Journal of Genomics最新文献

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Identification and Characterization of a Potential Antibiotic Producing Strain of Pantoea ananatis. 一种潜在抗生素生产菌株的鉴定和特征描述。
Journal of Genomics Pub Date : 2022-02-07 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.70066
Michael J LaGier, Mark McDaniel, Alyssa Ragner, Amber Castillo
{"title":"Identification and Characterization of a Potential Antibiotic Producing Strain of <i>Pantoea ananatis</i>.","authors":"Michael J LaGier, Mark McDaniel, Alyssa Ragner, Amber Castillo","doi":"10.7150/jgen.70066","DOIUrl":"10.7150/jgen.70066","url":null,"abstract":"<p><p>Antibiotic resistance continues to be a significant public health challenge. Soil bacteria represent a potential source of yet to be discovered antimicrobials. The screening of Iowa (United States) soils yielded the identification of a strain of <i>Pantoea ananatis</i> (MMB-1), which displayed an antimicrobial-producing phenotype against a bacterium (<i>Bacillus subtilis</i>) representative of Gram-positive bacteria. Crude, organic, extracts of MMB-1 retained the anti-microbial activity. The draft genome of strain MMB-1 contains a total of 4,634,340 bp, and 4,624 protein-encoding genes. Consistent with phenotypic observation, the genome of MMB-1 encodes for a number of putative secondary metabolite biosynthetic gene clusters, including those known to be involved in the production of the antibiotics lankacidin C and bottromycin. This study increases our overall understanding of <i>Panteoa</i> as a group, and is also consistent with the notion that members of this genus have significant potential as useful natural product producers.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"26-32"},"PeriodicalIF":0.0,"publicationDate":"2022-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39908203","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
Circ-0036602 Acts As a Sponge of MiR-34a-5p and MiR-431-5p to Promote Cervical Cancer Proliferation and Invasion. Circ-0036602作为MiR-34a-5p和MiR-431-5p的海绵促进宫颈癌的增殖和侵袭
Journal of Genomics Pub Date : 2022-01-11 eCollection Date: 2022-01-01 DOI: 10.7150/jgen.62458
Xia Ye, Biqing Zhu, Jingjing Han, Jian Huang, Yaqin Wu
{"title":"Circ-0036602 Acts As a Sponge of MiR-34a-5p and MiR-431-5p to Promote Cervical Cancer Proliferation and Invasion.","authors":"Xia Ye,&nbsp;Biqing Zhu,&nbsp;Jingjing Han,&nbsp;Jian Huang,&nbsp;Yaqin Wu","doi":"10.7150/jgen.62458","DOIUrl":"https://doi.org/10.7150/jgen.62458","url":null,"abstract":"<p><p><b>Background</b>: Cervical cancer (CC) is one of the most common female malignancies worldwide. An increasing body of evidence suggests that circular RNAs (circRNAs) participate in the pathogenesis of various cancers, including CC. However, the expression profile and underlying molecular mechanisms remain largely unknown. <b>Methods</b>: In this study, high throughput sequencing was applied to identify circRNA in HPV-16 positive CC tissues. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression in CC tissues and cell lines. RNase R treatment, gel-electrophoresis, and RNA fluorescent <i>in situ</i> hybridization (FISH) were used to characterize the circRNAs. Subsequently, the Cell Counting Kit-8 assay (CCK8), transwell and wound healing assays were performed to assess circRNA function. Meanwhile, dual-luciferase reporter and western blot were used to clarify the associated molecular mechanisms. <b>Results</b>: Circ0036602 was upregulated in HPV-16 positive CC and correlated with a poor prognosis. Moreover, circ0036602 expression significantly correlated with the clinicopathologic characteristics. Knockdown of circ0036602 inhibited CC cell proliferation, migration, and invasion. Further studies showed that circ0036602 could bind to miR-34-5p and miR-431-5p to regulate the expression of the target gene HMGB1. <b>Conclusions</b>: Taken together, our findings suggest that circ0036602 is a tumor-promoting circRNA that promotes CC cells by sponging miR-34-5p and miR-431-5p to regulate HMGB1. Circ0036602 has huge prospects as a potential therapeutic target for CC patients.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"16-25"},"PeriodicalIF":0.0,"publicationDate":"2022-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39908202","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: 4
Comparative analysis of mRNA transcripts of HT-29 cell line expressed in identical quantities for pathogenic E. coli strains UM146 and UM147 with control Escherichia coli Nissle 1917. 致病性大肠杆菌UM146和UM147与对照大肠杆菌Nissle 1917表达量相同的HT-29细胞系mRNA转录物的比较分析
Journal of Genomics Pub Date : 2022-01-01 DOI: 10.7150/jgen.67277
Roman Kotłowski
{"title":"Comparative analysis of mRNA transcripts of HT-29 cell line expressed in identical quantities for pathogenic <i>E. coli</i> strains UM146 and UM147 with control <i>Escherichia coli</i> Nissle 1917.","authors":"Roman Kotłowski","doi":"10.7150/jgen.67277","DOIUrl":"https://doi.org/10.7150/jgen.67277","url":null,"abstract":"<p><p>Aim of study was comparative analysis of mRNA transcripts of HT-29 cell line, expressed in identical quantities for the combination of pathogenic and non-pathogenic <i>Escherichia coli</i> strains. HT-29 confluent monolayers infection with two pathogenic <i>E. coli</i> strains UM146 and UM147 resulted in two sets of mRNA transcripts that were identical with RNA transcripts obtained for non-pathogenic one strain <i>E. coli</i> Nissle 1917. In this study genome-wide experiments were conducted using expression microarray-system. Only one common mRNA transcript coding for CCDC65 gene was equally expressed by HT-29 cells after incubation challenge with three different <i>E. coli</i> strains used. This gene and its bacterial analogue are important in the ciliary or flagellar motility, respectively. Altogether, 78 and 81 HT-29 mRNA transcripts for <i>E. coli</i> UM146 and <i>E. coli</i> UM147 had identical RNA quantity in comparison to the response obtained for non-pathogenic <i>E. coli</i> Nissle 1917 interactions with HT-29 monolayers. Specific analysis using REACTOME and agriGO terms enrichment data-mining tools as well as word-cloud analysis allowed for identification the most important processes characteristic during HT-29 cell line infections for each pathogenic <i>E. coli</i> strain used. The importance of results may contribute to recognition of those processes during bacterial infections that are identical with processes arising from human interaction with non-pathogenic strains that belong to the same bacterial species.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39892103","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
Genetic Dissection of the Mixing Properties of Wheat Flour (Triticum aestivum L.) Using Unconditional and Conditional QTL Mapping. 小麦粉混合特性的遗传分析使用无条件和条件QTL映射。
Journal of Genomics Pub Date : 2022-01-01 DOI: 10.7150/jgen.67253
Haixia Yu, Yuling An, Aiping Wang, Xin Guan, Jichun Tian, Tangyuan Ning, Kexin Fan, Hao Li, Qianqian Liu, Dongxue Wang, Jiansheng Chen
{"title":"Genetic Dissection of the Mixing Properties of Wheat Flour (<i>Triticum aestivum</i> L.) Using Unconditional and Conditional QTL Mapping.","authors":"Haixia Yu,&nbsp;Yuling An,&nbsp;Aiping Wang,&nbsp;Xin Guan,&nbsp;Jichun Tian,&nbsp;Tangyuan Ning,&nbsp;Kexin Fan,&nbsp;Hao Li,&nbsp;Qianqian Liu,&nbsp;Dongxue Wang,&nbsp;Jiansheng Chen","doi":"10.7150/jgen.67253","DOIUrl":"https://doi.org/10.7150/jgen.67253","url":null,"abstract":"<p><p>Wheat (<i>Triticum aestivum</i> L.) flour mixing properties are essential quality parameters in the dough development process. Limited research on superior alleles for mixing properties has restricted their molecular improvement, and other factors related to the complex traits have been ignored. A molecular map of 9576 polymorphic markers in the RIL population (F<sub>8:9</sub>) (Shannong01-35/Gaocheng9411) was constructed to evaluate mixing property effects in three environments. The parents were selected with markedly distinct high-molecular-weight glutenin subunits (HMW-GS). This study not only evaluated mixing properties using conventional unconditional QTL mapping but also evaluated the relationships between protein-related traits using conditional QTL mapping. The analyses identified most additive QTLs for major mixing properties on chromosomes 1A, 1B, and 1D. Two major loci (<i>1A.1-15</i> and <i>1D-1</i>) associated with mixing properties have confirmed the important contributions of Glu-A1 and Glu-D1 to wheat quality at the QTL level, which were mainly affected by the gluten index. Another important locus, <i>1B.1-24</i> (associated with midline peak value and midline peak width, with high phenotypic variations explained), might represent a new variation distinct from <i>Glu-B1.</i> The favored alleles came from Gaocheng9411. Several mixing properties shared the same QTLs (<i>1B.1-6</i> and <i>1A.1-15</i>), indicating tight linkage or pleiotropism. Genotype-by-environment (G×E) interactions were also investigated in the present study. The QTL results in our study may improve our understanding of the genetic interrelationships between mixing properties and protein-related traits.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":" ","pages":"8-15"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39892105","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
Draft genomes of non-nitrogen-fixing Frankia strains. 绘制非固氮法兰克菌株的基因组。
Journal of Genomics Pub Date : 2021-10-22 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.65429
Camila Carlos-Shanley, Trina Guerra, Dittmar Hahn
{"title":"Draft genomes of non-nitrogen-fixing <i>Frankia</i> strains.","authors":"Camila Carlos-Shanley,&nbsp;Trina Guerra,&nbsp;Dittmar Hahn","doi":"10.7150/jgen.65429","DOIUrl":"https://doi.org/10.7150/jgen.65429","url":null,"abstract":"<p><p>In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing <i>Frankia</i> that were isolated from the root nodules of <i>Coriaria nepalensis</i> and <i>Alnus glutinosa</i>, genospecies CN and Ag, respectively<i>.</i> Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"68-75"},"PeriodicalIF":0.0,"publicationDate":"2021-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39560969","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: 4
Draft Genome Sequences and Genomic Analysis for Pigment Production in Bacteria Isolated from Blue Discolored Soymilk and Tofu. 从蓝变性豆浆和豆腐中分离的细菌的基因组序列草图和色素生产的基因组分析。
Journal of Genomics Pub Date : 2021-09-23 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.65500
Marina E De León, Harriet S Wilson, Guillaume Jospin, Jonathan A Eisen
{"title":"Draft Genome Sequences and Genomic Analysis for Pigment Production in Bacteria Isolated from Blue Discolored Soymilk and Tofu.","authors":"Marina E De León,&nbsp;Harriet S Wilson,&nbsp;Guillaume Jospin,&nbsp;Jonathan A Eisen","doi":"10.7150/jgen.65500","DOIUrl":"https://doi.org/10.7150/jgen.65500","url":null,"abstract":"<p><p>Cold-tolerant bacteria are known to contaminate and cause defects in refrigerated foods. Defects in food products can be observed as changes in appearance, texture, and/or flavor that detract from the product's intended look, feel, or taste. Two distinct organisms were cultured from blue pigmented soymilk and tofu that had been left opened and expired in a home refrigerator. The blue coloration was reproduced when isolates were cultured in fresh, sterile soymilk. These strains also produced a variety of colony color morphologies when cultured on different media types. We report two draft genome sequences of the potential causative agents of blue discoloration of soy foods, <i>Pseudomonas carnis</i> strains UCD_MED3 and UCD_MED7 as well as the 16S rRNA gene sequences of co-occurring strains isolated from the defective soy samples but that did not cause blue discoloration when cultured in fresh soymilk; <i>Serratia liquefaciens</i> strains UCD_MED2 and UCD_MED5.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"55-67"},"PeriodicalIF":0.0,"publicationDate":"2021-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8490086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39540819","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: 2
Identification of a novel pathogenic variant in PALB2 and BARD1 genes by a multigene sequencing panel in triple negative breast cancer in Morocco. 通过多基因测序小组在摩洛哥三阴性乳腺癌中鉴定一种新的PALB2和BARD1基因致病变异。
Journal of Genomics Pub Date : 2021-09-18 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.61713
Abdelilah Laraqui, Mathias Cavaillé, Nancy Uhrhammer, Oubaida ElBiad, Yannick Bidet, Hicham El Rhaffouli, Hicham El Anaz, Driss Moussaoui Rahali, Jaouad Kouach, Khaled Guelzim, Bouabid Badaoui, Abderrahman AlBouzidi, Mohammed Oukabli, Rachid Tanz, Yasser Sbitti, Mohammed Ichou, Khaled Ennibi, Yassine Sekhsokh, Yves-Jean Bignon
{"title":"Identification of a novel pathogenic variant in <i>PALB2</i> and <i>BARD1</i> genes by a multigene sequencing panel in triple negative breast cancer in Morocco.","authors":"Abdelilah Laraqui,&nbsp;Mathias Cavaillé,&nbsp;Nancy Uhrhammer,&nbsp;Oubaida ElBiad,&nbsp;Yannick Bidet,&nbsp;Hicham El Rhaffouli,&nbsp;Hicham El Anaz,&nbsp;Driss Moussaoui Rahali,&nbsp;Jaouad Kouach,&nbsp;Khaled Guelzim,&nbsp;Bouabid Badaoui,&nbsp;Abderrahman AlBouzidi,&nbsp;Mohammed Oukabli,&nbsp;Rachid Tanz,&nbsp;Yasser Sbitti,&nbsp;Mohammed Ichou,&nbsp;Khaled Ennibi,&nbsp;Yassine Sekhsokh,&nbsp;Yves-Jean Bignon","doi":"10.7150/jgen.61713","DOIUrl":"10.7150/jgen.61713","url":null,"abstract":"<p><p>Pathogenic variants (PVs) in <i>BRCA</i> genes have been mainly associated with an increasing risk of triple negative breast cancer (TNBC). The contribution of PVs in non-BRCA genes to TNBC seems likely since the processing of homologous recombination repair of double-strand DNA breaks involves several genes. Here, we investigate the susceptibility of genetic variation of the <i>BRCA</i> and non-<i>BRCA</i> genes in 30 early-onset Moroccan women with TNBC. <b>Methods:</b> Targeted capture-based next generation sequencing (NGS) method was performed with a multigene panel testing (MGPT) for variant screening. Panel sequencing was performed with genes involved in hereditary predisposition to cancer and candidate genes whose involvement remains unclear using Illumina MiSeq platform. Interpretation was conducted by following the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) criteria. <b>Results:</b> PVs were identified in 20% (6/30) of patients with TNBC. Of these, 16.7% (5/30) carried a <i>BRCA</i> PV [10% (3/30) in <i>BRCA1</i>, 6.7% (2/30) in <i>BRCA2</i>] and 6.6% (2/30) carried a non-<i>BRCA</i> PV. The identified PVs in <i>BRCA</i> genes (<i>BRCA1</i> c.798_799delTT, <i>BRCA1</i> c.3279delC, <i>BRCA2</i> c.1310_1313del, and <i>BRCA2</i> c.1658T>G) have been reported before and were classified as pathogenic. The identified founder PVs <i>BRCA1</i> c.798_799del and <i>BRCA2</i> c.1310_1313delAAGA represented 10% (3/30). Our MGPT allowed identification of several sequence variations in most investigated genes, among which we found novel truncating variations in <i>PALB2</i> and <i>BARD1</i> genes. The <i>PALB2</i> c.3290dup and <i>BARD1</i> c.1333G>T variants are classified as pathogenic. We also identified 42 variants of unknown/uncertain significance (VUS) in 70% (21/30) of patients with TNBC, including 50% (21/42) missense variants. The highest VUS rate was observed in <i>ATM</i> (13%, 4/30). Additionally, 35.7% (15/42) variants initially well-known as benign, likely benign or conflicting interpretations of pathogenicity have been reclassified as VUS according to ACMG-AMP. <b>Conclusions:</b> <i>PALB2</i> and <i>BARD1</i> along with <i>BRCA</i> genetic screening could be helpful for a larger proportion of early-onset TNBC in Morocco.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"43-54"},"PeriodicalIF":0.0,"publicationDate":"2021-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8490085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39540818","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: 4
Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India. 临床百日咳杆菌ST2株与印度疫苗参考株的遗传多样性比较
Journal of Genomics Pub Date : 2021-09-03 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.58823
Naresh Chand Sharma, Shalini Anandan, Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi Sethuvel, Karthick Vasudevan, Dhirendra Kumar, Sushil Kumar Gupta, Lucky Sangal, Balaji Veeraraghavan
{"title":"Genetic Diversity of Clinical <i>Bordetella Pertussis</i> ST2 Strains in comparison with Vaccine Reference Strains of India.","authors":"Naresh Chand Sharma,&nbsp;Shalini Anandan,&nbsp;Naveen Kumar Devanga Ragupathi,&nbsp;Dhiviya Prabaa Muthuirulandi Sethuvel,&nbsp;Karthick Vasudevan,&nbsp;Dhirendra Kumar,&nbsp;Sushil Kumar Gupta,&nbsp;Lucky Sangal,&nbsp;Balaji Veeraraghavan","doi":"10.7150/jgen.58823","DOIUrl":"https://doi.org/10.7150/jgen.58823","url":null,"abstract":"<p><p><b>Objectives:</b> Pertussis is a highly contagious disease of the respiratory tract caused by <i>Bordetella pertussis</i>, a bacterium that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical <i>B. pertussis</i> strains from India for the first time. <b>Methods:</b> Complete genome sequencing was performed for two <i>B. pertussis</i> strains using Ion Torrent PGM and Oxford nanopore sequencing method. Data was assembled <i>de novo</i> and the sequence annotation was performed through PATRIC and NCBI server. Downstream analyses of the isolates were performed using CGE server databases for antimicrobial resistance genes, plasmids, and sequence types. The phylogenetic analysis was performed using Roary. <b>Results:</b> The analysis revealed insertional elements flanked by IS<i>481</i>, which has been previously regarded as the important component for bacterial evolution. The two <i>B. pertussis</i> clinical strains exhibited diversity through genome degradation when compared to whole-cell vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. <b>Conclusion:</b> The genome information of Indian clinical <i>B. pertussis</i> strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"38-42"},"PeriodicalIF":0.0,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8437686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39419942","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: 3
Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity. 南非和尼日利亚凝固酶阴性葡萄球菌基因组序列分析凸显环境驱动的异质性
Journal of Genomics Pub Date : 2021-05-13 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.53019
Tawanda Elias Maguvu, Adegboyega Oyedele Oladipo, Cornelius Carlos Bezuidenhout
{"title":"Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity.","authors":"Tawanda Elias Maguvu, Adegboyega Oyedele Oladipo, Cornelius Carlos Bezuidenhout","doi":"10.7150/jgen.53019","DOIUrl":"10.7150/jgen.53019","url":null,"abstract":"<p><p>Here, we report high-quality annotated draft genomes of eight coagulase-negative staphylococci (CoNS) isolates obtained from South Africa and Nigeria. We explored the prevalence of antibiotic resistance and virulence genes, their association with mobile genetic elements. The pan-genomic analysis highlighted the environmentally driven heterogeneity of the isolates. Isolates from Nigeria had at least one gene for cadmium resistance/tolerance, these genes were not detected in isolates from South Africa. In contrast, isolates from South Africa had a <i>tetM</i> gene, which was not detected among the isolates from Nigeria. The observed genomic heterogeneity correlates with anthropogenic activities in the area where the isolates were collected. Moreover, the isolates used in this study possess an open pan-genome, which could easily explain the environmentally driven heterogeneity.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"9 ","pages":"26-37"},"PeriodicalIF":0.0,"publicationDate":"2021-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39023802","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
Draft genome sequences of three filamentous cyanobacteria isolated from brackish habitats. 绘制从微咸生境中分离的三种丝状蓝藻的基因组序列。
Journal of Genomics Pub Date : 2021-02-17 eCollection Date: 2021-01-01 DOI: 10.7150/jgen.53678
Joanne Sarah Boden, Michele Grego, Henk Bolhuis, Patricia Sánchez-Baracaldo
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引用次数: 2
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