Special Issue "Feature Paper 2012"

Guest Editor
Prof. Dr. J. Peter W. Young
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Website: http://www.york.ac.uk/biology/research/ecology-evolution/j-peter-w-young/
E-Mail: jpy1@york.ac.uk
Phone: +44 1904 328630
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity

Submission

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Type of Paper: Review
Title: Origins of Entirely New Genes
Author: Kenji Ikehara
Affiliation: Nara Study Center of The Open University of Japan; E-Mail: sc58059@cc.nara-wu.ac.jp
Abstract: Two main theories have been proposed for the origins of new genes. One is the duplication theory proposed by S. Ohno (1970) and the other is the exon shuffling theory provided by Gilbert et al. (1997). But, it must be pointed out that both theories are insufficient for explaining the origins of new genes, since the ideas require pre-existing ancestor genes. On the other hand, I have proposed another hypothesis for creation of entirely new genes or the first family genes, suggesting that they were created from non-stop frames on anti-sense sequences of GC-rich genes or GC-NSF(a), and of double-stranded GC-rich (SNS)n and (GNC)n genes in the respective eras of the universal, SNS and GNC genetic codes, where S and N mean G or C and one of four nucleotides, respectively. In parallel, I have presented protein 0th-order structures or specific amino acid compositions, in which random joining of amino acids could produce water-soluble globular proteins at a high probability, such as 10 amino acids encoded by SNS and GNC-encoding [GADV]-amino acids, where [GADV] means glycine [G], alanine [A], aspartic acid [D] and valine [V]. In this review, I will discuss on the principle and the reason why entirely new genes could be produced from those anti-sense sequences of the GC-rich genes, base on a view point of the protein 0th-order structures, which contribute to form globular proteins with slightly flexible structures more than extant proteins.

Type of Paper: Article
Title: Ancestral Prokaryotic Genome Reconstruction at the Gene and Replicon Scales
Authors: Kuan Yang, Lenwood S. Heath, and Joao C. Setubal
Affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748  sala 911, 05508-000 São Paulo, SP, Brazil; E-Mail: joao.c.setubal@gmail.com
Abstract: While a large number of computational methods exist for gene-centric phylogenyanalysis, not much has been done for detailed ancestral genome reconstruction. Accurate ancestral genome reconstruction can be understood as a phylogenetic study with more de-tails than a phylogenetic tree reconstruction. We developed a new computational system (REGEN) for ancestral bacterial genome reconstruction at both gene and replicon level. RE-GEN reconstructs gene content, a set of contiguous gene runs, and replicon structure for each genome. Furthermore, along each branch of the phylogenetic tree, it reconstructs possible evolutionary events, including gene level events such as insertion and deletion, and replicon level events such as replicon fission and fusion. The reconstruction can be carried out using either the maximum parsimony or maximum likelihood method. The system has been extensively evaluated using both real and simulated data and applied to a group of species in the Rhizobiales order in α-proteobacteria. To the authors knowledge, this system is the first attempt to perform model-free neighboring gene pairs based ancestral genome reconstruction supporting both maximum parsimony and maximum likelihood methods at both gene and replicon scales.

Type of Paper: Review
Title: Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Authors: Federica Torri ^1,2, Ivo D. Dinov ^2,3, Alen Zamanyan ³, Sam Hobel ³, Alex Genco ³, Petros Petrosyan ³, Andrew P. Clark ⁴, Zhizhong Liu ³, Paul Eggert ^3,5, Jonathan Pierce ³, James A. Knowles ⁴, Joseph Ames ², Carl Kesselman ², Arthur W. Toga ^2,3, Steven G. Potkin ^1,2, Marquis P. Vawter ⁶ and Fabio Macciardi ^{1,2 *}
Affiliations: ¹ Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA 92617, USA; E-Mails: ftorri@uci.edu (F.T.); sgpotkin@uci.edu (S.G.P.); fmacciar@uci.edu (F.M.)
² Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, CA 90292, USA; E-Mails: ivo.dinov@loni.ucla.edu (I.D.D.); jdames@uci.edu (J.A.); toga@loni.ucla.edu (A.W.T.)
³ Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, CA 90095, USA; E-Mails: Alen.Zamanyan@loni.ucla.edu (A.Z.); shobel87@gmail.com (S.H.); alexgenco@gmail.com (A.G.); Petros.Petrosyan@loni.ucla.edu (P.P.); zhizhong.liu@loni.ucla.edu (Z.L.); eggert@cs.ucla.edu (P.E.); jonathan.pierce@loni.ucla.edu (J.P.);
⁴ Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, CA 90033, USA; E-Mail: carl@isi.edu (C.K.)
⁵ Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA; E-Mails: clarkap@usc.edu (A.P.C.); knowles@med.usc.edu (J.K.)
⁶ Functional Genomics Laboratory, Department of Psychiatry And Human Behavior, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; E-Mail: mvawter@uci.edu (M.P.V.)
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 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.

Type of Paper: Review
Title: The Information Content of Genomes
Author: Mark E. Samuels
Affiliation: Department of Medicine, University of Montreal, Centre de Recherche du CHU Ste-Justine, Montreal, PQ, Canada H3T 1C5; Canada; E-Mail: mark.e.samuels@umontreal.ca
Abstract: With the advent of high throughput DNA sequencing technologies, it has become feasible to determine the sequence of whole genomes. There are now large numbers of completed microbial genomes, sequenced essentially to completion, as well as significant numbers of metazoan species (animal – across multiple phyla, and plant) sequenced to near completion. In most cases, only one or a few representative genomes of each metazoan species have been sequenced, but further cost reductions make it likely that this will change in the near future. On the other hand, numerous individual human genomes have been sequenced, some of which data are fully accessible via public databases. The availability of such extensive collections of sequence data allows experimental studies of hitherto more theoretical questions in developmental and evolutionary biology. One such is the information content contained in genomes. This question is inextricably related to the concept of complexity in biological systems. This article will briefly review the literature on complexity and alternative ways to measure it, and will document attempts to apply such measures to genomes, but with a fresh viewpoint stimulated by the explosion of new experimental data.

Type of Paper: Review
Title: Recruitment of Transcription Complexes to Enhancers and the Role of Enhancer Transcription.
Authors: Jared Stees ¹, Fred Varn ¹, John Strouboulis ² and Jörg Bungert ¹
Affiliations: ¹ Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville 32610, FL, USA; E-Mail: jbungert@ufl.edu
² Institute of Molecular Oncology, BSRC Alexander Fleming, Varkiza, Greece; E-Mail: strouboulis@fleming.gr
Abstract: Enhancer elements regulate the tissue-and developmental stage specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we review the current literature on enhancer function and discuss how transcription of enhancers or enhancer generated transcripts could contribute to the regulation of gene expression during the differentiation of cells.