Pub Date : 2023-09-01Epub Date: 2023-09-27DOI: 10.5808/gi.23035
Ayesha Zeba, Kanagaraj Sekar, Anjali Ganjiwale
The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics (MD) simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis (RIN) for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.
{"title":"M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study.","authors":"Ayesha Zeba, Kanagaraj Sekar, Anjali Ganjiwale","doi":"10.5808/gi.23035","DOIUrl":"10.5808/gi.23035","url":null,"abstract":"<p><p>The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics (MD) simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis (RIN) for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.</p>","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"21 3","pages":"e41"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.
{"title":"A genome‑wide approach to the systematic and comprehensive analysis of LIM gene family in sorghum (Sorghum bicolor L.).","authors":"Md Abdur Rauf Sarkar, Salim Sarkar, Md Shohelul Islam, Fatema Tuz Zohra, Shaikh Mizanur Rahman","doi":"10.5808/gi.23007","DOIUrl":"10.5808/gi.23007","url":null,"abstract":"<p><p>The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.</p>","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"21 3","pages":"e36"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Beom-Soon Choi, Seon Kang Choi, Nam-Soo Kim, I. Choi
BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as “query” or “target” in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.
{"title":"NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer","authors":"Beom-Soon Choi, Seon Kang Choi, Nam-Soo Kim, I. Choi","doi":"10.5808/gi.22053","DOIUrl":"https://doi.org/10.5808/gi.22053","url":null,"abstract":"BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as “query” or “target” in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43666790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Permutation testing is a robust and popular approach for significance testing in genomic research that has the advantage of reducing inflated type 1 error rates; however, its computational cost is notorious in genome-wide association studies (GWAS). Here, we developed a supercomputing-aided approach to accelerate the permutation testing for GWAS, based on the message-passing interface (MPI) on parallel computing architecture. Our application, called MPI-GWAS, conducts MPI-based permutation testing using a parallel computing approach with our supercomputing system, Nurion (8,305 compute nodes, and 563,740 central processing units [CPUs]). For 107 permutations of one locus in MPI-GWAS, it was calculated in 600 s using 2,720 CPU cores. For 107 permutations of ~30,000–50,000 loci in over 7,000 subjects, the total elapsed time was ~4 days in the Nurion supercomputer. Thus, MPI-GWAS enables us to feasibly compute the permutation-based GWAS within a reason-able time by harnessing the power of parallel computing resources.
{"title":"MPI-GWAS: a supercomputing-aided permutation approach for genome-wide association studies","authors":"H. Paik, Yongseong Cho, S. Cho, Oh-Kyoung Kwon","doi":"10.5808/gi.22001","DOIUrl":"https://doi.org/10.5808/gi.22001","url":null,"abstract":"Permutation testing is a robust and popular approach for significance testing in genomic research that has the advantage of reducing inflated type 1 error rates; however, its computational cost is notorious in genome-wide association studies (GWAS). Here, we developed a supercomputing-aided approach to accelerate the permutation testing for GWAS, based on the message-passing interface (MPI) on parallel computing architecture. Our application, called MPI-GWAS, conducts MPI-based permutation testing using a parallel computing approach with our supercomputing system, Nurion (8,305 compute nodes, and 563,740 central processing units [CPUs]). For 107 permutations of one locus in MPI-GWAS, it was calculated in 600 s using 2,720 CPU cores. For 107 permutations of ~30,000–50,000 loci in over 7,000 subjects, the total elapsed time was ~4 days in the Nurion supercomputer. Thus, MPI-GWAS enables us to feasibly compute the permutation-based GWAS within a reason-able time by harnessing the power of parallel computing resources.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49372531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Teck Yew Wong, S. Menaga, Chi-Ying F. Huang, S. H. Ho, S. Gan, Y. Lim
2-Methoxy-1,4-naphthoquinone (MNQ) has been shown to cause cytotoxic towards various cancer cell lines. This study is designed to investigate the regulatory effect of MNQ on the key cancer genes in mitogen-activated protein kinase, phosphoinositide 3-kinase, and nuclear factor кB signaling pathways. The expression levels of the genes were compared at different time point using polymerase chain reaction arrays and Ingenuity Pathway Analysis was performed to identify gene networks that are most significant to key cancer genes. A total of 43 differentially expressed genes were identified with 21 up-regulated and 22 down-regulated genes. Up-regulated genes were involved in apoptosis, cell cycle and act as tumor suppressor while down-regulated genes were involved in anti-apoptosis, angiogenesis, cell cycle and act as transcription factor as well as proto-oncogenes. MNQ exhibited multiple regulatory effects on the cancer key genes that targeting at cell proliferation, cell differentiation, cell transformation, apoptosis, reduce inflammatory responses, inhibits angiogenesis and metastasis.
{"title":"2-Methoxy-1,4-naphthoquinone (MNQ) regulates cancer key genes of MAPK, PI3K, and NF-κB pathways in Raji cells","authors":"Teck Yew Wong, S. Menaga, Chi-Ying F. Huang, S. H. Ho, S. Gan, Y. Lim","doi":"10.5808/gi.21041","DOIUrl":"https://doi.org/10.5808/gi.21041","url":null,"abstract":"2-Methoxy-1,4-naphthoquinone (MNQ) has been shown to cause cytotoxic towards various cancer cell lines. This study is designed to investigate the regulatory effect of MNQ on the key cancer genes in mitogen-activated protein kinase, phosphoinositide 3-kinase, and nuclear factor кB signaling pathways. The expression levels of the genes were compared at different time point using polymerase chain reaction arrays and Ingenuity Pathway Analysis was performed to identify gene networks that are most significant to key cancer genes. A total of 43 differentially expressed genes were identified with 21 up-regulated and 22 down-regulated genes. Up-regulated genes were involved in apoptosis, cell cycle and act as tumor suppressor while down-regulated genes were involved in anti-apoptosis, angiogenesis, cell cycle and act as transcription factor as well as proto-oncogenes. MNQ exhibited multiple regulatory effects on the cancer key genes that targeting at cell proliferation, cell differentiation, cell transformation, apoptosis, reduce inflammatory responses, inhibits angiogenesis and metastasis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41964367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
NorJasmin Hussin, I. A. Azmir, Y. Esa, A. Ahmad, Faezah Mohd Salleh, P. N. S. Jahari, K. Munian, H. Gan
The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.
对世界上最小的鲤科鱼——原基因幼鱼(Paedocypris progenetica)的两个线粒体全基因组进行了测序和组装。有丝分裂基因组P1-P的环状DNA分子。progenetica和S3-P。原基因体长度分别为16,827和16,616 bp，编码13个蛋白质编码基因、22个转移RNA基因、2个核糖体RNA基因和1个控制区。progenetica的基因排列与其他Paedocypris种相同。BLAST和系统发育分析显示，来自霹雳州和雪兰莪州的两种Paedocypris有丝分裂基因组序列存在差异。P. progenetica的环状DNA分子产生标准的脊椎动物基因排列，总核苷酸组成为a 33.0%， T 27.2%， C 23.5%， G 15.5%。该种的总AT含量与其他属其他种一致。黄杨对照区gc -负偏和AT-正偏分别显示丰富的遗传变异性和AT核苷酸偏倚。本研究结果提供了基因组变异信息，增强了对原遗传假单胞虫有丝分裂基因组的认识。之后，它们可以为系统发育分析和群体遗传学数据提供非常有价值的新见解。
{"title":"Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak","authors":"NorJasmin Hussin, I. A. Azmir, Y. Esa, A. Ahmad, Faezah Mohd Salleh, P. N. S. Jahari, K. Munian, H. Gan","doi":"10.5808/gi.21081","DOIUrl":"https://doi.org/10.5808/gi.21081","url":null,"abstract":"The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46106618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj
Vibrio harveyi belongs to the family Vibrionaceae of class Gammaproteobacteria. Around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness) in humans. A large number of bacterial particles can be found in the infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the bacteria. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against the most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as have a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computers revealed that the vaccination might elicit immune reactions Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.
{"title":"Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach","authors":"Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj","doi":"10.5808/gi.21065","DOIUrl":"https://doi.org/10.5808/gi.21065","url":null,"abstract":"Vibrio harveyi belongs to the family Vibrionaceae of class Gammaproteobacteria. Around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness) in humans. A large number of bacterial particles can be found in the infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the bacteria. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against the most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as have a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computers revealed that the vaccination might elicit immune reactions Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43799386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Human exposure to pollutants has been on the rise. Thus, researchers have been focused on understanding the effect of these compounds on human health, especially on the genetic information by using various tests, among them the somatic mutation and recombination tests (SMARTs). It is a sensitive and accurate method applicable to genotoxicity analysis. Here, a comprehensive bibliometric analysis of SMART assays in genotoxicity studies was performed to assess publication trends of this field. Data were extracted from the Web of Science database and analyzed by the bibliometric tools HistCite, Biblioshiny (RStudio), VOSViewer, and CiteSpace. Results have shown an increase in the last 10 years in terms of publication. A total of 392 records were published in 96 sources mainly from Brazil, Spain, and Turkey. Research collaboration networks between countries and authors were performed. Based on document co-citation, five large research clusters were identified and analyzed. The youngest research frontier emphasized on nanoparticles. With this study, how research trends evolve over years was demonstrated. Thus, international collaboration could be enhanced, and a promising field could be developed.
人类接触污染物的程度一直在上升。因此，研究人员一直致力于通过各种测试了解这些化合物对人类健康的影响，特别是对遗传信息的影响，其中包括体细胞突变和重组测试(SMARTs)。它是一种灵敏、准确的遗传毒性分析方法。本文对遗传毒性研究中的SMART分析进行了全面的文献计量学分析，以评估该领域的发表趋势。数据从Web of Science数据库中提取，并通过文献计量工具HistCite、Biblioshiny (RStudio)、VOSViewer和CiteSpace进行分析。结果显示，在过去10年里，论文发表量有所增加。共发表了392条记录，主要来自巴西、西班牙和土耳其的96个来源。在国家和作者之间建立了研究协作网络。基于文献共被引，确定并分析了5个大型研究集群。最年轻的研究前沿是纳米颗粒。这项研究展示了多年来研究趋势的演变。因此，可以加强国际合作，并可以发展一个有前途的领域。
{"title":"Publication trends of somatic mutation and recombination tests research: a bibliometric analysis (1984‒2020)","authors":"Ghada Tagorti, B. Kaya","doi":"10.5808/gi.21083","DOIUrl":"https://doi.org/10.5808/gi.21083","url":null,"abstract":"Human exposure to pollutants has been on the rise. Thus, researchers have been focused on understanding the effect of these compounds on human health, especially on the genetic information by using various tests, among them the somatic mutation and recombination tests (SMARTs). It is a sensitive and accurate method applicable to genotoxicity analysis. Here, a comprehensive bibliometric analysis of SMART assays in genotoxicity studies was performed to assess publication trends of this field. Data were extracted from the Web of Science database and analyzed by the bibliometric tools HistCite, Biblioshiny (RStudio), VOSViewer, and CiteSpace. Results have shown an increase in the last 10 years in terms of publication. A total of 392 records were published in 96 sources mainly from Brazil, Spain, and Turkey. Research collaboration networks between countries and authors were performed. Based on document co-citation, five large research clusters were identified and analyzed. The youngest research frontier emphasized on nanoparticles. With this study, how research trends evolve over years was demonstrated. Thus, international collaboration could be enhanced, and a promising field could be developed.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48753660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
2022 Korea Genome Organization This is an open-access article distributed under the terms of the Creative Commons Attribution license (http://creativecommons. org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In this issue, there are two review articles, eight original articles, one genome archive, and two application notes. In this editorial, I would like to focus on the two review articles, as well as two original articles and one application note on genome-wide association studies (GWAS). Recent rapid advances in single-cell RNA sequencing have made it possible to recognize a variety of previously unidentified subpopulations and rare cell states in tumors and the immune system based on single-cell gene expression profiles. Single-cell RNA sequencing is the topic of the first review article, by Dr. Jong-Il Kim’s group (Seoul National University College of Medicine, Korea). This review addresses the current development of methods for constructing single-cell epigenomic libraries, including multi-omics tools with important elements and additional requirements for the future, focusing on DNA methylation, chromatin accessibility, and histone post-translational modification. Single-cell epigenomic libraries help to understand the principles of comprehensive gene regulation that determine cell fate through transcripts alone and the resulting output of gene expression programs. The corresponding single-cell epigenome is expected to elucidate the mechanisms involved in the origin and maintenance of a comprehensive single-cell transcriptome. This review insightfully summarizes current research trends in the field of cellular differentiation and disease development at the single-cell level, moving toward the single-cell epigenome. The second review, led by Dr. Tung (Dagon University, Myanmar), deals with recent developments in whole-genome sequencing technologies. While the analysis of whole-genome sequencing data requires highly sophisticated bioinformatics tools, many researchers do not have the bioinformatics capabilities to analyze the genomic data and are therefore unable to take maximum advantage of whole-genome sequencing. This review provides a practical guide on a set of bioinformatics tools available online to analyze whole-genome sequence data of bacterial genomes and presents a description of their web interfaces. Now, I would like to turn to three articles about GWAS. The main goal of GWAS is the identification of causal variants associated with the phenotype of interest. All GWAS introduce appropriate statistical models to explain the phenotype and then to perform statistical tests. An important challenge in this post-GWAS era is to increase statistical power by using better statistical models and tests, and to investigate the causal effects between modifiable risk factors and the phenotypes via Mendelian randomization (MR). The first article, t
{"title":"Editor’s introduction to this issue (G&I 20:1, 2022)","authors":"Taesung Park","doi":"10.5808/gi.20.1.e1","DOIUrl":"https://doi.org/10.5808/gi.20.1.e1","url":null,"abstract":"2022 Korea Genome Organization This is an open-access article distributed under the terms of the Creative Commons Attribution license (http://creativecommons. org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In this issue, there are two review articles, eight original articles, one genome archive, and two application notes. In this editorial, I would like to focus on the two review articles, as well as two original articles and one application note on genome-wide association studies (GWAS). Recent rapid advances in single-cell RNA sequencing have made it possible to recognize a variety of previously unidentified subpopulations and rare cell states in tumors and the immune system based on single-cell gene expression profiles. Single-cell RNA sequencing is the topic of the first review article, by Dr. Jong-Il Kim’s group (Seoul National University College of Medicine, Korea). This review addresses the current development of methods for constructing single-cell epigenomic libraries, including multi-omics tools with important elements and additional requirements for the future, focusing on DNA methylation, chromatin accessibility, and histone post-translational modification. Single-cell epigenomic libraries help to understand the principles of comprehensive gene regulation that determine cell fate through transcripts alone and the resulting output of gene expression programs. The corresponding single-cell epigenome is expected to elucidate the mechanisms involved in the origin and maintenance of a comprehensive single-cell transcriptome. This review insightfully summarizes current research trends in the field of cellular differentiation and disease development at the single-cell level, moving toward the single-cell epigenome. The second review, led by Dr. Tung (Dagon University, Myanmar), deals with recent developments in whole-genome sequencing technologies. While the analysis of whole-genome sequencing data requires highly sophisticated bioinformatics tools, many researchers do not have the bioinformatics capabilities to analyze the genomic data and are therefore unable to take maximum advantage of whole-genome sequencing. This review provides a practical guide on a set of bioinformatics tools available online to analyze whole-genome sequence data of bacterial genomes and presents a description of their web interfaces. Now, I would like to turn to three articles about GWAS. The main goal of GWAS is the identification of causal variants associated with the phenotype of interest. All GWAS introduce appropriate statistical models to explain the phenotype and then to perform statistical tests. An important challenge in this post-GWAS era is to increase statistical power by using better statistical models and tests, and to investigate the causal effects between modifiable risk factors and the phenotypes via Mendelian randomization (MR). The first article, t","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49173955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kyunghyuk Park, Min Chul Jeon, Bokyung Kim, Bukyoung Cha, Jong-Il Kim
The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.
{"title":"Experimental development of the epigenomic library construction method to elucidate the epigenetic diversity and causal relationship between epigenome and transcriptome at a single-cell level","authors":"Kyunghyuk Park, Min Chul Jeon, Bokyung Kim, Bukyoung Cha, Jong-Il Kim","doi":"10.5808/gi.21078","DOIUrl":"https://doi.org/10.5808/gi.21078","url":null,"abstract":"The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44772237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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