains low amounts of specific bioactive compounds, which are challenging to isolate easily. Currently, scientists are attempting to increase bioactive molecules' production from medicinal plants in different ways or to synthesize them chemically. The genomic tools helped to understand medicinal plants' genome organization and led to manipulating genes responsible for various biosynthesis pathways. Metabolic engineering has made it possible to enhance the production of secondary metabolites by introducing manipulated biosynthetic pathways to attain high levels of desirable bioactive molecules. Metabolic engineering is a promising approach for improving the production of secondary metabolites over a short time period. In this review, we have highlighted the scope of various biotechnological approaches for metabolic engineering to enhance the production of secondary metabolites for pharmaceutical applications in T. hemsleyanum. Also, we summarized the progress made in metabolic engineering for bioactive molecule enhancement in T. hemsleyanum. It may lead to reducing the destruction of the natural habitat of T. hemsleyanum and conserving them through the cost-effective production of bioactive molecules in the future.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"54 47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135533055","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

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":"201 1","pages":"0"},"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

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":"23 5","pages":"353-368"},"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

Circular RNA Involvement in Aging and Longevity. 环状RNA参与衰老和长寿。

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220927110258

Ruize Niu, Jia Liu

{"title":"Circular RNA Involvement in Aging and Longevity.","authors":"Ruize Niu, Jia Liu","doi":"10.2174/1389202923666220927110258","DOIUrl":"https://doi.org/10.2174/1389202923666220927110258","url":null,"abstract":"Background: Circular RNAs (circRNAs) are transcribed by RNA polymerase II and are mostly generated by the back-splicing of exons in the protein-coding gene. Massive circRNAs are reported to be differentially expressed in different species, implicating their prospects as aging biomarkers or regulators in the aging progression.Methods: The possible role of circRNAs in aging and longevity was reviewed by the query of circRNAs from literature reports related to tissue, organ or cellular senescence, and individual longevity.Results: A number of circRNAs have been found to positively and negatively modulate aging and longevity through canonical aging pathways in the invertebrates Caenorhabditis elegans and Drosophila. Recent studies have also shown that circRNAs regulate age-related processes and pathologies such various mammalian tissues, as the brain, serum, heart, and muscle. Besides, three identified representative circRNAs (circSfl, circGRIA1, and circNF1-419) were elucidated to correlate with aging and longevity.Conclusion: This review outlined the current studies of circRNAs in aging and longevity, highlighting the role of circRNAs as a biomarker of aging and as a regulator of longevity.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 5","pages":"318-325"},"PeriodicalIF":2.6,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e3/38/CG-23-318.PMC9878857.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484051","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: 1