Current Genomics最新文献

{"title":"The Complete Chloroplast Genome Sequence of <i>Cicer bijugum</i>, Genome Organization, and Comparison with Related Species.","authors":"Melih Temel,&nbsp;Yasin Kaymaz,&nbsp;Duygu Ateş,&nbsp;Abdullah Kahraman,&nbsp;Muhammed Bahattin Tanyolaç","doi":"10.2174/1389202923666220211113708","DOIUrl":"https://doi.org/10.2174/1389202923666220211113708","url":null,"abstract":"<p><strong>Background: </strong>Chickpea is one of Turkey's most significant legumes, and because of its high nutritional value, it is frequently preferred in human nourishment.Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants.</p><p><strong>Objective: </strong>Current study aimed at revealing complete chloroplast genome sequence of one of the wild type <i>Cicer</i> species, <i>Cicer bijugum,</i> and comparing its genome with cultivated <i>Cicer</i> species, <i>Cicer arietinum,</i> by using bioinformatics analysis tools. Except for <i>Cicer arietinum</i>, there has been no study on the chloroplast genome sequence of <i>Cicer</i> species.Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type <i>Cicer</i> species, <i>Cicer bijugum,</i> and compare the chloroplast genome of <i>Cicer bijugum</i> with the cultivated one <i>Cicer arietinum.</i></p><p><strong>Methods: </strong>In this study, we sequenced the whole chloroplast genome of <i>Cicer bijugum</i>, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, <i>Cicer arietinum</i>, by using online bioinformatics analysis tools.</p><p><strong>Results: </strong>We determined the size of the chloroplast genome of <i>C. bijugum</i> as 124,804 bp and found that <i>C. bijugum</i> did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the <i>C. bijugum</i> chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15, and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that <i>C. bijugum</i> was phylogenetically closer to cultivated chickpea as compared to the other species.</p><p><strong>Conclusion: </strong>It is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary, and genetic engineering studies with chickpea species.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 1","pages":"50-65"},"PeriodicalIF":2.6,"publicationDate":"2022-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d0/9b/CG-23-50.PMC9199535.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40582299","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}

{"title":"Molecular Characterization of Upper Tract Urothelial Carcinoma for Precision Therapeutics and Non-invasive Diagnostics.","authors":"Emiko Sugawara,&nbsp;Kei Koyama,&nbsp;Kentaro Inamura","doi":"10.2174/1389202923666220204155828","DOIUrl":"https://doi.org/10.2174/1389202923666220204155828","url":null,"abstract":"<jats:sec>\u0000<jats:title />\u0000<jats:p />\u0000</jats:sec>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 1","pages":"2-4"},"PeriodicalIF":2.6,"publicationDate":"2022-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d4/37/CG-23-2.PMC9199533.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40582300","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}

{"title":"A Combinational Approach for More Efficient miRNA Biosensing.","authors":"Cheolho Lee","doi":"10.2174/1389202923666220204160912","DOIUrl":"https://doi.org/10.2174/1389202923666220204160912","url":null,"abstract":"<p><p>MicroRNAs, short single-stranded noncoding RNAs ranging in length from 18 ~ 24 bp, are found in all kingdoms of eukaryotes and even viruses. It was found that miRNAs are involved in a variety of biological processes, and their intracellular aberrant expression is related to diseases and abnormalities in the immune system. Since then, it has been considered essential to develop an efficient miRNA detection system. In this review, the limitations of traditional scheme-based miRNA detection methods are compared and analyzed. In particular, nucleic acid amplification-based miRNA detection methods and nanomaterial-based miRNA detection methods, which are widely used as a biosensing platform because of various features and advantages, such as high sensitivity, specificity, and simplicity, are analyzed. Based on this analysis, the latest examples of a combination of the advantages of nucleic acid amplification and those of nanomaterials are examined to suggest the characteristics of the next-generation miRNA biosensing.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 1","pages":"5-25"},"PeriodicalIF":2.6,"publicationDate":"2022-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ab/c7/CG-23-5.PMC9199536.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40582302","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}

{"title":"Preface","authors":"C. Neri","doi":"10.2174/138920292301220407100625","DOIUrl":"https://doi.org/10.2174/138920292301220407100625","url":null,"abstract":"This book is about automotive user interfaces. In the last years the importance of user interfaces for in-vehicle usage has increased strongly. Different studies show that over 80% of today’s innovations in the automotive industry are based on car electronics and its software. These innovations can be categorized into hidden technologies (e.g., ASP, ESP), comfort functions (e.g., navigation, communication, entertainment) or driver assistance (e.g., distance checking). Especially the last two categories have to be configurable by the driver and therefore require a certain amount of driver interaction. This results in a need for a modern and consistent automotive user interface which on the one hand allows the configuration of these systems and on the other hand conforms to the specialized requirements of the automotive industry. Some of these requirements are: the interaction devices have to be integrated into a limited space; the automotive user interface has to be intuitively usable and adaptable, since drivers generally do not get an extensive explanation and the automotive user interface has to be very easy to use and should distract the driver as little as possible from his main task of driving. The increased complexity of automotive user interfaces, the importance of using consumer electronic devices like smartphones in the car as well as autonomous driving has induced a lot of research at universities and industrial companies. The specific chapters in this book cover a relatively broad spectrum of detailed research topics in the area of automotive user interfaces concerning, e.g. usability and user experience, interaction techniques and technologies, applications, etc. This book provides an outstanding overview as well as deep insights into the area of automotive user interfaces, which is an important topic in the field of human– computer interaction. Besides aiming to be a reference in its area, this book is intended as a very significant and valuable source for professional practitioners, researchers as well as senior and postgraduate computer science and engineering students.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"1 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43073545","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}

{"title":"Exploring the Lethality of Human-Adapted Coronavirus Through Alignment-Free Machine Learning Approaches Using Genomic Sequences.","authors":"Rui Yin, Zihan Luo, Chee Keong Kwoh","doi":"10.2174/1389202923666211221110857","DOIUrl":"10.2174/1389202923666211221110857","url":null,"abstract":"<p><strong>Background: </strong>A newly emerging novel coronavirus appeared and rapidly spread worldwide and World Health Organization declared a pandemic on March 11, 2020. The roles and characteristics of coronavirus have captured much attention due to its power of causing a wide variety of infectious diseases, from mild to severe, on humans. The detection of the lethality of human coronavirus is key to estimate the viral toxicity and provide perspectives for treatment.</p><p><strong>Methods: </strong>We developed an alignment-free framework that utilizes machine learning approaches for an ultra-fast and highly accurate prediction of the lethality of human-adapted coronavirus using genomic sequences. We performed extensive experiments through six different feature transformation and machine learning algorithms combining digital signal processing to identify the lethality of possible future novel coronaviruses using existing strains.</p><p><strong>Results: </strong>The results tested on SARS-CoV, MERS-CoV and SARS-CoV-2 datasets show an average 96.7% prediction accuracy. We also provide preliminary analysis validating the effectiveness of our models through other human coronaviruses. Our framework achieves high levels of prediction performance that is alignment-free and based on RNA sequences alone without genome annotations and specialized biological knowledge.</p><p><strong>Conclusion: </strong>The results demonstrate that, for any novel human coronavirus strains, this study can offer a reliable real-time estimation for its viral lethality.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"583-595"},"PeriodicalIF":1.8,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8922323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42322549","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}

{"title":"<i>In-Silico</i> and <i>In-Vitro</i> Analysis of Human <i>SOS1</i> Protein Causing Noonan Syndrome - A Novel Approach to Explore the Molecular Pathways.","authors":"Vinoth Sigamani, Sheeja Rajasingh, Narasimman Gurusamy, Arunima Panda, Johnson Rajasingh","doi":"10.2174/1389202922666211130144221","DOIUrl":"10.2174/1389202922666211130144221","url":null,"abstract":"<p><strong>Aims: </strong>Perform <i>in-silico</i> analysis of human <i>SOS1</i> mutations to elucidate their pathogenic role in Noonan syndrome (NS).</p><p><strong>Background: </strong>NS is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, <i>SOS1</i>, RAF1, and KRAS genes. NS is thought to affect approximately 1 in 1000. NS patients suffer different pathogenic effects depending on the mutations they carry. Analysis of the mutations would be a promising predictor in identifying the pathogenic effect of NS.</p><p><strong>Methods: </strong>We performed computational analysis of the <i>SOS1</i> gene to identify the pathogenic nonsynonymous single nucleotide polymorphisms (nsSNPs) th a t cause NS. <i>SOS1</i> variants were retrieved from the SNP database (dbSNP) and analyzed by <i>in-silico</i> tools I-Mutant, iPTREESTAB, and MutPred to elucidate their structural and functional characteristics.</p><p><strong>Results: </strong>We found that 11 nsSNPs of <i>SOS1</i> that were linked to NS. 3D modeling of the wild-type and the 11 nsSNPs of <i>SOS1</i> showed that <i>SOS1</i> interacts with cardiac proteins GATA4, TNNT2, and ACTN2. We also found that GRB2 and HRAS act as intermediate molecules between <i>SOS1</i> and cardiac proteins. Our <i>in-silico</i> analysis findings were further validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying <i>SOS1</i> gene variant c.1654A>G (NSiCMCs) and compared to control human skin fibroblast-derived iCMCs (C-iCMCs). Our <i>in vitro</i> data confirmed that the <i>SOS1</i>, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs when compared to C-iCMCs.</p><p><strong>Conclusion: </strong>This is the first <i>in-silico</i> and <i>in vitro</i> study demonstrating that 11 nsSNPs of <i>SOS1</i> play deleterious pathogenic roles in causing NS.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"526-540"},"PeriodicalIF":2.6,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8905634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48533369","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}

{"title":"Comparative Genomics and Evolution of Avian Specialized Traits.","authors":"Lei Wu, Xiaolu Jiao, Dezhi Zhang, Yalin Cheng, Gang Song, Yanhua Qu, Fumin Lei","doi":"10.2174/1389202923666211227143952","DOIUrl":"10.2174/1389202923666211227143952","url":null,"abstract":"<p><p>Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits <i>via</i> comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"496-511"},"PeriodicalIF":1.8,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8905638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42523309","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}

{"title":"Raising Climate-Resilient Crops: Journey From the Conventional Breeding to New Breeding Approaches.","authors":"Yashika Gaba, Ashwani Pareek, Sneh Lata Singla-Pareek","doi":"10.2174/1389202922666210928151247","DOIUrl":"10.2174/1389202922666210928151247","url":null,"abstract":"<p><strong>Background: </strong>In order to meet the demands of the ever-increasing human population, it has become necessary to raise climate-resilient crops. Plant breeding, which involves crossing and selecting superior gene pools, has contributed tremendously towards achieving this goal during the past few decades. The relatively newer methods of crop improvement based on genetic engineering are relatively simple, and targets can be achieved in an expeditious manner. More recently emerged genome editing technique using CRISPR has raised strong hopes among plant scientists for precise integration of valuable traits and removal of undesirable ones.</p><p><strong>Conclusion: </strong>Genome editing using Site-Specific Nucleases (SSNs) is a good alternative to the plant breeding and genetic engineering approaches as it can modify the genomes specifically and precisely at the target site in the host genome. Another added advantage of the genome editing approach is the simpler biosafety regulations that have been adopted by many countries for commercialization of the products thus generated. This review provides a critical assessment of the available methods for improving the stress tolerance in crop plants. Special emphasis has been given on genome editing approach in light of the diversity of tools, which are being discovered on an everyday basis and the practical applications of the same. This information will serve as a beginner's guide to initiate the crop improvement programs as well as giving technical insight to the expert to plan the research strategically to tackle even multigenic traits in crop plants.</p>","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"450-467"},"PeriodicalIF":1.8,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8886625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47324936","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}

{"title":"Genes, Genomes and Germplasm for Climate-Smart Agriculture-Part-III.","authors":"Girdhar K Pandey, Viswanathan Chinnusamy, Sangram K Lenka","doi":"10.2174/138920292206211230181546","DOIUrl":"10.2174/138920292206211230181546","url":null,"abstract":"","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"391-392"},"PeriodicalIF":1.8,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8886629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44702611","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}

{"title":"Identification of Potential Pleiotropic Genes for Immune and Skeletal Diseases Using Multivariate MetaCCA Analysis","authors":"P. He, Rong-Rong Cao, F. Deng, S. Lei","doi":"10.2174/1389202923666211223115214","DOIUrl":"https://doi.org/10.2174/1389202923666211223115214","url":null,"abstract":"Background Immune and skeletal systems physiologically and pathologically interact with each other. Immune and skeletal diseases may share potential pleiotropic genetics factors, but the shared specific genes are largely unknown. Objective This study aimed to investigate the overlapping genetic factors between multiple diseases (including rheumatoid arthritis (RA), psoriasis, osteoporosis, osteoarthritis, sarcopenia, and fracture). Methods The canonical correlation analysis (metaCCA) approach was used to identify the shared genes for six diseases by integrating genome-wide association study (GWAS)-derived summary statistics. The versatile Gene-based Association Study (VEGAS2) method was further applied to refine and validate the putative pleiotropic genes identified by metaCCA. Results About 157 (p<8.19E-6), 319 (p<3.90E-6), and 77 (p<9.72E-6) potential pleiotropic genes were identified shared by two immune diseases, four skeletal diseases, and all of the six diseases, respectively. The top three significant putative pleiotropic genes shared by both immune and skeletal diseases, including HLA-B, TSBP1, and TSBP1-AS1 (p<E-300), were located in the major histocompatibility complex (MHC) region. Nineteen of 77 putative pleiotropic genes identified by metaCCA analysis were associated with at least one disease in the VEGAS2 analysis. Specifically, the majority (18) of these 19 putative validated pleiotropic genes were associated with RA. Conclusion The metaCCA method identified some pleiotropic genes shared by the immune and skeletal diseases. These findings help to improve our understanding of the shared genetic mechanisms and signaling pathways underlying immune and skeletal diseases.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"22 1","pages":"596 - 606"},"PeriodicalIF":2.6,"publicationDate":"2021-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46316451","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}