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Genome-wide end-sequenced BAC resources for the NOD/MrkTac and NOD/ShiLtJ mouse genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting beta-cells by an autoimmune driven process. NOD mice represent a valuable tool for studying the genetics of T1D and for evaluating therapeutic interventions. Here we describe the development and characterization by end-sequencing of bacterial artificial chromosome (BAC) libraries derived from NOD/MrkTac (DIL NOD) and NOD/ShiLtJ (CHORI-29), two commonly used NOD substrains. The DIL NOD library is composed of 196,032 BACs and the CHORI-29 library is composed of 110,976 BACs. The average depth of geno...
Source: Genomics - November 9, 2009 Category: Genetics & Stem Cells Authors: Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM, Nefedov M, de Jong PJ, Lyons P, Wicker L, Todd J, Hayashizaki Y, Gulban O, Danska J, Harrow J, Hubbard T, Rogers J, Adams DJ Tags: Genomics Source Type: journals

Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mycosporine-like amino acids (MAAs) are a family of more than 20 compounds having absorption maxima between 310 - 362 nm. These compounds are well known for their UV-absorbing/screening role in various organisms and seem to have evolutionary significance. In the present investigation we tested four cyanobacteria e.g., Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 6301, for their ability to synthesize MAA and conducted genomic and phylogenetic analysis to identify the possible set of genes that might be involved in the biosynthesis of these compounds. Out of th...
Source: Genomics - October 28, 2009 Category: Genetics & Stem Cells Authors: Singh SP, Klisch M, Sinha RP, Häder DP Tags: Genomics Source Type: journals

A mutation in gene CNGA3 is associated with day blindness in sheep.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lambs with congenital day blindness show diminished cone function, which is characteristic of achromatopsia, a congenital disorder described in humans and dogs. To identify gene(s) associated with sheep day blindness, we investigated mutations in the CNGA3, CNGB3, and GNAT2 genes which have been associated with achromatopsia. Sequencing the coding regions of those genes from four affected and eight non-affected lambs showed that all affected lambs were homozygous for a mutation in the CNGA3 gene that changes amino acid R236 to a stop codon. By PCR-RFLP-based testing, homozygosity for the stop codon mutation was detecte...
Source: Genomics - October 26, 2009 Category: Genetics & Stem Cells Authors: Reicher S, Seroussi E, Gootwine E Tags: Genomics Source Type: journals

Reexpression of LGI1 in glioma cells results in dysregulation of genes implicated in the canonical axon guidance pathway.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The LGI1 gene suppresses invasion in glioma cells and predisposes to epilepsy. In a gene expression array comparison between parental cells and T98G cell clones forced to express LGI1, we demonstrate that the canonical axon guidance pathway is the most significantly affected. In particular, aspects of axon guidance that involve reorganization of the actin cytoskeleton, which is also involved in cell movement and invasion, were affected. Analysis of actin fiber organization using fluorescence microscopy demonstrated that different T98G cell clones expressing the exogenous LGI1 gene show high levels of stress fibers comp...
Source: Genomics - October 12, 2009 Category: Genetics & Stem Cells Authors: Kunapuli P, Lo K, Hawthorn L, Cowell JK Tags: Genomics Source Type: journals

Integrated Molecular Analysis Suggests a Three-Class Model for Low-Grade Gliomas: A Proof-of-Concept Study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Integration of genomic, transcriptomic, and morphologic data for class discovery suggests a three class model for low-grade gliomas. Class I represents tumors with molecular similarity to pilocytic astrocytomas, class II tumors are similar to 1p/19q codeleted oligodendrogliomas, and class III represents infiltrative low-grade gliomas. This classification is similar to current clinical paradigms for low-grade gliomas; our work suggests a molecular basis for such models. This classification may supplement or may serve as the basis for a molecular pathologic alternative to current grading schemes for low-grade gl...
Source: Genomics - October 12, 2009 Category: Genetics & Stem Cells Authors: Marko NF, Prayson RA, Barnett GH, Weil RJ Tags: Genomics Source Type: journals

Distribution of DNA methylation, CpGs and CpG islands in human isochores.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, there are more CpG targets that remain unmethylated in the GC-richest, gene-richest isochores in comparison with the other isochores. This conclusion supports the idea that the widespread methylation under consideration here has a general inhibitory effect on gene expression. PMID: 19800400 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - September 29, 2009 Category: Genetics & Stem Cells Authors: Varriale A, Bernardi G Tags: Genomics Source Type: journals

Identification of novel stress-regulated microRNAs from Oryza sativa L.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are a type of small non-coding RNA found in eukaryotes. They play a key role in gene expression by down-regulating gene expression, and are involved in the environment stress response in plants. Although a large number of miRNAs have been identified from Arabidopsis, few studies have focused on Oryza sativa miRNAs, especially on stress related miRNAs. Five cDNA libraries of small RNAs from rice seedlings treated with cold, dehydration, salinity, and abscisic acid (ABA), as well as wild-type seedlings, were constructed. Seven rice novel miRNAs were identified by Northern analysis, and their expression...
Source: Genomics - September 27, 2009 Category: Genetics & Stem Cells Authors: Jian X, Zhang L, Li G, Zhang L, Wang X, Cao X, Fang X, Chen F Tags: Genomics Source Type: journals

Peptidomics and genomics analysis of novel antimicrobial peptides from the frog, Rana nigrovittata.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Much attention has been paid on amphibian peptides for their wide-ranging pharmacological properties, clinical potential, and gene-encoded origin. More than 300 antimicrobial peptides (AMPs) from amphibians have been studied. Peptidomics and genomics analysis combined with functional test including microorganism-killing, histamine releasing and mast cell degranulation were used to investigate antimicrobial peptide diversity. 34 novel AMPs from skin secretions of Rana nigrovittata were identified in current work, and they belong to 9 families, including 6 novel families. Other three families are classified into rugosin,...
Source: Genomics - September 20, 2009 Category: Genetics & Stem Cells Authors: Ma Y, Liu C, Liu X, Wu J, Yang H, Wang Y, Li J, Yu H, Lai R Tags: Genomics Source Type: journals

Genome-scale screening and molecular characterization of membrane-bound transcription factors in Arabidopsis and rice.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Controlled proteolytic activation of membrane-bound transcription factors (MTFs) is recently emerging as a versatile way of rapid transcriptional responses to environmental changes in plants. Here, we report genome-scale identification of putative MTFs in the Arabidopsis and rice genomes. The Arabidopsis and rice genomes have at least 85 and 45 MTFs, respectively, in virtually all major transcription factor families. Of particular interest is the NAC MTFs (designated NTLs): there are at least 18 NTLs in Arabidopsis and 5 NTL members (OsNTLs) in rice. While the full-size OsNTL forms are associated with the membranes, tr...
Source: Genomics - September 16, 2009 Category: Genetics & Stem Cells Authors: Kim SG, Lee S, Seo PJ, Kim SK, Kim JK, Park CM Tags: Genomics Source Type: journals

Identifying errors in avian influenza virus gene sequences and implications for data usage of public databases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Public gene sequence databases have become important research tools to understand viruses and other organisms. Evidence suggests that the identifying information for some of the sequences in these databases might not belong to the sequences they are associated with. We developed two tests to conduct a comprehensive analysis of all published sequences of the hemaglutinin and neuramidase genes of avian influenza viruses (AIVs) to identify sequences that may have been misclassified. One test identified sequence pairs with highly similar nucleotide sequences despite a difference of several years between their sampling date...
Source: Genomics - September 16, 2009 Category: Genetics & Stem Cells Authors: Li J, Zu Dohna H, Miller J, Cardona CJ, Carpenter TE Tags: Genomics Source Type: journals

Improved gene targeting in C. elegans using counter selection and Flp-mediated marker excision.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene targeting is widely used for the precise manipulation of genes. However, in the model organism C. elegans non-transposon mediated gene targeting remains laborious, and as a result has not been widely used. One obstacle to the wider use of this approach is the difficulty of identifying homologous recombination events amongst non-specific events. To improve gene targeting in C. elegans, we used a counter selection approach to reduce the number of false positives; this involved using unc-119 as a positive selection marker and GFP as a counter selection marker which is lost during homologous recombination. This method...
Source: Genomics - September 7, 2009 Category: Genetics & Stem Cells Authors: Vázquez-Manrique RP, Legg JC, Olofsson B, Ly S, Baylis HA Tags: Genomics Source Type: journals

Bacterial genomic G+C composition- eliciting environmental adaptation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacterial genomes reflect their adaptation strategies through nucleotide usage trends found in their chromosome composition. Bacteria, unlike eukaryotes contain a wide range of genomic G+C. This wide variability may be viewed as a response to environmental adaptation. Two overarching trends are observed across bacterial genomes, the first, correlates genomic G+C to environmental niches and lifestyle, whilst the other utilises intra-genomic G+C incongruence to delineate horizontally transferred material. In this review, we focus on the influence of several properties including biochemical, genetic flows, selection biase...
Source: Genomics - September 7, 2009 Category: Genetics & Stem Cells Authors: Mann S, Chen YP Tags: Genomics Source Type: journals

TULIP1 haploinsufficiency with brain development delay.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A novel microdeletion of 14q13.1q13.3 was identified in a patient with developmental delay and intractable epilepsy. The 2.8-Mb deletion included 15 genes, of which TULIP1 was the only gene highly expressed in the brain. Western blotting revealed reduced amount of TULIP1 in cell lysates derived from immortalized lymphocytes of the patient, suggesting the association bewteen TULIP1 haploinsufficiency and the patient's phenotype, then 140 patients were screened for TULIP1 mutations and four missense mutations were identified. Although all four missense mutations were common with parents, reduced TULIP1 was observed in th...
Source: Genomics - September 1, 2009 Category: Genetics & Stem Cells Authors: Shimojima K, Komoike Y, Tohyama J, Takahashi S, Páez MT, Nakagawa E, Goto Y, Ohno K, Ohtsu M, Oguni H, Osawa M, Higashinakagawa T, Yamamoto T Tags: Genomics Source Type: journals

Ontological Discovery Environment: A system for integrating gene-phenotype associations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The wealth of genomic technologies has enabled biologists to rapidly ascribe phenotypic characters to biological substrates. Central to effective biological investigation is the operational definition of the process under investigation. We propose an elucidation of categories of biological characters, including disease relevant traits, based on natural endogenous processes and experimentally observed biological networks, pathways and systems rather than on externally manifested constructs and current semantics such as disease names and processes. The Ontological Discovery Environment (ODE) is an Internet accessible res...
Source: Genomics - September 1, 2009 Category: Genetics & Stem Cells Authors: Baker EJ, Jay JJ, Philip VM, Zhang Y, Li Z, Kirova R, Langston MA, Chesler EJ Tags: Genomics Source Type: journals

Enabling Technologies of Genomic-Scale Sequence Enrichment for Targeted High-Throughput-Sequencing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Next-generation-sequencing has still not reached its full potential due to the technical inability of effectively targeting desired genomic regions of interest. Once available, methods adressing this bottleneck will dramatically reduce cost and enable the efficient analysis of complex samples. Recently, a number of possible approaches for genomic-scale sequence enrichment have been reported using different strategies. All methods basically rely on sequence-specific nucleic acid hybridization, however, they differ in several aspects such as the use of solid phase versus solution phase hybridization, probe design and ove...
Source: Genomics - August 27, 2009 Category: Genetics & Stem Cells Authors: Summerer D Tags: Genomics Source Type: journals

Isolation of cancer specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The antisense promoter of human LINE-1 (L1) retroelements can direct transcription of adjacent unique genomic sequences generating chimeric RNAs, which can perturb transcription of neighbouring genes. As L1 elements constitute 17% of the human genome, chimeric transcription is potentially widespread, but the extent to which this occurs is largely unknown. Using a genome-wide screen we have isolated novel chimeric transcripts that are unique to breast cancer cell lines, primary tumours and colon cancer cells. Expression of the cancer specific chimeric transcripts can be induced in non-malignant breast epithelial cells b...
Source: Genomics - August 27, 2009 Category: Genetics & Stem Cells Authors: Cruickshanks HA, Tufarelli C Tags: Genomics Source Type: journals

YY1-dependent transcriptional regulation of the human GDAP1 gene.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Charcot-Marie-Tooth disease (CMT) is a heritable neurodegenerative condition, some types of which (notably CMT4A) are caused by mutations in the GDAP1 gene that encodes a protein of unknown molecular function implicated in regulation of mitochondrial fission. Here we present for the first time a functional analysis of the GDAP1 gene promoter which we found to be transcriptionally regulated by YY1, a broadly studied factor that seems to be involved in regulating many of the same cellular phenomena as GDAP1. We show that GDAP1 is broadly expressed in cancer cell lines of different tissue origin, contrasting with the rest...
Source: Genomics - August 27, 2009 Category: Genetics & Stem Cells Authors: Ratajewski M, Pulaski L Tags: Genomics Source Type: journals

Structural differentiation of the three eukaryotic RNA polymerases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
All eukaryotes have three different RNA polymerases (RNAPs) which transcribe different types of genes. RNA polymerase I transcribes rRNA genes, RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes, and RNA polymerase III transcribes tRNA and 5S rRNA genes. Here, we use an in silico approach to identify putative functional differences between these three RNAPs. Our results show that cleft loops are the most conserved regions of RNAPs, but that these regions have several significant length differences between the three RNAPs. There were also significant shifts in the rates of evolution of some amino acid si...
Source: Genomics - August 27, 2009 Category: Genetics & Stem Cells Authors: Carter R, Drouin G Tags: Genomics Source Type: journals

The plasticity of the mammalian transcriptome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The dogmatic view of RNA as a mere necessity in the transfer of information between DNA and proteins has during recent years come into question. Novel approaches and new technology has revealed an unprecedented level of inherent complexity in the mammalian transcriptome. Here, the majority of nucleotides are expressed, in sharp contrast to the approximately 1.2 % of the human genome harboring protein coding information. Also, >50 % of genomic loci contain antisense and interleaved transcription, a conservative estimate since non-coding RNA is highly regulated between tissues and developmental stages, which has only ...
Source: Genomics - August 26, 2009 Category: Genetics & Stem Cells Authors: Lindberg J, Lundeberg J Tags: Genomics Source Type: journals

ReTRN: a retriever of real transcriptional regulatory network and expression data for evaluating structure learning algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One of the important goals in systems biology is to infer transcription network based on gene expression data. Validation of the reconstructed network often requires benchmark datasets, e.g. gene expression data, which are usually unattainable. Synthetic datasets are therefore often needed to test the structure learning algorithms in a fast and reproducible manner. However, due to the lack of knowledge about the gene expression profiles, synthetic datasets may not resemble the biological reality. Here we present a computational tool, namely, ReTRN (Real Transcriptional Regulatory Networks) for extracting subnetworks fr...
Source: Genomics - August 23, 2009 Category: Genetics & Stem Cells Authors: Li Y, Zhu Y, Bai X, Cai H, Ji W, Guo D Tags: Genomics Source Type: journals

Convergent Random Forest Predictor: Methodology for predicting drug response from genome-scale data applied to anti-TNF response.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biomarker development for prediction of patient response to therapy is one of the goals of molecular profiling of human tissues. Due to the large number of transcripts, relatively limited number of samples, and high variability of data, identification of predictive biomarkers is a challenge for data analysis. Furthermore, many genes may be responsible for drug response differences, but often only a few are sufficient for accurate prediction. Here we present an analysis approach, the Convergent Random Forest (CRF) method, for the identification of highly predictive biomarkers. The aim is to select from genome-wide expre...
Source: Genomics - August 18, 2009 Category: Genetics & Stem Cells Authors: Bienkowska J, Dagin G, Batliwalla F, Allaire N, Roubenoff R, Gregersen P, Carulli J Tags: Genomics Source Type: journals

A Discovery of Novel microRNAs in the Silkworm (Bombyx mori) Genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are pivotal regulators involved in various physiological and pathological processes via their post-transcriptional regulation of gene expressions. We sequenced 14 libraries of small RNAs constructed from samples spanning the life cycle of silkworms, and discovered 52 novel miRNAs previously not known in animals and verified 45 of them using stem-loop RT-PCR. Our genome-wide analyses of 27 species-specific miRNAs suggest they arise from transposable elements, protein-coding genes duplication/transposition and random foldback sequences; which is consistent with the idea that novel animal miRNAs may evo...
Source: Genomics - August 18, 2009 Category: Genetics & Stem Cells Authors: Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J Tags: Genomics Source Type: journals

Identification of significant regional genetic variations using continuous CNV values in aCGH data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we propose a method, shifted ANOVA, to detect significantly altered regions. This method, based on the standard ANOVA, analyzes changes in copy number variation for regions. The selected regions have the group effect only, but no effect within samples and no interactive effects. The performance of the proposed method is evaluated from the homogeneity and classification accuracies of the selected regions. Shifted ANOVA may identify new candidate genes neighboring known because it detects significantly altered chromosomal regions, rather than independent probes. PMID: 19699295 [PubMed - as supplied by publ...
Source: Genomics - August 18, 2009 Category: Genetics & Stem Cells Authors: Kim KY, Lee GY, Kim J, Jeung HC, Chung HC, Rha SY Tags: Genomics Source Type: journals

Hemophilia B is a quasi-quantitative condition with certain mutations showing phenotypic plasticity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hemophilia B has been considered as a classical monogenetic disorder with complete penetrance. Here, we observed that its allelic spectrum encompasses mutations that show least phenotypic variation as well as those showing phenotypic plasticity, thereby establishing hemophilia B as a quasi-quantitative condition with variable expressivity. Thus, we relocate it from simple monogenic diseases with complete penetrance into a space that marks the conceptual continuum of Mendelian to complex diseases. By computational analysis, we show that mutations showing phenotypic variation were characterized by relatively less conserv...
Source: Genomics - August 18, 2009 Category: Genetics & Stem Cells Authors: Chavali S, Ghosh S, Bharadwaj D Tags: Genomics Source Type: journals

The transcriptional regulation of protein complexes; a cross-species perspective.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The extent of co-expression of the components of a comprehensive set of 244 multi-subunit protein complexes over large DNA microarray data sets was investigated in S. cerevisiae, A. thaliana, C. elegans, D. melanogaster and H. sapiens. Co-expression amongst the components of protein complexes is substantial and occurs in all the species studied, reflecting the importance of regulation at the level of the transcript. Complexes that are conserved in all species, and tend to be associated with very fundamental biological processes, are significantly more likely to have co-expressed components, indicating the fundamental a...
Source: Genomics - August 17, 2009 Category: Genetics & Stem Cells Authors: Webb EC, Westhead DR Tags: Genomics Source Type: journals

Relative quantitation of restriction fragment length polymorphic DNAs via DNA melting analysis provides an effective way to determine allele frequencies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To accurately and precisely estimate the allele frequencies in DNA pools for a cost-effective approach to correlate genetic variations to phenotypic traits, we exploited differential melting kinetics between restriction fragment length polymorphic DNAs. The allele frequencies of two SNPs in a series of DNA mixtures with known allelic compositions of the SNPs were determined by analyzing the meltings of restricted PCR amplicons, yielding a result with a root mean square error (RMSE) of 0.014 relative to the expected values and a standard deviation (SD) of 0.018 from triplicate measurements. This method was then applied ...
Source: Genomics - August 13, 2009 Category: Genetics & Stem Cells Authors: Yu H, Koo I, Jeong S Tags: Genomics Source Type: journals

Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over the past decade genomic approaches have begun to revolutionise the study of animal diversity. In particular, genome sequencing programmes have spread beyond the traditional model species to encompass an increasing diversity of animals from many different phyla, as well as unicellular eukaryotes that are closely related to the animals. Whole genome sequences allow researchers to establish, with reasonable confidence, the full complement of any particular family of genes in a genome. Comparison of gene complements from appropriate genomes can reveal the evolutionary history of gene families, indicating when both gen...
Source: Genomics - August 9, 2009 Category: Genetics & Stem Cells Authors: Shimeld SM, Degnan B, Luke GN Tags: Genomics Source Type: journals

Pleiotropic Effects of RecQ in Deinococcus radiodurans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In Deinococcus radiodurans, there is a unique RecQ homolog (DR1289) with three-tandem HRDC domains. Deletion of drrecQ resulted in a low doubling rate and sensitivity to hydrogen peroxide. Here, we used cDNA microarray and biochemical assays to explore the physiological changes in the drrecQ mutant. The expressions of genes with predicted functions involved in iron homeostasis, antioxidant system, electron transport, and energy metabolism were significantly altered in response to drrecQ disruption. More reactive oxygen species (ROS) was accumulated in drrecQ mutant strain when compared to wild type. In addition, ICP-MS...
Source: Genomics - August 9, 2009 Category: Genetics & Stem Cells Authors: Chen H, Huang L, Hua X, Ying L, Hu Y, Wang C, Chen W, Yu X, Xu Z, Tian B, Hu S, Hua Y Tags: Genomics Source Type: journals

Identification of methods for use of formalin-fixed, paraffin embedded tissue samples in RNA expression profiling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Formalin-fixed paraffin embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent bioanlyzer, and amplification of the 28S ribosomal RNA, were p...
Source: Genomics - August 2, 2009 Category: Genetics & Stem Cells Authors: Roberts L, Bowers J, Sensinger K, Lisowski A, Getts R, Anderson MG Tags: Genomics Source Type: journals

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study we de_ne a set of 2,827 short ultraconserved promoter regions (SUPR) in 5kb upstream regions of 1,268 human protein-coding genes using a de_nition of 98% identity for at least 30bp in 7 mammalian species. Our analysis shows that SUPRs are enriched in genes playing a role in regulation and development. Many of the genes having a SUPR-containing promoter have additional alternative promoters that do not contain SUPRs. Comparison of such promoters by CAGE tag, EST, and Solexa read analysis revealed that SUPR-associated transcripts show a signi_cantly higher mean expression than transcripts associated with non-SU...
Source: Genomics - August 2, 2009 Category: Genetics & Stem Cells Authors: Rodelsperger C, Kohler S, Schulz MH, Manke T, Bauer S, Robinson PN Tags: Genomics Source Type: journals

Structural Analysis of 83-kb Genomic DNA from Thellungiella halophila: Sequence Features and Microcolinearity between Salt Cress and Arabidopsis thaliana.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Salt cress (Thellungiella halophila) has become a desirable plant model for molecular analysis of the mechanisms of salt tolerance. Analysis of its physiological action and expressed EST has resulted in better understanding. However, less is known about its genomic features. Here we determined a continuous sequence approximately 83 kb from a salt cress BAC clone, providing the first insight into the genomic feature for this species. The gene density is approximately one gene per 3.6 kb in this sequence. Many types of repetitive sequences are present in this salt cress sequence, including LTR-retroelementsDNA transponso...
Source: Genomics - July 27, 2009 Category: Genetics & Stem Cells Authors: Deng Z, Li Y, Xia R, Wang W, Huang X, Zhang L, Zhang S, Yang C, Zhang Y, Chen M, Xie Q Tags: Genomics Source Type: journals

14-3-3 proteins: insights from genome-wide studies in yeast.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
1433 proteins form a family of highly conserved, acidic, dimeric proteins. These proteins have been identified in all eukaryotic species investigated, often in multiple isoforms, up to 13 in the plant Arabidopsis thaliana. Hundreds of proteins, from diverse eukaryotic organisms, implicated in numerous cellular processes, have been identified as binding partners of 14-3-3 proteins. Therefore, the major activity of 14-3-3 proteins seems to be its ability to bind other intracellular proteins. Binding to 14-3-3 proteins may result in a conformational change of the protein required for its full activity or for inhibition of...
Source: Genomics - July 21, 2009 Category: Genetics & Stem Cells Authors: van Heusden GP Tags: Genomics Source Type: journals

A genome-wide screen in Saccharomyces cerevisiae Reveals Pathways affected By Arsenic Toxicity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have used Saccharomyces cerevisiae to identify toxicologically important proteins and pathways involved in arsenic-induced toxicity and carcinogenicity in humans. We performed a systemic screen of the complete set of 4,733 haploid S. cerevisiae single gene deletion mutants to identify those that have decreased or increased growth, relative to wild-type, after exposure to sodium arsenite (NaAsO(2)). IC(50) values for all mutants were determined to further validate our results. Ultimately we identified 248 mutants sensitive to arsenite and 5 mutants resistant to arsenite exposure. We analyzed the proteins correspondin...
Source: Genomics - July 20, 2009 Category: Genetics & Stem Cells Authors: Zhou X, Arita A, Ellen TP, Liu X, Bai J, Rooney JP, Kurtz AD, Klein CB, Dai W, Begley TJ, Costa M Tags: Genomics Source Type: journals

Conserved miRNAs analysis in Gossypium hirsutum through small RNAs sequencing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, to analyze the miRNAs in cotton, a small RNA library of the sequences from 18 to 26 nt of Gossypium hirsutum seedling have been built by high-throughput sequencing. In this library, 34 conserved miRNA families were identified by homology search and the miRNA sequences of them were also found in the library. Furthermore, potential targets of these conserved miRNA families were predicted in cotton TC library. However, based on the mature miRNAs and their miR sequences, only 8 conserved miRNA encoding loci (miR156, miR157a, miR157b, miR162, miR164, miR393, miR399, miR827) were identified from cotton EST sequenc...
Source: Genomics - July 19, 2009 Category: Genetics & Stem Cells Authors: Ruan MB, Zhao YT, Meng ZH, Wang XJ, Yang WC Tags: Genomics Source Type: journals

Evolutionary Developmental Genomics: at the 2008 meeting of the European Society for Evolutionary Developmental Biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19615437 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - July 13, 2009 Category: Genetics & Stem Cells Authors: Ferrier DE, Martinez P Tags: Genomics Source Type: journals

Localization of Type 1 Diabetes susceptibility in the Ancestral Haplotype 18.2 by high density SNP mapping.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Previous studies have suggested that the ancestral haplotype 18.2 (AH18.2) carries additional susceptibility gene to Type 1 Diabetes (T1D) on the Major Histocompatibility Complex (MHC). We analyzed 10 DR3/TNFa1b5 homozygous subjects in order to establish the conservation of the AH18.2 and then compared this conserved region with other DR3 haplotype, the AH8.1. The Illumina's HumanHap550 Bead chip was used to perform an extensive genotyping of the MHC region. The AH18.2 was highly conserved between DDR1 and HLA-DQA1 genes; therefore most probably the second susceptibility gene is located within this region. We can exclu...
Source: Genomics - July 6, 2009 Category: Genetics & Stem Cells Authors: Santiago JL, Li W, Lee A, Martinez A, Chandrasekaran A, Fernandez-Arquero M, Khalili H, de la Concha EG, Urcelay E, Gregersen PK Tags: Genomics Source Type: journals

A mutation of the WFDC1 gene is responsible for multiple ocular defects in cattle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Multiple ocular defects (MOD) in cattle is an autosomal recessive hereditary disorder characterized by dysplasia of the lens, retinal detachment, persistence of the hyaloid artery, and microphthalmia. The locus responsible for MOD has been mapped to the proximal region of bovine chromosome 18. In the present study, we refined the localization of the MOD locus to a 1.0-Mb interval by haplotype analysis using a pedigree of affected animals. Comparison of nucleotide sequence of genes in this region revealed a one-nucleotide insertion in the WFDC1 gene, which resulted in a frame shift mutation and premature termination cod...
Source: Genomics - June 28, 2009 Category: Genetics & Stem Cells Authors: Abbasi AR, Khalaj M, Tsuji T, Tanahara M, Uchida K, Sugimoto Y, Kunieda T Tags: Genomics Source Type: journals

Estimating the age of retrotransposon subfamilies using maximum likelihood.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a maximum likelihood model to estimate the age of retrotransposon subfamilies. This method is designed around a master gene model which assumes a constant retrotransposition rate. The statistical properties of this model and an ad hoc estimation procedure are compared using two simulated data sets. We also test whether each estimation procedure is robust to violation of the master gene model. According to our results, both estimation procedures are accurate under the master gene model. While both methods tend to overestimate ages under the intermediate model, the maximum likelihood estimate is significantly less...
Source: Genomics - June 28, 2009 Category: Genetics & Stem Cells Authors: Marchani EE, Xing J, Witherspoon DJ, Jorde LB, Rogers AR Tags: Genomics Source Type: journals

Identification of FAM46D as a novel Cancer/Testis antigen using EST data and serological analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cancer/Testis Antigens (CTAs) are immunogenic proteins with a restricted expression pattern in normal tissues and aberrant expression in different types of tumors being considered promising candidates for immunotherapy. We used the alignment between EST sequences and the human genome sequence to identify novel CT genes. By examining the EST tissue composition of known CT clusters we defined parameters for the selection of 1,184 EST clusters corresponding to putative CT genes. The expression pattern of 70 CT gene candidates was evaluated by RT-PCR in 21 normal tissues, 17 tumor cell lines and 160 primary tumors. We were...
Source: Genomics - June 16, 2009 Category: Genetics & Stem Cells Authors: Bettoni F, Filho FC, Grosso DM, Galante PA, Parmigiani RB, Geraldo MV, Henrique-Silva F, Oba-Shinjo SM, Marie SK, Soares FA, Brentani HP, Simpson AJ, de Souza SJ, Camargo AA Tags: Genomics Source Type: journals

An Integrated Approach to Infer Causal Associations among Gene Expression, Genotype Variation, and Disease.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene expression data and genotype variation data are now capable of providing genome-wide patterns across many different clinical conditions. However, the separate analysis of these data has limitations in elucidating the complex network of gene interactions underlying complex traits, such as common human diseases. More information about the identity of key driver genes of common diseases comes from integrating these two heterogeneous types of data. We developed a two-step procedure to characterize complex diseases by integrating genotype variation data and gene expression data. The first step elucidates the causal rel...
Source: Genomics - June 16, 2009 Category: Genetics & Stem Cells Authors: Lee E, Cho S, Kim K, Park T Tags: Genomics Source Type: journals

An extended anchored linkage map and virtual mapping for the American mink genome based on homology to human and dog.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report we present an extended linkage map of the American mink (Neovison vison) consisting of 157 microsatellite markers and comprising at least one linkage group for each of the autosomes. Each linkage group has been assigned to a chromosome and oriented by fluorescence in situ hybridization (FISH) and/or by means of human/dog/mink comparative homology. The average interval between markers is 8.5 cM and the linkage groups collectively span 1340 cM. In addition, 217 and 275 mink microsatellites have been placed on human and dog genomes, respectively. In conjunction with the existing comparative human/dog/mink data,...
Source: Genomics - June 8, 2009 Category: Genetics & Stem Cells Authors: Anistoroaei R, Ansari S, Farid A, Benkel B, Karlskov-Mortensen P, Christensen K Tags: Genomics Source Type: journals

Genetic contribution of chemokine receptor 2 (CCR2) polymorphisms towards increased serum total IgE levels in Indian asthmatics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The chemokine (C-C motif) receptors (CCR) 2 and 5 are members of a large family of G protein-coupled receptors, playing important roles in asthma pathogenesis. Using standard sequencing techniques, a total of 15 single nucleotide and 8 insertion/deletion polymorphisms (DIPs) (5 novels) were identified in and around these two genes. None of the studied polymorphisms (N=7, selected on the basis on linkage disequilibrium) was associated with asthma in a case (N=315) - control (N=337) study and showed no evidence for non-random transmission to individuals with asthma/atopy in Indian pedigrees (n=235). However, multilocus h...
Source: Genomics - June 8, 2009 Category: Genetics & Stem Cells Authors: Batra J, Ghosh B Tags: Genomics Source Type: journals

Candidate Agtr2 influenced genes and pathways identified by expression profiling in the developing brain of Agtr2(-/y) mice.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides insight into Agtr2 influenced candidate genes and suggests that expression dysregulation of these genes may modulate Agtr2 actions in the brain that influences learning and memory. PMID: 19501643 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - June 5, 2009 Category: Genetics & Stem Cells Authors: Pawlowski TL, Heringer-Walther S, Cheng CH, Archie JG, Chen CF, Walther T, Srivastava AK Tags: Genomics Source Type: journals

Critical evaluation of the FANTOM3 non-coding RNA transcripts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We studied the genomic positions of 38,129 putative ncRNAs from the RIKEN dataset in relation to protein-coding genes. We found that the dataset has 41% sense, 6% antisense, 24% intronic and 29% intergenic transcripts. Interestingly, 17,678 (47%) of the FANTOM3 transcripts were found to potentially be internally primed from longer transcripts. The highest fraction of these transcripts was found among the intronic transcripts and as many as 77% or 6929 intronic transcripts were both internally primed and unspliced. We defined a filtered subset of 8535 transcripts that did not overlap with protein-coding genes, did not c...
Source: Genomics - June 5, 2009 Category: Genetics & Stem Cells Authors: Nordström KJ, Mirza MA, Almén MS, Gloriam DE, Fredriksson R, Schiöth HB Tags: Genomics Source Type: journals

Estimation of bacterial species phylogeny through oligonucleotide frequency distances.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Classification of bacteria is mainly based on sequence comparisons of certain homologous genes such as 16S rRNA. Recently there are challenges to classify bacteria using oligonucleotide frequency pattern of nonhomologous sequences. However, the evolutionary significance of oligonucleotides longer than tetra-nucleotide is not studied well. We performed phylogenetic analysis by using the Euclidean distances calculated from the di to deca-nucleotide frequencies in bacterial genomes, and compared these oligonucleotide frequency-based tree topologies with those for 16S rRNA gene and concatenated seven genes. When oligonucle...
Source: Genomics - May 31, 2009 Category: Genetics & Stem Cells Authors: Takahashi M, Kryukov K, Saitou N Tags: Genomics Source Type: journals

Genome-wide analysis reveals increased levels of transcripts related with infectivity in peanut lectin non-agglutinated promastigotes of Leishmania infantum.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Metacyclic promastigotes are transmitted during bloodmeals after development inside the gut of the sandfly vector. The isolation from axenic cultures of procyclic and metacyclic promastigotes by peanut lectin agglutination followed by differential centrifugation is controversial in Leishmania infantum. The purpose of this study has been to isolate both fractions simultaneously from the same population in stationary phase of axenic culture and compare their expression profiles by whole-genome shotgun DNA microarrays. The 317 genes found with meaningful values of stage-specific regulation demonstrate that negative select...
Source: Genomics - May 31, 2009 Category: Genetics & Stem Cells Authors: Alcolea PJ, Alonso A, Sánchez-Gorostiaga A, Moreno-Paz M, Gómez MJ, Ramos I, Parro V, Larraga V Tags: Genomics Source Type: journals

An evolutionarily conserved nested gene pair - Mab21 and Lrba/Nbea in metazoan.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The embedding of one gene in another as a nested gene pair is a unique phenomenon of gene clustering in the metazoan genome. A gene-centric paralogous genomic sequence comparison strategy was used in this study to align these paralogous nested pairs, Mab21l2-Lrba and Mab21l1-Nbea, to identify the associated paralogous non-coding elements (pNEs) they shared. A majority of these pNEs in the Mab21l2-Lrba locus display tissue-specific enhancer activities recapitulating the expression profiles of Mab21l2 and Mab21l1. Since these enhancers are spread into the introns of Lrba, dissociation of the two genes will likely disrupt...
Source: Genomics - May 28, 2009 Category: Genetics & Stem Cells Authors: Tsang WH, Shek KF, Lee TY, Chow KL Tags: Genomics Source Type: journals

Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To provide a framework for studies to understand the contribution of SALT OVERLY SENSITIVE1 (SOS1) to salt tolerance in Thellungiella halophila, we sequenced and annotated a 193-kb T. halophila BAC containing a putative SOS1 locus (ThSOS1) and compared the sequence to the orthologous 146-kb region of the genome of its salt-sensitive relative, Arabidopsis thaliana. Overall, the two sequences were colinear, but three major expansion/contraction regions in T. halophila were found to contain five Long Terminal Repeat retrotransposons, MuDR DNA transposons and intergenic sequences that contribute to the 47.8-kb size variati...
Source: Genomics - May 27, 2009 Category: Genetics & Stem Cells Authors: Nah G, Pagliarulo CL, Mohr PG, Luo M, Sisneros N, Yu Y, Collura K, Currie J, Goicoechea JL, Wing RA, Schumaker KS Tags: Genomics Source Type: journals

Differentially Expressed Genes Strongly Correlated with Femur Strength in Rats.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The region of chromosome 1q33-q54 harbors quantitative trait loci (QTL) for femur strength in COP X DA and F344 X LEW F2 rats. The purpose of this study is to identify the genes within this QTL region that contribute to the variation in femur strength. Microarray analysis was performed using RNA extracted from femurs of COP, DA, F344 and LEW rats. Genes differentially expressed in the 1q33-q54 region among these rat strains were then ranked based on the strength of correlation with femur strength in F2 animals derived from these rats. A total of 214 genes in this QTL region were differentially expressed among all rat s...
Source: Genomics - May 27, 2009 Category: Genetics & Stem Cells Authors: Alam I, Sun Q, Koller DL, Liu L, Liu Y, Edenberg HJ, Li J, Foroud T, Turner CH Tags: Genomics Source Type: journals

Evidence for potential functionality of nuclearly-encoded humanin isoforms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Humanin (HN) is a recently identified neuroprotective and antiapoptotic peptide derived from a portion of the mitochondrial DNA sequence. We provide bioinformatic and expression data suggesting the existence of 13 nuclear loci predicted to maintain the open reading frames of 15 distinct full-length HN-like peptides. At least ten of these nuclear HN genes are expressed in human tissues, and respond to staurosporine (STS) and beta-carotene. Sequence comparisons of the nuclear HN isoforms and their homologues in other species reveal two consensus motifs, encompassing residues 5-11 (GFS/NCLLL), and 14-19 (SEIDLP/S). Prolin...
Source: Genomics - May 26, 2009 Category: Genetics & Stem Cells Authors: Bodzioch M, Lapicka-Bodzioch K, Zapala B, Kamysz W, Kiec-Wilk B, Dembinska-Kiec A Tags: Genomics Source Type: journals