Genomics & informatics最新文献_第7页

Whole genome sequence analyses of thermotolerant Bacillus sp. isolates from food. 耐高温芽孢杆菌全基因组序列分析。

Genomics & informatics Pub Date : 2023-09-01 Epub Date: 2023-09-27 DOI: 10.5808/gi.23030

Phornphan Sornchuer, Kritsakorn Saninjuk, Pholawat Tingpej

{"title":"Whole genome sequence analyses of thermotolerant Bacillus sp. isolates from food.","authors":"Phornphan Sornchuer, Kritsakorn Saninjuk, Pholawat Tingpej","doi":"10.5808/gi.23030","DOIUrl":"10.5808/gi.23030","url":null,"abstract":"The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"21 3","pages":"e35"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184738","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}

引用次数: 0

Molecular docking Study of Nuciferine as a Tyrosinase Inhibitor and Its Therapeutic Potential for Hyperpigmentation. 芥子碱作为酪氨酸酶抑制剂的分子对接研究及其对色素沉着过度的治疗潜力。

Genomics & informatics Pub Date : 2023-09-01 Epub Date: 2023-09-14 DOI: 10.5808/gi.23054

Veerabhuvaneshwari Veerichetty, Iswaryalakshmi Saravanabavan

{"title":"Molecular docking Study of Nuciferine as a Tyrosinase Inhibitor and Its Therapeutic Potential for Hyperpigmentation.","authors":"Veerabhuvaneshwari Veerichetty, Iswaryalakshmi Saravanabavan","doi":"10.5808/gi.23054","DOIUrl":"10.5808/gi.23054","url":null,"abstract":"Melanin is synthesized by tyrosinase to protect the skin from ultraviolet light. However, overproduction and accumulation of melanin can result in hyperpigmentation and skin melanoma. Tyrosinase inhibitors are commonly used in the treatment of hyperpigmentation. Natural tyrosinase inhibitors are often favored over synthetic ones due to the potential side effects of the latter, which can include skin irritation, allergies, and other adverse reactions. Nuciferine, an alkaloid derived from Nelumbo nucifera, exhibits potent antioxidant and anti-proliferative properties. This study focused on the in silico screening of nuciferine for anti-tyrosinase activity, using kojic acid, ascorbic acid, and resorcinol as standards. The tyrosinase protein target was selected through homology modeling. The residues of the substrate binding pocket and active site pockets were identified for the purposes of grid box optimization and docking. Nuciferine demonstrated a binding energy of -7.0 kcal/mol and a Ki of 5 µM, both of which were comparatively higher than the corresponding values of kojic acid, which showed -5.3 kcal/mol and 122 µM respectively. Therefore, nuciferine is a potent natural tyrosinase inhibitor and shows promising potential for application in the treatment of hyperpigmentation and skin melanoma.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"21 3","pages":"e43"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184734","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}

引用次数: 0

M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study. 登革热病毒M蛋白低聚为五聚体通道蛋白：计算机分析研究。

Genomics & informatics Pub Date : 2023-09-01 Epub Date: 2023-09-27 DOI: 10.5808/gi.23035

Ayesha Zeba, Kanagaraj Sekar, Anjali Ganjiwale

{"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":"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.","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}

引用次数: 0

In-silico and structure-based assessment to evaluate pathogenicity of missense mutations associated with non-small cell lung cancer identified in the Eph-ephrin class of proteins. 对Eph-ephrin类蛋白质中鉴定的与非小细胞肺癌癌症相关的错义突变的致病性进行原位和结构评估。

Genomics & informatics Pub Date : 2023-09-01 Epub Date: 2023-09-27 DOI: 10.5808/gi.22069

Shubhashish Chakraborty, Reshita Baruah, Neha Mishra, Ashok K Varma

{"title":"In-silico and structure-based assessment to evaluate pathogenicity of missense mutations associated with non-small cell lung cancer identified in the Eph-ephrin class of proteins.","authors":"Shubhashish Chakraborty, Reshita Baruah, Neha Mishra, Ashok K Varma","doi":"10.5808/gi.22069","DOIUrl":"10.5808/gi.22069","url":null,"abstract":"Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"21 3","pages":"e30"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184731","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}

引用次数: 0

A genome‑wide approach to the systematic and comprehensive analysis of LIM gene family in sorghum (Sorghum bicolor L.). 系统全面分析高粱LIM基因家族的全基因组方法。

Genomics & informatics Pub Date : 2023-09-01 Epub Date: 2023-09-27 DOI: 10.5808/gi.23007

Md Abdur Rauf Sarkar, Salim Sarkar, Md Shohelul Islam, Fatema Tuz Zohra, Shaikh Mizanur Rahman

{"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":"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.","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}

引用次数: 0

NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer NBLAST:一个基于图形用户界面的双向BLAST软件，带有点图查看器

Genomics & informatics Pub Date : 2022-09-01 DOI: 10.5808/gi.22053

Beom-Soon Choi, Seon Kang Choi, Nam-Soo Kim, I. Choi

引用次数: 1

MPI-GWAS: a supercomputing-aided permutation approach for genome-wide association studies MPI-GWAS：一种用于全基因组关联研究的超计算辅助排列方法

Genomics & informatics Pub Date : 2022-03-01 DOI: 10.5808/gi.22001

H. Paik, Yongseong Cho, S. Cho, Oh-Kyoung Kwon

引用次数: 0

2-Methoxy-1,4-naphthoquinone (MNQ) regulates cancer key genes of MAPK, PI3K, and NF-κB pathways in Raji cells 2-甲氧基-1,4-萘醌(MNQ)调控Raji细胞中MAPK、PI3K、NF-κB通路的肿瘤关键基因

Genomics & informatics Pub Date : 2022-03-01 DOI: 10.5808/gi.21041

Teck Yew Wong, S. Menaga, Chi-Ying F. Huang, S. H. Ho, S. Gan, Y. Lim

引用次数: 1

Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach 用免疫信息学方法设计一种新的针对鱼类哈维氏弧菌感染的信使核糖核酸疫苗

Genomics & informatics Pub Date : 2022-03-01 DOI: 10.5808/gi.21065

Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj

{"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}

引用次数: 10

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak 来自马来西亚半岛、雪兰莪州和霹雳州泥炭沼泽的世界上最小的鱼，progenetica Paedocypris的第一个有丝分裂基因组的特征

Genomics & informatics Pub Date : 2022-03-01 DOI: 10.5808/gi.21081

NorJasmin Hussin, I. A. Azmir, Y. Esa, A. Ahmad, Faezah Mohd Salleh, P. N. S. Jahari, K. Munian, H. Gan

{"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}

引用次数: 2