Bioinformatics of Genome Regulation and Structure/ Systems Biology最新文献

{"title":"Comparative genomic analysis of moderate bacteriophages of alfalfa root nodule bacteria","authors":"V. Muntyan, A. Kozlova, A. Afonin, A. N. Muntyan, E. Dzyubenko, M. Kabilov, E. Antonova, M. Roumiantseva","doi":"10.18699/bgrs/sb-2020-138","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-138","url":null,"abstract":"The bacteriophage AP300 infecting Sinorhizobium meliloti was isolated from soil sample from mountainous region of Dagestan, which belongs to the Caucasus Center for Legume Variety under the grant RSF 17-16-01095. The AP300 genome was annotated and its similarity to bacteriophage vB MloP_Lo5R7ANS (NC_025431; Podoviridae family) infecting Mesorhizobium loti strains was revealed. It was found that insertion frequency of the Mesorhizobium phage vB MloP_Lo5R7ANS-like sequences in the chromosomes of S. meliloti strains was 6.591 • 10-4. In the chromosomes of 4 strains of Sinorhizobium meliloti isolated in geographically different regions from soils and nodules of alfalfa plants, intact vB MloP_Lo5R7ANS-like prophages were detected. The 46.39-57.14% ORFs of AP300 and 4 prophages were homologous to ORFs of vB MloP_Lo5R7ANS. The 18 ORFs from mentioned above ORFs were identified in all studied sequences and they were similar to those in vB MloP_Lo5R7ANS. The other 7.22-15.79% ORFs were homologous to other phages. ORFs encoding virion components: head, capsid, tail, virion, integrase were detected in soil bacteriophage AP300 and in all studied prophages determined in rhizobia symbionts of alfalfa. It was revealed that Sinorhizobium prophages could be phylogenetically related not only to Sinorhizobium phages, but also to phages of Mesorhizobium. Tail tubular protein A in all studied sequences has structural differences from the currently known TTPA Klebsiella phage KP32 (pdb5MU4), it has specific sites of post- translational modification, which can probably determine the specificity of interaction with EPS of nodule bacteria of alfalfa.","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130436398","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}

{"title":"How miRNAs can protect humans from coronaviruses COVID-19, SARS-CoV, and MERS-CoV","authors":"A. Ivashchenko, A. Rakhmetullina, D. Aisina","doi":"10.21203/rs.3.rs-16264/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-16264/v1","url":null,"abstract":"\u0000 Viral diseases cause significant harm to human health and often cause high mortality. In the past twenty years, humanity has undergone infection by SARS-CoV (severe acute respiratory syndrome), MERS-CoV (Middle East respiratory syndrome) and COVID-19 coronaviruses, which spread from animals to humans and from person to person. These diseases have led to large economic losses. To fight coronaviruses and other viruses, it is proposed to use miRNAs, which regulate protein synthesis at the translational level. MirTarget program was used to determine the following binding characteristics: the locations of miRNA binding sites in the 3'UTR, 5'UTR, and CDS; the free energy interaction ∆G between miRNA and mRNA; the ΔG/ΔGm value, where ΔGm is equal to the free energy binding of miRNA with its full complementary nucleotide sequence; and the nucleotide interaction schemes between miRNAs and mRNAs. Out of 2565 miRNAs, miR-4778-3p, miR-6864-5p and miR-5197-3p were identified as the most effectively interacting with the gRNA of SARS-CoV, MERS-CoV and COVID-19, respectively. Based on the miR-4778-3p, miR-6864-5p and miR-5197-3p sequences, complete complementary miRNA (cc-miR) binding sites in the gRNA coronaviruses were created. The detected binding sites of these cc-miRs did not form intramolecular complexes in the 2D structure of the gRNA of SARS-CoV, MERS-CoV, and COVID-19 with a value of more than 85%. Therefore, the cc-miRs will bind gRNA at these sites without competition. The cc-miRs for SARS-CoV, MERS-CoV, and COVID-19 did not have target genes among the 17508 human coding genes with a ΔG/ΔGm of more than 85%, which implies the absence of side effects of these cc-miRs on the translation of human mRNAs. cc-miRs can be used as therapeutic agents by incorporating them into exosomes or other vesicles and introducing them into the blood or lung by inhalation. The introduction of cc-miR into the blood will suppress the reproduction of the virus in the blood and in all organs into which it can enter. The proposed method of inhibiting the reproduction of coronaviruses can be used for other viruses.","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129684816","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}

{"title":"Effects of melatonin and SkQ1 long-term treatment during aging and development AMD-like retinopathy","authors":"","doi":"10.18699/bgrs/sb-2020-406","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-406","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123168086","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}

{"title":"Is there a fecundity/longevity trade-off under heat stress?","authors":"","doi":"10.18699/bgrs/sb-2020-393","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-393","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124257515","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}

{"title":"Evolution of proteins involved in response to ROS","authors":"","doi":"10.18699/bgrs/sb-2020-398","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-398","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127150756","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}

{"title":"New approach to genome-wide automated inference of bacterial transcription factor binding sites","authors":"","doi":"10.18699/bgrs/sb-2020-046","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-046","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127449092","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}

{"title":"X-chromosome Inactivation in American Mink iPSCs","authors":"","doi":"10.18699/bgrs/sb-2020-310","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-310","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124817883","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}

{"title":"Recognition of flavivirus species on the base of coding genome sequences","authors":"","doi":"10.18699/bgrs/sb-2020-091","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-091","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124820131","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}

{"title":"Difference between younger and older adults in post-task traces after creative task performance matches PASA model","authors":"","doi":"10.18699/bgrs/sb-2020-402","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-402","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125887242","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}

{"title":"Experimental substantiation of transdermal transport of photosensitizers by fractional laser photothermolysis(FLP)","authors":"","doi":"10.18699/bgrs/sb-2020-300","DOIUrl":"https://doi.org/10.18699/bgrs/sb-2020-300","url":null,"abstract":"","PeriodicalId":199580,"journal":{"name":"Bioinformatics of Genome Regulation and Structure/ Systems Biology","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126191403","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}