Konstantinos Giannopoulos, Maria Gazouli, Klio Chatzistefanou, Anthi Bakouli, Marilita M Moschos
{"title":"The Genetic Background of Central Serous Chorioretinopathy: A Review on Central Serous Chorioretinopathy Genes.","authors":"Konstantinos Giannopoulos, Maria Gazouli, Klio Chatzistefanou, Anthi Bakouli, Marilita M Moschos","doi":"10.7150/jgen.55545","DOIUrl":"https://doi.org/10.7150/jgen.55545","url":null,"abstract":"<p><p>Central serous chorioretinopathy is characterized by neurosensory detachment of the central retina secondary to fluid leakage through the retinal pigment epithelium. Though it has an incidence of 9,9 per 100.000 in men and 1,7 per 100.000 in women, it is the fourth most common retinal disorder. Central serous chorioretinopathy patients present with blurred vision, central scotoma, metamorphopsia, micropsia and mild color discrimination. It is usually a self-limited disorder with nearly none or minimal visual impairment but in some patients the disease persists and may cause severe visual impairment. Central serous chorioretinopathy pathophysiology is not well understood. Choroid, retinal pigment epithelium and hormonal pathways seem to play important roles in central serous chorioretinopathy pathophysiology. Also, familial cases of the disease indicate that there is a genetic background. The identification of certain disease genes could lead to the development of better diagnostic and therapeutic approaches for central serous chorioretinopathy patients.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"10-19"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7806452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38828019","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}
{"title":"Draft Genome Sequence of <i>Enterobacter</i> sp. AS-1, a Potential Eurytrophic Recombination Host.","authors":"Yuki Iwasaki, Yuya Itoiri, Sota Ihara, Hironaga Akita, Mamoru Oshiki, Zen-Ichiro Kimura","doi":"10.7150/jgen.53040","DOIUrl":"https://doi.org/10.7150/jgen.53040","url":null,"abstract":"<p><p>Strain AS-1 was isolated from laboratory-scale activated sludge collected in Japan. This strain not only grows on rich medium, including R2A medium, but also forms colonies on medium lacking organic matter other than agar (water agar), indicating it could be used as a eurytrophic recombinant host in material production processes. Here, we present a draft genome sequence of <i>Enterobacter</i> sp. AS-1, which consists of a total of 24 contigs containing 5,207,146 bp, with a GC content of 55.64%, and comprising 4,921 predicted coding sequences. Based on 16S rRNA gene sequence analysis, strain AS-1 was designated as <i>Enterobacter</i> sp. AS-1.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"6-9"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39123432","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}
{"title":"Isolation, draft genome sequencing and identification of <i>Enterobacter roggenkampii</i> CCI9.","authors":"Hironaga Akita, Yuya Itoiri, Noriyo Takeda, Zen-Ichiro Kimura, Hiroyuki Inoue, Akinori Matsushika","doi":"10.7150/jgen.46294","DOIUrl":"https://doi.org/10.7150/jgen.46294","url":null,"abstract":"<p><p>Strain CCI9, which was isolated from leaf soil collected in Japan, was capable of growth on poor-nutrient medium, at temperatures of 10°C to 45°C, at pHs of 4.5 to 10, and in the presence of 7.0% NaCl. We determined a draft genome sequence of strain CCI9, which consists of a total of 28 contigs containing 4,644,734 bp with a GC content of 56.1%. This assembly yielded 4,154 predicted coding sequences. Multilocus sequence analysis (MLSA) based on <i>atpD</i>, <i>gyrB</i>, <i>infB,</i> and <i>rpoB</i> gene sequences were performed to further identify strain CCI9. The MLSA revealed that strain CCI9 clustered tightly with <i>Enterobacter roggenkampii</i> EN-117<sup>T</sup>. Moreover, the average nucleotide identity value (98.6%) between genome sequences of strain CCI9 and <i>E. roggenkampii</i> EN-117<sup>T</sup> exceeds the cutoff value for prokaryotic subspecies delineation. Therefore, strain CCI9 was identified as <i>E. roggenkampii</i> CCI9. To clarify differences between <i>E. roggenkampii</i> EN-117<sup>T</sup> and CCI9, the coding proteins were compared against the eggNOG database.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39123430","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}
Journal of GenomicsPub Date : 2020-09-23eCollection Date: 2020-01-01DOI: 10.7150/jgen.51181
Samira Mansour, Erik Swanson, Céline Pesce, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa
{"title":"Draft Genome Sequences for the <i>Frankia</i> sp. strains CgS1, CcI156 and CgMI4, Nitrogen-Fixing Bacteria Isolated from <i>Casuarina</i> sp. in Egypt.","authors":"Samira Mansour, Erik Swanson, Céline Pesce, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa","doi":"10.7150/jgen.51181","DOIUrl":"https://doi.org/10.7150/jgen.51181","url":null,"abstract":"<p><p><i>Frankia</i> sp. strains CgS1, CcI156 and CgMI4 were isolated from <i>Casuarina glauca</i> and C. <i>cunninghamiana</i> nodules. Here, we report the 5.26-, 5.33- and 5.20-Mbp draft genome sequences of <i>Frankia</i> sp. strains CgS1, CcI156 and CgMI4, respectively. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"84-88"},"PeriodicalIF":0.0,"publicationDate":"2020-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.51181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38468302","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}
Journal of GenomicsPub Date : 2020-08-29eCollection Date: 2020-01-01DOI: 10.7150/jgen.50468
Takashi Kitano, Choong-Gon Kim, Naruya Saitou
{"title":"Nucleotide sequencing of the HoxA gene cluster using Gorilla fosmid clones.","authors":"Takashi Kitano, Choong-Gon Kim, Naruya Saitou","doi":"10.7150/jgen.50468","DOIUrl":"https://doi.org/10.7150/jgen.50468","url":null,"abstract":"<p><p>We sequenced the western gorilla (<i>Gorilla gorilla</i>) HoxA cluster region using seven fosmid clones, and found that the total tiling path sequence was 214,185 bp from the 5' non-genic region of HoxA1 to the 3' non-genic region of Evx1. We compared the nucleotide sequence with the gorilla genome sequence in the NCBI database, and the overall proportion of nucleotide difference was estimated to be 0.0005-0.0007. These estimates are lower than overall genomic polymorphism in gorillas.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"80-83"},"PeriodicalIF":0.0,"publicationDate":"2020-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.50468","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38481460","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}
Journal of GenomicsPub Date : 2020-07-03eCollection Date: 2020-01-01DOI: 10.7150/jgen.42790
Belen Gonzalez-Santamarina, Anne Busch, Silvia Garcia-Soto, Mostafa Y Abdel-Glil, Jörg Linde, Reinhard Fries, Diana Meemken, Helmut Hotzel, Herbert Tomaso
{"title":"Draft genome sequence of multi-resistant <i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Rissen strain 19CS0416 isolated from Vietnam reveals <i>mcr-1</i> plasmid mediated resistance to colistin already in 2013.","authors":"Belen Gonzalez-Santamarina, Anne Busch, Silvia Garcia-Soto, Mostafa Y Abdel-Glil, Jörg Linde, Reinhard Fries, Diana Meemken, Helmut Hotzel, Herbert Tomaso","doi":"10.7150/jgen.42790","DOIUrl":"https://doi.org/10.7150/jgen.42790","url":null,"abstract":"<p><p>We report the first draft genome sequence of a <i>Salmonella</i> strain with plasmid-mediated resistance to colistin encoded by <i>mcr-1</i> gene in Vietnam. <i>Salmonella enterica subsp. enterica</i> serovar Rissen was isolated from a Vietnamese pig slaughterhouse in 2013. We can confirm that <i>mcr-1</i> gene is identical to the first reported <i>mcr-1</i> gene of the <i>Escherichia coli</i> strain SHP45, isolated in 2015 from a Chinese pig. The plasmid containing this gene in the strain 19CS0416 was highly related (96.86% identity) to the plasmid (pHNSHP45) contained in this Chinese strain. Moreover, this plasmid was determined to be 100% identical to a plasmid (p13P477T-7) belonging to an <i>Escherichia coli</i> (13P477T) found in Hong Kong during the same year in pigs. Our results will aid in understanding the dissemination of <i>mcr-1</i> gene in East Asia, dating back to as early as 2013.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"76-79"},"PeriodicalIF":0.0,"publicationDate":"2020-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.42790","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38283674","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}
Journal of GenomicsPub Date : 2020-06-29eCollection Date: 2020-01-01DOI: 10.7150/jgen.48656
Anne Busch, Helmut Hotzel, Ulrich Methner
{"title":"Complete genome and plasmid sequences of a multidrug-resistant Salmonella enterica subsp. enterica serovar Panama isolate from a German cattle farm.","authors":"Anne Busch, Helmut Hotzel, Ulrich Methner","doi":"10.7150/jgen.48656","DOIUrl":"https://doi.org/10.7150/jgen.48656","url":null,"abstract":"<p><p>We describe a rare isolate of Salmonella enterica subsp. enterica serovar Panama with an extended-spectrum β-lactamase (ESBL) profile from a German cattle-fattening farm. Applying two next-generation sequencing methods we generated sequences of the genome as well as the plasmids; assembled the draft genome sequence of Salmonella enterica subsp. enterica serovar Panama isolate 18PM0209. Antimicrobial resistance genes, virulence-associated genes and plasmids were analyzed using bioinformatics. Occurrence of multidrug-resistant <i>Salmonella</i> serovars at cattle-fattening farms indicate the need of enhanced surveillance to prevent further spread of these organisms.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"71-75"},"PeriodicalIF":0.0,"publicationDate":"2020-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.48656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38283673","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}
Journal of GenomicsPub Date : 2020-05-18eCollection Date: 2020-01-01DOI: 10.7150/jgen.41196
Dylan Beeber, Frédéric Jj Chain
{"title":"crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications.","authors":"Dylan Beeber, Frédéric Jj Chain","doi":"10.7150/jgen.41196","DOIUrl":"https://doi.org/10.7150/jgen.41196","url":null,"abstract":"<p><p>The success of CRISPR/Cas9 gene editing applications relies on the efficiency of the single guide RNA (sgRNA) used in conjunction with the Cas9 protein. Current sgRNA design software vary in the details they provide on sgRNA sequence efficiency and usually limit organism choice to a list of developer-selected species. The <i>crispRdesignR</i> package aims to address these limitations by providing comprehensive sequence features of the generated sgRNAs in a single program, which allows users to predict sgRNA efficiency and design sgRNA sequences for systems that currently do not have optimized efficiency scoring methods. <i>crispRdesignR</i> reports extensive information on all designed sgRNA sequences with robust off-target calling and annotation and can be run in a user-friendly graphical interface. The <i>crispRdesignR</i> package is implemented in R and has fully editable code for specialized purposes including sgRNA design in user-provided genomes. The package is platform independent and extendable, with its source code and documentation freely available at https://github.com/dylanbeeber/crispRdesignR.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"62-70"},"PeriodicalIF":0.0,"publicationDate":"2020-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.41196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38006908","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}
{"title":"Draft genome sequence of <i>Actinomadura</i> sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway.","authors":"Hisayuki Komaki, Enjuro Harunari, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Kannika Duangmal, Arinthip Thamchaipenet, Yasuhiro Igarashi","doi":"10.7150/jgen.44650","DOIUrl":"10.7150/jgen.44650","url":null,"abstract":"<p><p><i>Actinomadura</i> sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of <i>Actinomadura</i> sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene (<i>t1pks</i>) clusters, a large <i>t1pks</i> cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"53-61"},"PeriodicalIF":0.0,"publicationDate":"2020-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7256010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38006907","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}
Journal of GenomicsPub Date : 2020-04-22eCollection Date: 2020-01-01DOI: 10.7150/jgen.43953
Indika Senevirathna, Dinesha Jayasundara, Joshua P Lefler, Kira L Chaiboonm, Janith Warnasekara, Suneth Agampodi, Michael A Matthias, Joseph M Vinetz
{"title":"Complete Genome Sequence of <i>Leptospira interrogans</i> Strains FMAS_KW1, FMAS_KW2 and FMAS_AW1 Isolated from Leptospirosis Patients from Karawanalla and Awissawella, Sri Lanka.","authors":"Indika Senevirathna, Dinesha Jayasundara, Joshua P Lefler, Kira L Chaiboonm, Janith Warnasekara, Suneth Agampodi, Michael A Matthias, Joseph M Vinetz","doi":"10.7150/jgen.43953","DOIUrl":"https://doi.org/10.7150/jgen.43953","url":null,"abstract":"<p><p>Leptospirosis is an important cause of acute undifferentiated fever and complex multisystem febrile diseases in the tropics and subtropics. Understanding the evolution of <i>Leptospira</i> especially as related to the clinical pathogenesis of leptospirosis is facilitated by systematic comparative genomic analysis of human-infecting isolates. Here, we announce the complete genome sequences of three <i>Leptospira</i> strains that were isolated from blood of humans with undifferentiated fever in Sri Lanka.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"49-52"},"PeriodicalIF":0.0,"publicationDate":"2020-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.43953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38006906","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}