465 results match your criteria Comparative and Functional Genomics [Journal]


Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon.

Comp Funct Genomics 2012 27;2012:628204. Epub 2012 Dec 27.

Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland ; Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014 Tartu, Estonia.

Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Read More

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http://dx.doi.org/10.1155/2012/628204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544263PMC
January 2013
10 Reads

Gemi: PCR primers prediction from multiple alignments.

Comp Funct Genomics 2012 19;2012:783138. Epub 2012 Dec 19.

Facultés de Médecine et de Pharmacie, Aix Marseille Université, URMITE, UM 63, CNRS 7278, INSERM, U1095, 13385 Marseille Cedex 05, France.

Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. Read More

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http://www.hindawi.com/journals/ijg/2012/783138/
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http://dx.doi.org/10.1155/2012/783138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535827PMC
January 2013
10 Reads

TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases.

Comp Funct Genomics 2012 18;2012:678761. Epub 2012 Nov 18.

Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida Y Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile ; Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.

Transposases (Tnps) are enzymes that participate in the movement of insertion sequences (ISs) within and between genomes. Genes that encode Tnps are amongst the most abundant and widely distributed genes in nature. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of ISs. Read More

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http://dx.doi.org/10.1155/2012/678761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506888PMC
December 2012
6 Reads

The α(1)AT and TIMP-1 Gene Polymorphism in the Development of Asthma.

Comp Funct Genomics 2012 21;2012:968267. Epub 2012 Nov 21.

CSIR-Institute of Genomics and Integrative Biology, University Campus, Mall Road, Delhi 110007, India ; Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001, India.

Asthma has been an inflammatory disorder accompanied by tissue remodeling and protease-antiprotease imbalance in lungs. The SNPs of alpha-1 antitrypsin (α(1)AT) and tissue inhibitor of metalloproteinase-1 (TIMP-1) genes were studied for their association with asthma. Genotyping of α(1)AT and TIMP-1 genes was performed in 202 asthmatics and 204 controls. Read More

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http://dx.doi.org/10.1155/2012/968267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512250PMC
December 2012
9 Reads

Comparative Analysis of MicroRNAs between Sporophyte and Gametophyte of Porphyra yezoensis.

Comp Funct Genomics 2012 26;2012:912843. Epub 2012 Sep 26.

Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Nanhai Road 7, Qingdao 266071, China ; School of Earth Science, Graduate University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China.

Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. Read More

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http://dx.doi.org/10.1155/2012/912843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463926PMC
October 2012
11 Reads

Correlation of aquaporins and transmembrane solute transporters revealed by genome-wide analysis in developing maize leaf.

Comp Funct Genomics 2012 26;2012:546930. Epub 2012 Sep 26.

College of Information Sciences and Engineering, Shandong Agricultural University, Shandong, Taian 271018, China ; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong, Taian 271018, China.

Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. Read More

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http://www.hindawi.com/journals/ijg/2012/546930/
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http://dx.doi.org/10.1155/2012/546930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463914PMC
October 2012
11 Reads

Epigenetic control of reprogramming and cellular differentiation.

Comp Funct Genomics 2012 17;2012:538639. Epub 2012 Sep 17.

Dulbecco Telethon Institute (DTI), IRCCS Fondazione Santa Lucia and European Brain Research Institute, 00143 Rome, Italy ; National Research Council, Institute of Translational Pharmacology, via Fosso del Cavaliere 100, 00133 Rome, Italy.

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http://dx.doi.org/10.1155/2012/538639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457607PMC
October 2012
8 Reads

Epigenetic regulation of B lymphocyte differentiation, transdifferentiation, and reprogramming.

Comp Funct Genomics 2012 26;2012:564381. Epub 2012 Aug 26.

Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avenida Gran Via s/n km 2.7, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.

B cell development is a multistep process that is tightly regulated at the transcriptional level. In recent years, investigators have shed light on the transcription factor networks involved in all the differentiation steps comprising B lymphopoiesis. The interplay between transcription factors and the epigenetic machinery involved in establishing the correct genomic landscape characteristic of each cellular state is beginning to be dissected. Read More

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http://dx.doi.org/10.1155/2012/564381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3444840PMC
September 2012
11 Reads

A systems approach and skeletal myogenesis.

Comp Funct Genomics 2012 6;2012:759407. Epub 2012 Sep 6.

Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan ; Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya, Tokyo 157-8535, Japan.

Skeletal myogenesis depends on the strict regulation of the expression of various gene subsets. Therefore, the understanding of genome wide gene regulation is imperative for elucidation of skeletal myogenesis. In recent years, systems approach has contributed to the understanding of various biological processes. Read More

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http://www.hindawi.com/journals/ijg/2012/759407/
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http://dx.doi.org/10.1155/2012/759407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443578PMC
September 2012
13 Reads

Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp.

Comp Funct Genomics 2012 6;2012:752867. Epub 2012 Sep 6.

School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.

Members of the Burkholderia family occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of available Burkholderia genomes has revealed a core set of 178 glycan-associated proteins shared by all Burkholderia of which 68 are homologous to known essential genes. Read More

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http://www.hindawi.com/journals/ijg/2012/752867/
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http://dx.doi.org/10.1155/2012/752867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443583PMC
September 2012
7 Reads

Empirical bayes model comparisons for differential methylation analysis.

Comp Funct Genomics 2012 22;2012:376706. Epub 2012 Aug 22.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.

A number of empirical Bayes models (each with different statistical distribution assumptions) have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e. Read More

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http://dx.doi.org/10.1155/2012/376706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432337PMC
September 2012
14 Reads

Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast.

Comp Funct Genomics 2012 16;2012:653174. Epub 2012 Aug 16.

Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Kueishan, Taoyuan 333, Taiwan.

Genetic robustness refers to a compensatory mechanism for buffering deleterious mutations or environmental variations. Gene duplication has been shown to provide such functional backups. However, the overall contribution of duplication-based buffering for genetic robustness is rather small. Read More

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http://dx.doi.org/10.1155/2012/653174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431050PMC
September 2012
27 Reads

Interactome of Radiation-Induced microRNA-Predicted Target Genes.

Comp Funct Genomics 2012 27;2012:569731. Epub 2012 Jun 27.

Department of Medical Laboratory and Radiation Sciences, University of Vermont, 302 Rowell Building, Burlington, VT 05405, USA.

The microRNAs (miRNAs) function as global negative regulators of gene expression and have been associated with a multitude of biological processes. The dysfunction of the microRNAome has been linked to various diseases including cancer. Our laboratory recently reported modulation in the expression of miRNA in a variety of cell types exposed to ionizing radiation (IR). Read More

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http://dx.doi.org/10.1155/2012/569731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424689PMC
August 2012
8 Reads

Comparative Analysis of SWIRM Domain-Containing Proteins in Plants.

Comp Funct Genomics 2012 17;2012:310402. Epub 2012 Jul 17.

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 51065, China.

Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. Read More

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http://dx.doi.org/10.1155/2012/310402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424641PMC
August 2012
8 Reads

Predictive models of gene regulation from high-throughput epigenomics data.

Comp Funct Genomics 2012 13;2012:284786. Epub 2012 Aug 13.

Computational Genomics, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain.

The epigenetic regulation of gene expression involves multiple factors. The synergistic or antagonistic action of these factors has suggested the existence of an epigenetic code for gene regulation. Highthroughput sequencing (HTS) provides an opportunity to explore this code and to build quantitative models of gene regulation based on epigenetic differences between specific cellular conditions. Read More

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http://dx.doi.org/10.1155/2012/284786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424690PMC
August 2012
8 Reads

Multidimensional scaling applied to histogram-based DNA analysis.

Comp Funct Genomics 2012 24;2012:289694. Epub 2012 Jul 24.

Department of Informatics Engineering, Institute of Engineering, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida 431, 4200-072 Porto, Portugal.

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. Read More

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http://dx.doi.org/10.1155/2012/289694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418642PMC
August 2012
6 Reads

Translational Control across Eukaryotes.

Authors:
Greco Hernández

Comp Funct Genomics 2012 12;2012:317690. Epub 2012 Jul 12.

Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Tlalpan, C.P. 14080, Mexico City, Mexico.

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http://dx.doi.org/10.1155/2012/317690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401530PMC
August 2012
6 Reads

Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis.

Comp Funct Genomics 2012 5;2012:957607. Epub 2012 Jul 5.

Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.

MicroRNAs (miRNAs) are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST)-based combined method was applied for the detection of miRNAs in Macaca fascicularis which is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases of Macaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. Read More

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http://dx.doi.org/10.1155/2012/957607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398586PMC
August 2012
11 Reads

Evolutionary conservation and diversification of the translation initiation apparatus in trypanosomatids.

Comp Funct Genomics 2012 8;2012:813718. Epub 2012 Jul 8.

Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel.

Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. Read More

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http://www.hindawi.com/journals/ijg/2012/813718/
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http://dx.doi.org/10.1155/2012/813718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399392PMC
August 2012
7 Reads

Turning on myogenin in muscle: a paradigm for understanding mechanisms of tissue-specific gene expression.

Comp Funct Genomics 2012 28;2012:836374. Epub 2012 Jun 28.

Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6.

Expression of the myogenin (Myog) gene is restricted to skeletal muscle cells where the transcriptional activator turns on a gene expression program that permits the transition from proliferating myoblasts to differentiating myotubes. The strict temporal and spatial regulation on Myog expression in the embryo makes it an ideal gene to study the developmental regulation of tissue-specific expression. Over the last 20 years, our knowledge of the regulation of Myog expression has evolved from the identification of the minimal promoter elements necessary for the gene to be transcribed in muscle, to a mechanistic understanding of how the proteins that bind these DNA elements work together to establish transcriptional competence. Read More

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http://www.hindawi.com/journals/ijg/2012/836374/
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http://dx.doi.org/10.1155/2012/836374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395204PMC
August 2012
7 Reads

Transposable elements are a significant contributor to tandem repeats in the human genome.

Comp Funct Genomics 2012 24;2012:947089. Epub 2012 Jun 24.

Department of Biological Sciences, Brock University, St. Catharines, ON, Canada L2S 3A1.

Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. Read More

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http://dx.doi.org/10.1155/2012/947089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389668PMC
August 2012
9 Reads

Intron Retention and TE Exonization Events in ZRANB2.

Comp Funct Genomics 2012 17;2012:170208. Epub 2012 Jun 17.

National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk 363-883, Republic of Korea.

The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2), contains arginine/serine-rich (RS) domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3) between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3). Read More

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http://dx.doi.org/10.1155/2012/170208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384923PMC
August 2012
9 Reads

Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists.

Comp Funct Genomics 2012 20;2012:134839. Epub 2012 Jun 20.

Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Read More

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http://dx.doi.org/10.1155/2012/134839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3388326PMC
August 2012
6 Reads

Global Transcriptional Analysis of Olfactory Genes in the Head of Pine Shoot Beetle, Tomicus yunnanensis.

Comp Funct Genomics 2012 18;2012:491748. Epub 2012 Jun 18.

Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming 650224, China.

The most important proteins involved in olfaction include odorant binding protein (OBP), chemosensory protein (CSP), olfactory receptor (OR), and gustatory receptor (GR). Despite that the exhaustive genomic analysis has revealed a large number of olfactory genes in a number of model insects, it is still poorly understood for most nonmodel species. This is mostly due to the reason that the small antenna is challenging for collection. Read More

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http://www.hindawi.com/journals/ijg/2012/491748/
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http://dx.doi.org/10.1155/2012/491748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385610PMC
August 2012
6 Reads

Epigenetic alterations in muscular disorders.

Authors:
Chiara Lanzuolo

Comp Funct Genomics 2012 18;2012:256892. Epub 2012 Jun 18.

CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Via Del Fosso di Fiorano 64, 00143 Rome, Italy.

Epigenetic mechanisms, acting via chromatin organization, fix in time and space different transcriptional programs and contribute to the quality, stability, and heritability of cell-specific transcription programs. In the last years, great advances have been made in our understanding of mechanisms by which this occurs in normal subjects. However, only a small part of the complete picture has been revealed. Read More

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http://dx.doi.org/10.1155/2012/256892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385594PMC
August 2012
6 Reads

The Distribution of eIF4E-Family Members across Insecta.

Comp Funct Genomics 2012 13;2012:960420. Epub 2012 Jun 13.

Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1.

Insects are part of the earliest faunas that invaded terrestrial environments and are the first organisms that evolved controlled flight. Nowadays, insects are the most diverse animal group on the planet and comprise the majority of extant animal species described. Moreover, they have a huge impact in the biosphere as well as in all aspects of human life and economy; therefore understanding all aspects of insect biology is of great importance. Read More

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http://dx.doi.org/10.1155/2012/960420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382400PMC
August 2012
7 Reads

Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application.

Comp Funct Genomics 2012 17;2012:373768. Epub 2012 Jun 17.

Department of Plant Pathology, University of Georgia, Tifton, GA, USA.

Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. Read More

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http://dx.doi.org/10.1155/2012/373768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382957PMC
August 2012
9 Reads

Tackling skeletal muscle cells epigenome in the next-generation sequencing era.

Comp Funct Genomics 2012 3;2012:979168. Epub 2012 Jun 3.

Department of Biomolecular Sciences and Biotechnology, University of Milano, Via Celoria 26, 20133 Milan, Italy.

Recent advances in high-throughput technologies have transformed methodologies employed to study cell-specific epigenomes and the approaches to investigate complex cellular phenotypes. Application of next-generation sequencing technology in the skeletal muscle differentiation field is rapidly extending our knowledge on how chromatin modifications, transcription factors and chromatin regulators orchestrate gene expression pathways guiding myogenesis. Here, we review recent biological insights gained by the application of next-generation sequencing techniques to decode the epigenetic profile and gene regulatory networks underlying skeletal muscle differentiation. Read More

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http://dx.doi.org/10.1155/2012/979168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371680PMC
August 2012
7 Reads

The stability of the induced epigenetic programs.

Authors:
Maria J Barrero

Comp Funct Genomics 2012 3;2012:434529. Epub 2012 Jun 3.

Center of Regenerative Medicine in Barcelona, Aiguader 88, 7th floor, 08003 Barcelona, Spain.

For many years scientists have been attracted to the possibility of changing cell identity. In the last decades seminal discoveries have shown that it is possible to reprogram somatic cells into pluripotent cells and even to transdifferentiate one cell type into another. In view of the potential applications that generating specific cell types in the laboratory can offer for cell-based therapies, the next important questions relate to the quality of the induced cell types. Read More

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http://dx.doi.org/10.1155/2012/434529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371670PMC
August 2012
6 Reads

UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes.

Comp Funct Genomics 2012 27;2012:520732. Epub 2012 May 27.

Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.

Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Read More

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http://dx.doi.org/10.1155/2012/520732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368176PMC
August 2012
22 Reads

Cytoplasmic Ribonucleoprotein Foci in Eukaryotes: Hotspots of Bio(chemical)Diversity.

Comp Funct Genomics 2012 27;2012:504292. Epub 2012 May 27.

Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, CP 1888 Florencio Varela, Argentina.

The life of an mRNA from transcription to degradation offers multiple control check points that regulate gene expression. Transcription, splicing, and translation have been widely studied for many years; however, in recent years, new layers of posttranscriptional and posttranslational control have been uncovered. They involve the regulation of the metabolism of mRNA in cytoplasmic foci. Read More

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http://dx.doi.org/10.1155/2012/504292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368187PMC
August 2012
6 Reads

Before It Gets Started: Regulating Translation at the 5' UTR.

Comp Funct Genomics 2012 28;2012:475731. Epub 2012 May 28.

Greehey Children's Cancer Research Institute, UTHSCSA, San Antonio, TX 78229-3900, USA.

Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g. Read More

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http://dx.doi.org/10.1155/2012/475731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368165PMC
August 2012
14 Reads

Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon.

Comp Funct Genomics 2012 28;2012:418208. Epub 2012 May 28.

Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China.

Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. Read More

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http://dx.doi.org/10.1155/2012/418208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368180PMC
August 2012
6 Reads

Human Genomic Deletions Generated by SVA-Associated Events.

Comp Funct Genomics 2012 20;2012:807270. Epub 2012 May 20.

Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.

Mobile elements are responsible for half of the human genome. Among the elements, L1 and Alu are most ubiquitous. They use L1 enzymatic machinery to move in their host genomes. Read More

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http://dx.doi.org/10.1155/2012/807270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3362811PMC
August 2012
11 Reads

Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes.

Comp Funct Genomics 2012 15;2012:287852. Epub 2012 May 15.

Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.

Restriction of proteins to discrete subcellular regions is a common mechanism to establish cellular asymmetries and depends on a coordinated program of mRNA localization and translation control. Many processes from the budding of a yeast to the establishment of metazoan embryonic axes and the migration of human neurons, depend on this type of cell polarization. How factors controlling transport and translation assemble to regulate at the same time the movement and translation of transported mRNAs, and whether these mechanisms are conserved across kingdoms is not yet entirely understood. Read More

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http://www.hindawi.com/journals/ijg/2012/287852/
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http://dx.doi.org/10.1155/2012/287852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361156PMC
August 2012
10 Reads

Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes.

Comp Funct Genomics 2012 14;2012:258284. Epub 2012 May 14.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Takifugu rubripes is teleost fish widely used in comparative genomics to understand the human system better due to its similarities both in number of genes and structure of genes. In this work we survey the fugu genome, and, using sensitive computational approaches, we identify the repertoire of putative protein kinases and classify them into groups and subfamilies. The fugu genome encodes 519 protein kinase-like sequences and this number of putative protein kinases is comparable closely to that of human. Read More

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http://dx.doi.org/10.1155/2012/258284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359783PMC
August 2012
7 Reads

On the Diversification of the Translation Apparatus across Eukaryotes.

Comp Funct Genomics 2012 14;2012:256848. Epub 2012 May 14.

Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080 Mexico City, Mexico.

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Read More

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http://dx.doi.org/10.1155/2012/256848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359775PMC
August 2012
8 Reads

Versatility of RNA-Binding Proteins in Cancer.

Authors:
Laurence Wurth

Comp Funct Genomics 2012 14;2012:178525. Epub 2012 May 14.

Gene Regulation Programme, Center for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain.

Posttranscriptional gene regulation is a rapid and efficient process to adjust the proteome of a cell to a changing environment. RNA-binding proteins (RBPs) are the master regulators of mRNA processing and translation and are often aberrantly expressed in cancer. In addition to well-studied transcription factors, RBPs are emerging as fundamental players in tumor development. Read More

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http://dx.doi.org/10.1155/2012/178525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359819PMC
August 2012
7 Reads

The role of translation initiation regulation in haematopoiesis.

Comp Funct Genomics 2012 9;2012:576540. Epub 2012 May 9.

Department of Pathology, Medical School, University of Malta, Msida MSD 2090, Malta.

Organisation of RNAs into functional subgroups that are translated in response to extrinsic and intrinsic factors underlines a relatively unexplored gene expression modulation that drives cell fate in the same manner as regulation of the transcriptome by transcription factors. Recent studies on the molecular mechanisms of inflammatory responses and haematological disorders indicate clearly that the regulation of mRNA translation at the level of translation initiation, mRNA stability, and protein isoform synthesis is implicated in the tight regulation of gene expression. This paper outlines how these posttranscriptional control mechanisms, including control at the level of translation initiation factors and the role of RNA binding proteins, affect hematopoiesis. Read More

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http://dx.doi.org/10.1155/2012/576540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357504PMC
August 2012
7 Reads

Pseudogenes.

Authors:
Yusuf Tutar

Comp Funct Genomics 2012 7;2012:424526. Epub 2012 May 7.

Department of Biochemistry, Faculty of Medicine, Cumhuriyet University, 58140 Sivas, Turkey.

Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called "genomic fossils" and treated as "junk DNA" several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Read More

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http://dx.doi.org/10.1155/2012/424526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352212PMC
August 2012
8 Reads

The eIF4F and eIFiso4F Complexes of Plants: An Evolutionary Perspective.

Comp Funct Genomics 2012 7;2012:287814. Epub 2012 May 7.

Department of Chemistry and Biochemistry and the Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.

Translation initiation in eukaryotes requires a number of initiation factors to recruit the assembled ribosome to mRNA. The eIF4F complex plays a key role in initiation and is a common target point for regulation of protein synthesis. Most work on the translation machinery of plants to date has focused on flowering plants, which have both the eIF4F complex (eIF4E and eIF4G) as well as the plant-specific eIFiso4F complex (eIFiso4E and eIFiso4G). Read More

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http://dx.doi.org/10.1155/2012/287814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352336PMC
August 2012
19 Reads

The Bic-C family of developmental translational regulators.

Comp Funct Genomics 2012 7;2012:141386. Epub 2012 May 7.

Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, Canada H3G 0B1.

Regulation of mRNA translation is especially important during cellular and developmental processes. Many evolutionarily conserved proteins act in the context of multiprotein complexes and modulate protein translation both at the spatial and the temporal levels. Among these, Bicaudal C constitutes a family of RNA binding proteins whose founding member was first identified in Drosophila and contains orthologs in vertebrates. Read More

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http://dx.doi.org/10.1155/2012/141386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352585PMC
August 2012
6 Reads

Regulation of Translation Initiation under Abiotic Stress Conditions in Plants: Is It a Conserved or Not so Conserved Process among Eukaryotes?

Comp Funct Genomics 2012 23;2012:406357. Epub 2012 Apr 23.

Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, 28049 Madrid, Spain.

For years, the study of gene expression regulation of plants in response to stress conditions has been focused mainly on the analysis of transcriptional changes. However, the knowledge on translational regulation is very scarce in these organisms, despite in plants, as in the rest of the eukaryotes, translational regulation has been proven to play a pivotal role in the response to different stresses. Regulation of protein synthesis under abiotic stress was thought to be a conserved process, since, in general, both the translation factors and the translation process are basically similar in eukaryotes. Read More

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http://www.hindawi.com/journals/ijg/2012/406357/
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http://dx.doi.org/10.1155/2012/406357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347718PMC
August 2012
12 Reads

The Complete Mitochondrial Genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and Its Phylogenetic Implication.

Comp Funct Genomics 2012 5;2012:328049. Epub 2012 Apr 5.

College of Life Sciences, Anhui Normal University, Wuhu 241000, China.

We here report the first complete mitochondrial (mt) genome of a skipper, Ctenoptilum vasava Moore, 1865 (Lepidoptera: Hesperiidae: Pyrginae). The mt genome of the skipper is a circular molecule of 15,468 bp, containing 2 ribosomal RNA genes, 24 putative transfer RNA (tRNA), genes including an extra copy of trnS (AGN) and a tRNA-like insertion trnL (UUR), 13 protein-coding genes and an AT-rich region. All protein-coding genes (PCGs) are initiated by ATN codons and terminated by the typical stop codon TAA or TAG, except for COII which ends with a single T. Read More

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http://dx.doi.org/10.1155/2012/328049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335176PMC
August 2012
37 Reads
11 Citations
2.030 Impact Factor

Functional genomic analysis of variation on beef tenderness induced by acute stress in angus cattle.

Comp Funct Genomics 2012 12;2012:756284. Epub 2012 Apr 12.

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.

Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Read More

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http://dx.doi.org/10.1155/2012/756284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3332163PMC
August 2012
11 Reads

Transcriptional Regulations on the Low-Temperature-Induced Floral Transition in an Orchidaceae Species, Dendrobium nobile: An Expressed Sequence Tags Analysis.

Comp Funct Genomics 2012 9;2012:757801. Epub 2012 Apr 9.

Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China.

Vernalization-induced flowering is a cold-relevant adaptation in many species, but little is known about the genetic basis behind in Orchidaceae species. Here, we reported a collection of 15017 expressed sequence tags (ESTs) from the vernalized axillary buds of an Orchidaceae species, Dendrobium nobile, which were assembled for 9616 unique gene clusters. Functional enrichment analysis showed that genes in relation to the responses to stresses, especially in the form of low temperatures, and those involving in protein biosynthesis and chromatin assembly were significantly overrepresented during 40 days of vernalization. Read More

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http://www.hindawi.com/journals/ijg/2012/757801/
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http://dx.doi.org/10.1155/2012/757801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328899PMC
August 2012
8 Reads

Expression, Purification, and Characterization of Ras Protein (BmRas1) from Bombyx mori.

Comp Funct Genomics 2012 29;2012:747539. Epub 2012 Mar 29.

Institute of Biochemistry, College of Life Sciences, Zhejiang Sci-Tech University, Zhejiang Province, Hangzhou 310018, China.

The Ras subfamily is the member of small G proteins superfamily involved in cellular signal transduction. Activation of Ras signaling causes cell growth, differentiation, and survival. Bombyx mori Ras-like protein (BmRas1) may belong to the Ras subfamily. Read More

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http://dx.doi.org/10.1155/2012/747539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3321280PMC
August 2012
8 Reads

PASSIOMA: Exploring Expressed Sequence Tags during Flower Development in Passiflora spp.

Comp Funct Genomics 2012 22;2012:510549. Epub 2012 Mar 22.

Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, 13083-860 Campinas, SP, Brazil.

The genus Passiflora provides a remarkable example of floral complexity and diversity. The extreme variation of Passiflora flower morphologies allowed a wide range of interactions with pollinators to evolve. We used the analysis of expressed sequence tags (ESTs) as an approach for the characterization of genes expressed during Passiflora reproductive development. Read More

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http://dx.doi.org/10.1155/2012/510549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318222PMC
August 2012
6 Reads

Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs.

Comp Funct Genomics 2012 16;2012:391546. Epub 2012 Feb 16.

Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Nicolás Cabrera, 1, Cantoblanco, 28049 Madrid, Spain.

The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. The majority of eukaryotic cellular mRNAs initiates translation by the cap-dependent or scanning mode of translation initiation, a mechanism that depends on the recognition of the m(7)G(5')ppp(5')N, known as the cap. However, mRNAs encoding proteins required for cell survival under stress bypass conditions inhibitory to cap-dependent translation; these mRNAs often harbor internal ribosome entry site (IRES) elements in their 5'UTRs that mediate internal initiation of translation. Read More

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http://dx.doi.org/10.1155/2012/391546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3321441PMC
August 2012
7 Reads

Generation and Analysis of Expressed Sequence Tags from Chimonanthus praecox (Wintersweet) Flowers for Discovering Stress-Responsive and Floral Development-Related Genes.

Comp Funct Genomics 2012 21;2012:134596. Epub 2012 Mar 21.

College of Horticulture and Landscape, Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, Southwest University, Chongqing 400715, China.

A complementary DNA library was constructed from the flowers of Chimonanthus praecox, an ornamental perennial shrub blossoming in winter in China. Eight hundred sixty-seven high-quality expressed sequence tag sequences with an average read length of 673.8 bp were acquired. Read More

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http://dx.doi.org/10.1155/2012/134596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318203PMC
August 2012
9 Reads