Special Issue "Feature Paper 2012"

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A special issue of Genes (ISSN 2073-4425).

Deadline for manuscript submissions: closed (30 September 2012)

Special Issue Editor

Guest Editor
Prof. Dr. J. Peter W. Young

Department of Biology, University of York, Heslington, York YO10 5DD, UK
Website | E-Mail
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity

Published Papers (6 papers)

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Research

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Open AccessArticle Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Genes 2012, 3(3), 545-575; doi:10.3390/genes3030545
Received: 6 July 2012 / Revised: 15 August 2012 / Accepted: 15 August 2012 / Published: 30 August 2012
Cited by 17 | PDF Full-text (2373 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches
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Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches in population genetics. These achievements have been made possible by next generation sequencing (NGS) technologies, which require substantial bioinformatics resources to analyze the dense and complex sequence data. The huge analytical burden of data from genome sequencing might be seen as a bottleneck slowing the publication of NGS papers at this time, especially in psychiatric genetics. We review the existing methods for processing NGS data, to place into context the rationale for the design of a computational resource. We describe our method, the Graphical Pipeline for Computational Genomics (GPCG), to perform the computational steps required to analyze NGS data. The GPCG implements flexible workflows for basic sequence alignment, sequence data quality control, single nucleotide polymorphism analysis, copy number variant identification, annotation, and visualization of results. These workflows cover all the analytical steps required for NGS data, from processing the raw reads to variant calling and annotation. The current version of the pipeline is freely available at http://pipeline.loni.ucla.edu. These applications of NGS analysis may gain clinical utility in the near future (e.g., identifying miRNA signatures in diseases) when the bioinformatics approach is made feasible. Taken together, the annotation tools and strategies that have been developed to retrieve information and test hypotheses about the functional role of variants present in the human genome will help to pinpoint the genetic risk factors for psychiatric disorders. Full article
(This article belongs to the Special Issue Feature Paper 2012)
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Open AccessArticle REGEN: Ancestral Genome Reconstruction for Bacteria
Genes 2012, 3(3), 423-443; doi:10.3390/genes3030423
Received: 8 June 2012 / Revised: 23 June 2012 / Accepted: 29 June 2012 / Published: 18 July 2012
Cited by 4 | PDF Full-text (550 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content,
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Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order. Full article
(This article belongs to the Special Issue Feature Paper 2012)
Open AccessArticle Clustering Rfam 10.1: Clans, Families, and Classes
Genes 2012, 3(3), 378-390; doi:10.3390/genes3030378
Received: 5 May 2012 / Revised: 4 June 2012 / Accepted: 15 June 2012 / Published: 5 July 2012
Cited by 1 | PDF Full-text (3062 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its
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The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes. Full article
(This article belongs to the Special Issue Feature Paper 2012)
Open AccessCommunication Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum
Genes 2012, 3(3), 361-377; doi:10.3390/genes3030361
Received: 10 June 2012 / Revised: 24 June 2012 / Accepted: 26 June 2012 / Published: 4 July 2012
Cited by 8 | PDF Full-text (691 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a
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The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis reveals two major sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa species in the region may have more than one introductory event, perhaps from Ethiopia. Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm that could be used to specifically detect Xcm by PCR-based methods. Full article
(This article belongs to the Special Issue Feature Paper 2012)
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Review

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Open AccessReview Radiobiology and Reproduction—What Can We Learn from Mammalian Females?
Genes 2012, 3(3), 521-544; doi:10.3390/genes3030521
Received: 20 June 2012 / Revised: 9 August 2012 / Accepted: 13 August 2012 / Published: 27 August 2012
Cited by 1 | PDF Full-text (292 KB) | HTML Full-text | XML Full-text
Abstract
Ionizing radiation damages DNA and induces mutations as well as chromosomal reorganizations. Although radiotherapy increases survival among cancer patients, this treatment does not come without secondary effects, among which the most problematic is gonadal dysfunction, especially in women. Even more, if radio-induced DNA
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Ionizing radiation damages DNA and induces mutations as well as chromosomal reorganizations. Although radiotherapy increases survival among cancer patients, this treatment does not come without secondary effects, among which the most problematic is gonadal dysfunction, especially in women. Even more, if radio-induced DNA damage occurs in germ cells during spermatogenesis and/or oogenesis, they can produce chromosomal reorganizations associated with meiosis malfunction, abortions, as well as hereditary effects. However, most of our current knowledge of ionizing radiation genotoxic effects is derived from in vitro studies performed in somatic cells and there are only some experimental data that shed light on how germ cells work when affected by DNA alterations produced by ionizing radiation. In addition, these few data are often related to mammalian males, making it difficult to extrapolate the results to females. Here, we review the current knowledge of radiobiology and reproduction, paying attention to mammalian females. In order to do that, we will navigate across the female meiotic/reproductive cycle/life taking into account the radiation-induced genotoxic effects analysis and animal models used, published in recent decades. Full article
(This article belongs to the Special Issue Feature Paper 2012)
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Open AccessReview The Role of Bromodomain Proteins in Regulating Gene Expression
Genes 2012, 3(2), 320-343; doi:10.3390/genes3020320
Received: 30 April 2012 / Revised: 11 May 2012 / Accepted: 17 May 2012 / Published: 29 May 2012
Cited by 20 | PDF Full-text (255 KB) | HTML Full-text | XML Full-text
Abstract
Histone modifications are important in regulating gene expression in eukaryotes. Of the numerous histone modifications which have been identified, acetylation is one of the best characterised and is generally associated with active genes. Histone acetylation can directly affect chromatin structure by neutralising charges
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Histone modifications are important in regulating gene expression in eukaryotes. Of the numerous histone modifications which have been identified, acetylation is one of the best characterised and is generally associated with active genes. Histone acetylation can directly affect chromatin structure by neutralising charges on the histone tail, and can also function as a binding site for proteins which can directly or indirectly regulate transcription. Bromodomains specifically bind to acetylated lysine residues on histone tails, and bromodomain proteins play an important role in anchoring the complexes of which they are a part to acetylated chromatin. Bromodomain proteins are involved in a diverse range of functions, such as acetylating histones, remodeling chromatin, and recruiting other factors necessary for transcription. These proteins thus play a critical role in the regulation of transcription. Full article
(This article belongs to the Special Issue Feature Paper 2012)

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