M. Krasnikova, I. Milyutina, V. K. Bobrova, A. Troitsky, A. Solovyev, S. Morozov
Transacting siRNA loci (TAS3-like) of a particular plant species are usually represented by several gene families. PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant Bryophyta taxa, namely, class Bryopsida (subclasses Bryidae and Dicranidae) and class Sphagnopsida. We found relatives of all four Physcomitrella patens (subclass Funariidae) TAS3-like loci in subclasses Bryidae and Dicranidae. Only representatives of subclass Bryidae encoded TAS3-like genes belonging to P. patens TAS3a and TAS3d families. On the other hand, only the members of order Grimmiales (subclass Dicranidae) encoded gene relatives of P. patens TAS3c family. These data indicate that moss ta-siRNA families have been long conserved during land plant evolution. However, P. patens TAS3-like loci were detected neither in two Sphagnum species from the earliest diverged moss class Sphagnopsida, nor in the Selaginella kraussiana from the earliest extant tracheophyta lineage, Lycopodiopsida.
{"title":"Molecular Diversity of miR390-Guided Transacting siRNA Precursor Genes in Lower Land Plants: Experimental Approach and Bioinformatics Analysis","authors":"M. Krasnikova, I. Milyutina, V. K. Bobrova, A. Troitsky, A. Solovyev, S. Morozov","doi":"10.1155/2011/703683","DOIUrl":"https://doi.org/10.1155/2011/703683","url":null,"abstract":"Transacting siRNA loci (TAS3-like) of a particular plant species are usually represented by several gene families. PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant Bryophyta taxa, namely, class Bryopsida (subclasses Bryidae and Dicranidae) and class Sphagnopsida. We found relatives of all four Physcomitrella patens (subclass Funariidae) TAS3-like loci in subclasses Bryidae and Dicranidae. Only representatives of subclass Bryidae encoded TAS3-like genes belonging to P. patens TAS3a and TAS3d families. On the other hand, only the members of order Grimmiales (subclass Dicranidae) encoded gene relatives of P. patens TAS3c family. These data indicate that moss ta-siRNA families have been long conserved during land plant evolution. However, P. patens TAS3-like loci were detected neither in two Sphagnum species from the earliest diverged moss class Sphagnopsida, nor in the Selaginella kraussiana from the earliest extant tracheophyta lineage, Lycopodiopsida.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"24 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2011-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81199245","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}
Arianne Tremblay, Parsa Hosseini, N. Alkharouf, Shuxian Li, B. Matthews
Soybean rust is caused by the obligate biotrophic fungus Phakopsora pachyrhizi, an exotic pathogen causing important yield losses in soybean production. We used an mRNA-Seq strategy to analyze the expression pattern of soybean genes and better understand molecular events occurring in soybean following the infection. cDNA libraries were constructed from RNA isolated from whole infected soybean leaves 10 days after inoculation with P. pachyrhizi and sequenced using an Illumina platform to identify soybean genes that are affected by pathogen growth. We obtained 15 million sequences corresponding to soybean genes. Forty-two percent of the genes were downregulated including genes encoding proteins involved in amino acid metabolism, carbohydrate metabolism, and transport facilitation; 31% were upregulated including genes encoding proteins involved in lipid metabolism, glycan biosynthesis, and signal transduction. Candidate host genes identified in this study will be manipulated to assay their potential to control soybean rust disease.
{"title":"Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing","authors":"Arianne Tremblay, Parsa Hosseini, N. Alkharouf, Shuxian Li, B. Matthews","doi":"10.1155/2011/827250","DOIUrl":"https://doi.org/10.1155/2011/827250","url":null,"abstract":"Soybean rust is caused by the obligate biotrophic fungus Phakopsora pachyrhizi, an exotic pathogen causing important yield losses in soybean production. We used an mRNA-Seq strategy to analyze the expression pattern of soybean genes and better understand molecular events occurring in soybean following the infection. cDNA libraries were constructed from RNA isolated from whole infected soybean leaves 10 days after inoculation with P. pachyrhizi and sequenced using an Illumina platform to identify soybean genes that are affected by pathogen growth. We obtained 15 million sequences corresponding to soybean genes. Forty-two percent of the genes were downregulated including genes encoding proteins involved in amino acid metabolism, carbohydrate metabolism, and transport facilitation; 31% were upregulated including genes encoding proteins involved in lipid metabolism, glycan biosynthesis, and signal transduction. Candidate host genes identified in this study will be manipulated to assay their potential to control soybean rust disease.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"6 1","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74247580","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}
S. Marzinotto, F. Sessa, A. Franzoni, A. Anselmi, L. Gastaldo, Silvia Mason, G. Damante, C. Beltrami, L. Mariuzzi
KRAS somatic mutations are found in 30–40% of colorectal cancer (CRC). Seven mutations in codons 12 and 13 of KRAS (95% of the observed human mutations) preclude the efficacy of anti-EGFR therapy for the treatment of CRC. Assessment of KRAS mutational status has become a standard procedure in the management of patients with CRC. Technically, KRAS mutation testing can be performed with different methods, characterized by distinct sensitivities and specificities. The present study analyzed KRAS in 182 CRC histological samples by using direct sequencing and a new kit based on a Real-Time Sequence-Specific Primers-PCR technology. The kit allowed to recover as positive 17 samples that were negative or unclear by sequencing, with a recovery rate equal to 13.82%. This study proposes a fast, sensitive, and high-throughput system to identify such seven described mutations of KRAS gene in CRC samples.
在30-40%的结直肠癌(CRC)中发现KRAS体细胞突变。KRAS密码子12和13的7个突变(占观察到的人类突变的95%)排除了抗egfr治疗结直肠癌的疗效。KRAS突变状态的评估已成为CRC患者管理的标准程序。从技术上讲，KRAS突变检测可以用不同的方法进行，具有不同的敏感性和特异性。本研究采用直接测序和基于Real-Time sequence specific primer - pcr技术的新试剂盒对182份结直肠癌组织学样本的KRAS进行了分析。试剂盒对17份测序阴性或不明确的样品恢复为阳性，回收率为13.82%。本研究提出了一种快速、灵敏、高通量的系统来鉴定CRC样本中这七种KRAS基因突变。
{"title":"KRAS Codons 12 and 13 Mutation Analysis: A Comparative Study between Direct Sequencing and a New Sensitive Real-Time PCR Assay","authors":"S. Marzinotto, F. Sessa, A. Franzoni, A. Anselmi, L. Gastaldo, Silvia Mason, G. Damante, C. Beltrami, L. Mariuzzi","doi":"10.1155/2011/895709","DOIUrl":"https://doi.org/10.1155/2011/895709","url":null,"abstract":"KRAS somatic mutations are found in 30–40% of colorectal cancer (CRC). Seven mutations in codons 12 and 13 of KRAS (95% of the observed human mutations) preclude the efficacy of anti-EGFR therapy for the treatment of CRC. Assessment of KRAS mutational status has become a standard procedure in the management of patients with CRC. Technically, KRAS mutation testing can be performed with different methods, characterized by distinct sensitivities and specificities. The present study analyzed KRAS in 182 CRC histological samples by using direct sequencing and a new kit based on a Real-Time Sequence-Specific Primers-PCR technology. The kit allowed to recover as positive 17 samples that were negative or unclear by sequencing, with a recovery rate equal to 13.82%. This study proposes a fast, sensitive, and high-throughput system to identify such seven described mutations of KRAS gene in CRC samples.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"15 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75295012","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}
K. Yamane, T. Nambu, T. Yamanaka, Chiho Mashimo, Chieko Sugimori, K. Leung, H. Fukushima
Rothia mucilaginosa is an opportunistic pathogen in the human oral cavity and pharynx. We found that R. mucilaginosa DY-18, a clinical isolate from a persistent apical periodontitis lesion, had biofilm-like structures. Similar structures were also observed on R. mucilaginosa ATCC25296. To further study these structures, we determined the complete genome sequence of DY-18 and found it a 2.26-Mb chromosome. Regarding stress responsive systems known to affect biofilm formation in many bacteria, DY-18 genome possessed only two sigma factor genes. One of these encoded an additional sigma factor whose promoter-binding activity may be regulated in response to environmental stimuli. Additionally, several genes assigned to two-component signal transduction systems were presented in this genome. To the best of our knowledge, this is the first complete genome of R. mucilaginosa species and our data raise the possibility that this organism regulates the biofilm phenotype through these stress responsive systems.
{"title":"Complete Genome Sequence of Rothia mucilaginosa DY-18: A Clinical Isolate with Dense Meshwork-Like Structures from a Persistent Apical Periodontitis Lesion","authors":"K. Yamane, T. Nambu, T. Yamanaka, Chiho Mashimo, Chieko Sugimori, K. Leung, H. Fukushima","doi":"10.1155/2010/457236","DOIUrl":"https://doi.org/10.1155/2010/457236","url":null,"abstract":"Rothia mucilaginosa is an opportunistic pathogen in the human oral cavity and pharynx. We found that R. mucilaginosa DY-18, a clinical isolate from a persistent apical periodontitis lesion, had biofilm-like structures. Similar structures were also observed on R. mucilaginosa ATCC25296. To further study these structures, we determined the complete genome sequence of DY-18 and found it a 2.26-Mb chromosome. Regarding stress responsive systems known to affect biofilm formation in many bacteria, DY-18 genome possessed only two sigma factor genes. One of these encoded an additional sigma factor whose promoter-binding activity may be regulated in response to environmental stimuli. Additionally, several genes assigned to two-component signal transduction systems were presented in this genome. To the best of our knowledge, this is the first complete genome of R. mucilaginosa species and our data raise the possibility that this organism regulates the biofilm phenotype through these stress responsive systems.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"65 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2010-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85672594","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}
E. Abdelwhab, H. Hafez, M. Aly, C. Grund, T. Harder
Highly pathogenic avian influenza H5N1 virus (HPAIV) continues to be a candidate of a further influenza virus pandemic. Egypt is the country worst affected by human cases of HPAIV H5N1 infection in 2009. Increased infection of preschool children and decreased mortality rates suggested subtle changes in the epidemiology of the infection. Among other factors, the evolution of several conspicuous viral genetic markers in the HA and NA genes of HPAIV H5N1 viruses of human cases from Egypt and their putative influence on biological virus characteristics described here may contribute to this situation.
{"title":"Increasing Prevalence of Unique Mutation Patterns in H5N1 Avian Influenza Virus HA and NA Glycoproteins from Human Infections in Egypt","authors":"E. Abdelwhab, H. Hafez, M. Aly, C. Grund, T. Harder","doi":"10.1155/2010/450823","DOIUrl":"https://doi.org/10.1155/2010/450823","url":null,"abstract":"Highly pathogenic avian influenza H5N1 virus (HPAIV) continues to be a candidate of a further influenza virus pandemic. Egypt is the country worst affected by human cases of HPAIV H5N1 infection in 2009. Increased infection of preschool children and decreased mortality rates suggested subtle changes in the epidemiology of the infection. Among other factors, the evolution of several conspicuous viral genetic markers in the HA and NA genes of HPAIV H5N1 viruses of human cases from Egypt and their putative influence on biological virus characteristics described here may contribute to this situation.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"92 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2010-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90429813","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}
A. Nederbragt, T. Rounge, Kyrre Kausrud, K. Jakobsen
Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.
{"title":"Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads","authors":"A. Nederbragt, T. Rounge, Kyrre Kausrud, K. Jakobsen","doi":"10.1155/2010/782465","DOIUrl":"https://doi.org/10.1155/2010/782465","url":null,"abstract":"Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. \u0000Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.","PeriodicalId":90934,"journal":{"name":"Next generation, sequencing & applications","volume":"188 1","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2010-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74434158","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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