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Genes, Volume 3, Issue 2 (June 2012), Pages 191-343

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Research

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Open AccessArticle Case Study of Sequence Capture Enrichment Technology: Identification of Variation Underpinning Developmental Syndromes in an Amniote Model
Genes 2012, 3(2), 233-247; doi:10.3390/genes3020233
Received: 6 January 2012 / Revised: 4 March 2012 / Accepted: 5 March 2012 / Published: 26 March 2012
Cited by 3 | PDF Full-text (400 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Chicken developmental mutants are valuable for discovering sequences and pathways controlling amniote development. Herein we applied the advanced technologies of targeted sequence genomic capture enrichment and next-generation sequencing to discover the causative element for three inherited mutations affecting craniofacial, limb and/or organ development.
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Chicken developmental mutants are valuable for discovering sequences and pathways controlling amniote development. Herein we applied the advanced technologies of targeted sequence genomic capture enrichment and next-generation sequencing to discover the causative element for three inherited mutations affecting craniofacial, limb and/or organ development. Since the mutations (coloboma, diplopodia-1 and wingless-2) were bred into a congenic line series and previously mapped to different chromosomes, each targeted mutant causative region could be compared to that of the other two congenic partners, thereby providing internal controls on a single array. Of the ~73 million 50-bp sequence reads, ~76% were specific to the enriched targeted regions with an average target coverage of 132-fold. Analysis of the three targeted regions (2.06 Mb combined) identified line-specific single nucleotide polymorphism (SNPs) and micro (1–3 nt) indels. Sequence content for regions indicated as gaps in the reference genome was generated, thus contributing to its refinement. Additionally, Mauve alignments were constructed and indicated putative chromosomal rearrangements. This is the first report of targeted capture array technology in an avian species, the chicken, an important vertebrate model; the work highlights the utility of employing advanced technologies in an organism with only a “draft stage” reference genome sequence. Full article
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Open AccessArticle Heritability of Radiation Response in Lung Cancer Families
Genes 2012, 3(2), 248-260; doi:10.3390/genes3020248
Received: 28 February 2012 / Revised: 7 March 2012 / Accepted: 22 March 2012 / Published: 29 March 2012
Cited by 2 | PDF Full-text (106 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Radiation sensitivity is assumed to be a cancer susceptibility factor due to impaired DNA damage signalling and repair. Relevant genetic factors may also determine the observed familial aggregation of early onset lung cancer. We investigated the heritability of radiation sensitivity in families of
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Radiation sensitivity is assumed to be a cancer susceptibility factor due to impaired DNA damage signalling and repair. Relevant genetic factors may also determine the observed familial aggregation of early onset lung cancer. We investigated the heritability of radiation sensitivity in families of 177 Caucasian cases of early onset lung cancer. In total 798 individuals were characterized for their radiation-induced DNA damage response. DNA damage analysis was performed by alkaline comet assay before and after in vitro irradiation of isolated lymphocytes. The cells were exposed to a dose of 4 Gy and allowed to repair induced DNA-damage up to 60 minutes. The primary outcome parameter Olive Tail Moment was the basis for heritability estimates. Heritability was highest for basal damage (without irradiation) 70% (95%-CI: 51%–88%) and initial damage (directly after irradiation) 65% (95%-CI: 47%–83%) and decreased to 20%–48% for the residual damage after different repair times. Hence our study supports the hypothesis that genomic instability represented by the basal DNA damage as well as radiation induced and repaired damage is highly heritable. Genes influencing genome instability and DNA repair are therefore of major interest for the etiology of lung cancer in the young. The comet assay represents a proper tool to investigate heritability of the radiation sensitive phenotype. Our results are in good agreement with other mutagen sensitivity assays. Full article
(This article belongs to the Special Issue Radiation-Related Cancer 25 Years After Chernobyl)
Open AccessCommunication A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter
Genes 2012, 3(2), 261-277; doi:10.3390/genes3020261
Received: 1 March 2012 / Revised: 30 March 2012 / Accepted: 31 March 2012 / Published: 12 April 2012
Cited by 24 | PDF Full-text (500 KB) | HTML Full-text | XML Full-text
Abstract
Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These
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Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These studies have demonstrated that Campylobacter populations are highly structured, with distinct genotypes associated with particular wild or domestic animal sources, and that chicken meat is the most likely source of most human infection in countries such as the UK. The availability of multiple whole genome sequences from Campylobacter isolates presents the prospect of identifying those genes or allelic variants responsible for host-association and increased human disease risk, but the diversity of Campylobacter genomes present challenges for such analyses. We present a gene-by-gene approach for investigating the genetic basis of phenotypes in diverse bacteria such as Campylobacter, implemented with the BIGSdb software on the pubMLST.org/campylobacter website. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessCommunication The Chernobyl Tissue Bank — A Repository for Biomaterial and Data Used in Integrative and Systems Biology Modeling the Human Response to Radiation
Genes 2012, 3(2), 278-290; doi:10.3390/genes3020278
Received: 2 April 2012 / Revised: 26 April 2012 / Accepted: 29 April 2012 / Published: 9 May 2012
Cited by 3 | PDF Full-text (202 KB) | HTML Full-text | XML Full-text
Abstract
The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer post Chernobyl, the
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The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer post Chernobyl, the Chernobyl Tissue Bank (CTB: www.chernobyltissuebank.com) was established in 1998. Thus far it is has collected biological samples from 3,861 individuals, and provided 27 research projects with 11,254 samples. The CTB was designed from its outset as a resource to promote the integration of research and clinical data to facilitate a systems biology approach to radiation related thyroid cancer. The project has therefore developed as a multidisciplinary collaboration between clinicians, dosimetrists, molecular biologists and bioinformaticians and serves as a paradigm for tissue banking in the omics era. Full article
(This article belongs to the Special Issue Radiation-Related Cancer 25 Years After Chernobyl)
Open AccessArticle The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence
Genes 2012, 3(2), 291-319; doi:10.3390/genes3020291
Received: 27 March 2012 / Revised: 2 May 2012 / Accepted: 8 May 2012 / Published: 16 May 2012
Cited by 3 | PDF Full-text (497 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species,
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The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales. Full article
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
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Review

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Open AccessReview From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens
Genes 2012, 3(2), 191-232; doi:10.3390/genes3020191
Received: 2 February 2012 / Revised: 29 February 2012 / Accepted: 29 February 2012 / Published: 26 March 2012
Cited by 10 | PDF Full-text (890 KB) | HTML Full-text | XML Full-text
Abstract
Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug
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Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
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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