Comparative and Functional Genomics
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Molecular Diversity of the Antimicrobial Domain of Beta-Defensin 3 and Homologous Peptides
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This report provides definite evidence of true orthology between these defensins and reveals molecular diversity of a mammalian specific domain responsible for their antimicrobial activity. Specifically, this analysis demonstrates that eleven amino acid residues of the antimicrobial domain have been mutated by positive selection to confer protein niche specialization. These data support the notion that natural selection acts as evolutionary force driving the proliferation and diversification of defensins and introduce a novel strategy for the design of more effective antibiotics. (Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - November 2, 2009 Category: Genetics & Stem Cells Source Type: journals
An Exon-Based Comparative Variant Analysis Pipeline to Study the Scale and Role of Frameshift and Nonsense Mutation in the Human-Chimpanzee DivergenceEmail this article to a colleague.
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The objective is to comparatively
analyze mutations specifically those that caused the frameshift and nonsense mutations and to assess their scale and potential impacts on human-chimpanzee divergence. Genomewide analysis of human and chimpanzee exons with ExonVar identified a number of species-specific, exon-disrupting mutations in chimpanzees but much fewer in humans. Many were found on genes involved in
important biological processes such as T cell lineage development, the pathogenesis of inflammatory diseases, and antigen induced cell death. A “less-is-more” model was previously established to illustrate the...
Source: Comparative and Functional Genomics - October 22, 2009 Category: Genetics & Stem Cells Source Type: journals
Physiological Function of Mycobacterial mtFabD, an Essential Malonyl-CoA:AcpM Transacylase of Type 2 Fatty Acid Synthase FASII, in Yeast mct1Δ CellsEmail this article to a colleague.
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Mycobacterium tuberculosis mtFabD is an essential malonyl-CoA:AcpM transacylase and is important for vital protein-protein interactions within type 2 fatty acid synthase FASII. mtFabD contacts KasA, KasB, FabH, InhA, and possibly also HadAB, HadBC, and FabG1/MabA. Disruption of mtFabD's interactions during FASII has been proposed for drug development. Here, the gene for a mitochondrially targeted mtFabD was ectopically expressed in Saccharomyces cerevisiae mct1Δ mutant cells lacking the corresponding mitochondrial malonyl-CoA transferase Mct1p, allowing the mutants to recover their abilities to respire on glycer...
Source: Comparative and Functional Genomics - October 21, 2009 Category: Genetics & Stem Cells Source Type: journals
Characterization of the Gene BmEm4, a Homologue of Drosophila E(spl)m4, from the Silkworm, Bombyx moriEmail this article to a colleague.
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The Drosophila E(spl)m4 gene contains some highly conserved motifs (such as the Brd box, GY box, K box, and CAAC motif) in its 3′ untranslated region (3′UTR). It was shown to be a microRNA target gene in Drosophila and to play an important role in the regulation of neurogenesis. We identified a homologue of the E(spl)m4 gene from Bombyx mori called BmEm4 and examined the expression patterns of BmEm4 mRNA and protein. There was a lack of correlation in the expression of the mRNA and protein between the different developmental stages, which raises the possibility of posttranscriptional regulation of the BmEm4 m...
Source: Comparative and Functional Genomics - October 12, 2009 Category: Genetics & Stem Cells Source Type: journals
Reverse Genetics for Functional Genomics of Phytopathogenic Fungi and OomycetesEmail this article to a colleague.
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Sequencing of over 40 fungal and oomycete genomes has been completed. The next major challenge in modern fungal/oomycete biology is now to translate this plethora of genome sequence information into biological functions. Reverse genetics has emerged as a seminal tool for functional genomics investigations. Techniques utilized for reverse genetics like targeted gene disruption/replacement, gene silencing, insertional mutagenesis, and targeting induced local lesions in genomes will contribute greatly to the understanding of gene function of fungal and oomycete pathogens. This paper provides an overview on high-throughput rev...
Source: Comparative and Functional Genomics - October 7, 2009 Category: Genetics & Stem Cells Source Type: journals
Classification of Nonenzymatic Homologues of Protein KinasesEmail this article to a colleague.
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Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases,
lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as
protein kinase, have been analysed. Using various sensitive sequence analysis methods, we
have recognized 82 PKLNKs from four higher eukaryotic organisms, namely, Homo sapiens, Mus musculus, Rattus norvegicus, and Drosophila melanogaster. On the basis of
their domain combination and function, PKLNKs have been classified mainly into four
categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein
interaction domain, (3) PKLNK...
Source: Comparative and Functional Genomics - September 28, 2009 Category: Genetics & Stem Cells Source Type: journals
Analysis of Array-CGH Data Using the R and Bioconductor Software SuiteEmail this article to a colleague.
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Conclusion. The implemented option for the determination of minimal altered regions (MARs) from a series of tumor samples is a step forward in the identification of new tumor suppressor genes or oncogenes. (Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - August 19, 2009 Category: Genetics & Stem Cells Source Type: journals
Anaplasma phagocytophilum and Anaplasma marginale Elicit Different Gene Expression Responses in Cultured Tick CellsEmail this article to a colleague.
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The objectives of this study were to characterize tick gene expression profile in Ixodes scapularis ticks and cultured ISE6 cells in response to infection with A. phagocypthilum and to compare tick gene expression responses in A. phagocytophilum- and A. marginale-infected tick cells by microarray and real-time RT-PCR analyses. The results of these studies demonstrated modulation of tick gene expression by A. phagocytophilum and provided evidence of different gene expression responses in tick cells infected with A. phagocytophilum and A. marginale. These differences in Anaplasma-tick interactions may reflect differences in ...
Source: Comparative and Functional Genomics - July 15, 2009 Category: Genetics & Stem Cells Source Type: journals
Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome DiversityEmail this article to a colleague.
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Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulatio...
Source: Comparative and Functional Genomics - July 12, 2009 Category: Genetics & Stem Cells Source Type: journals
A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thalianaEmail this article to a colleague.
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Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the ME...
Source: Comparative and Functional Genomics - July 5, 2009 Category: Genetics & Stem Cells Source Type: journals
UK CropNetEmail this article to a colleague.
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This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC). (Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - June 30, 2009 Category: Genetics & Stem Cells Source Type: journals
Accurate Prediction of Protein Functional Class from Sequence in the Mycobacterium tuberculosis and Escherichia coli Genomes Using Data MiningEmail this article to a colleague.
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The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with...
Source: Comparative and Functional Genomics - June 30, 2009 Category: Genetics & Stem Cells Source Type: journals
Molecular Characterization and Tissue Localization of an F-Box
Only Protein from Silkworm, Bombyx moriEmail this article to a colleague.
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The eukaryotic F-box protein family is characterized by an F-box motif that has been shown to be critical for the controlled degradation of regulatory proteins. We identified a
gene encoding an F-box protein from a cDNA library of silkworm pupae, which has an
ORF of 1821 bp, encoding a predicted 606 amino acids. Bioinformatic analysis on the
amino acid sequence shows that BmFBXO21 has a low degree of similarity to proteins
from other species, and may be related to the regulation of cell-cycle progression. We
have detected the expression pattern of BmFBXO21 mRNA and protein and performed
immunohistochemistry at three differ...
Source: Comparative and Functional Genomics - June 25, 2009 Category: Genetics & Stem Cells Source Type: journals
Advancing Post-Genome Data and System Integration through Machine LearningEmail this article to a colleague.
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Research on biological data integration has traditionally focused on the development of
systems for the maintenance and interconnection of databases. In the next few years,
public and private biotechnology organisations will expand their actions to promote the
creation of a post-genome semantic web. It has commonly been accepted that artificial
intelligence and data mining techniques may support the interpretation of huge amounts of
integrated data. But at the same time, these research disciplines are contributing to the
creation of content markup languages and sophisticated programs able to exploit the
constraints and pre...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
MicroCore: Mapping Genome Expression to Cell Pathways and NetworksEmail this article to a colleague.
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The MicroCore toolkit is a suite of analysis programs for microarray and proteomics
data that is open source and programmed exclusively in Java. MicroCore provides
a flexible and extensible environment for the interpretation of functional genomics
data through visualization. The first version of the application (downloadable from
the MicroCore website: http://www.ucl.ac.uk/oncology/MicroCore/microcore.htm),
implements two programs—PIMs (protein interaction maps) and MicroExpress—and
is soon to be followed by an extended version which will also feature a fuzzy
k-means clustering application and a Java-based R p...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
In This IssueEmail this article to a colleague.
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(Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Protein Interactions from Complexes: A Structural PerspectiveEmail this article to a colleague.
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By combining crystallographic information with protein-interaction data
obtained through traditional experimental means, this paper determines
the most appropriate method for generating protein-interaction networks
that incorporate data derived from protein complexes. We propose that
a combined method should be considered; in which complexes
composed of five chains or less are decomposed using the matrix
model, whereas the spoke model is used to derive pairwise interactions
for those with six chains or more. The results presented here should
improve the accuracy and relevance of studies investigating the
topology of protei...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Frequency of Cancer Genes on the Chicken Z Chromosome and Its Human Homologues: Implications for Sex Chromosome EvolutionEmail this article to a colleague.
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It has been suggested that there are special evolutionary forces that act on sex chromosomes. Hemizygosity of the X chromosome in male mammals has led to selection for male-advantage genes, and against genes posing extreme risks of tumor development. A similar bias against cancer genes should also apply to the Z chromosome that is present as a single copy in female birds. Using comparative database analysis, we found that there was no significant underrepresentation of cancer genes on the chicken Z, nor on the Z-orthologous regions of human chromosomes 5 and 9. This result does not support the hypothesis that genes involve...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Protein Coevolution and Isoexpression in Yeast Macromolecular ComplexesEmail this article to a colleague.
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Previous studies in the yeast Saccharomyces cerevisiae have shown that genes encoding subunits of macromolecular complexes have similar evolutionary rates (K) and expression levels (E). Besides, it is known that the expression of a gene is a strong predictor of its rate of evolution (i.e., E and K are correlated). Here we show that intracomplex variation of subunit expression correlates with intracomplex variation of their evolutionary rates (using two different measures of dispersion). However, a similar trend was observed for randomized complexes. Therefore, using a mathematical transformation, we created new variables c...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Identification and Analysis of Novel Amino-Acid Sequence Repeats in Bacillus anthracis str. Ames Proteome Using Computational ToolsEmail this article to a colleague.
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We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus
anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residu...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Normalisation of Multicondition cDNA Macroarray DataEmail this article to a colleague.
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Conclusions. The SCS normalisation results using 16 macroarray
data sets from a Bacillus subtilis experiment confirm that the method
is capable of reducing undesirable experimental variation whilst retaining important
biological information. The ease and speed of implementation mean that this method
can be easily adapted to other multicondition time/strain series single colour array data. (Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
eGenomics: Cataloguing Our Complete Genome Collection IIIEmail this article to a colleague.
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This meeting report summarizes the proceedings of the “eGenomics:
Cataloguing our Complete Genome Collection III” workshop held
September 11–13, 2006, at the National Institute for Environmental
eScience (NIEeS), Cambridge, United Kingdom.
This 3rd workshop of the Genomic Standards Consortium was divided into two parts.
The first half of the three-day workshop was dedicated to reviewing the genomic
diversity of our current and future genome and metagenome collection, and
exploring linkages to a series of existing projects through formal presentations.
The second half was dedicated ...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Comparison of Envelope-Related Genes in Unicellular and Filamentous CyanobacteriaEmail this article to a colleague.
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To elucidate the evolution of cyanobacterial envelopes and the relation between gene content and environmental adaptation, cell envelope structures and components of unicellular and filamentous cyanobacteria were analyzed in comparative genomics. Hundreds of envelope biogenesis genes were divided into 5 major groups and annotated according to their conserved domains and phylogenetic profiles. Compared to unicellular species, the gene numbers of filamentous cyanobacteria expanded due to genome enlargement effect, but only few gene families amplified disproportionately, such as those encoding waaG and glycosyl transferase 2....
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) GenomeEmail this article to a colleague.
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Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure tha...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis ResearchEmail this article to a colleague.
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Two-dimensional gel-electrophoresis (2-DE) images show the expression levels of
several hundreds of proteins where each protein is represented as a blob-shaped spot of
grey level values. The spot detection, that is, the segmentation process has to be efficient as
it is the first step in the gel processing. Such extraction of information is a very complex
task. In this paper, we propose a novel spot detector that is basically a morphology-based
method with the use of a seeded region growing as a central paradigm and
which relies on the spot correlation information. The method is tested on our synthetic
as well as on real ge...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Expression Divergence of Tandemly Arrayed Genes in Human and MouseEmail this article to a colleague.
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Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide PolymorphismsEmail this article to a colleague.
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The large amounts of EST sequence data available from a
single species of an organism as well as for several species
within a genus provide an easy source of identification of
intra- and interspecies single nucleotide polymorphisms
(SNPs). In the case of model organisms, the data available are
numerous, given the degree of redundancy in the deposited EST
data. There are several available bioinformatics tools that
can be used to mine this data; however, using them requires a
certain level of expertise: the tools have to be used
sequentially with accompanying format conversion and steps
like clu...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
The Progress on Genetic Analysis of Nasopharyngeal CarcinomaEmail this article to a colleague.
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Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research. (Source: Comparative and Functional Genomics)
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Accurate Localization of the Integration Sites of Two Genomic Islands at Single-Nucleotide Resolution in the Genome of Bacillus cereus ATCC 10987Email this article to a colleague.
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We have identified two genomic islands, that is,
BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987,
based on comparative analysis with Bacillus cereus ATCC 14579.
Furthermore, by using the cumulative GC profile and performing homology
searches between the two genomes, the integration sites of the two genomic
islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between
159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of
ORF BCE4594 and the start of the intergenic sequence immediately following...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome: A Systems ApproachEmail this article to a colleague.
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To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved 53% proteome coverage. To study the differential protein expression in response to sub-MIC antibiotics in the context of protein interaction networks, we inferred P. multocida Pm70 protein interaction network from orthologous proteins. We then overlaid the differential protein expression data onto the P. multocida protein interaction network to study the bacterial response. We identified proteins that could enhance antimicr...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Comparative Analysis of CpG Islands in Four Fish GenomesEmail this article to a colleague.
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There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafish). Our results suggest that Takai and Jones' (2002) algorithm is most suitable for comparative analysis of CGIs in the fish genome. Then, we performed a systematic analysis of CGIs in the four fish genomes using Takai and Jon...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
The Creatine Transporter Gene Paralogous at 16p11.2 Is Expressed in Human BrainEmail this article to a colleague.
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We report on the clinical, cytogenetic, and molecular findings in a boy with autism carrying a de novo translocation t(7;16)(p22.1;p11.2). The chromosome 16 breakpoint disrupts the paralogous SLC6A8 gene also called SLC6A10 or CT2. Predicted translation of exons and RT-PCR analysis reveal specific expression of the creatine transporter paralogous in testis and brain. Several studies reported on the role of X-linked creatine transporter mutations in individuals with mental retardation, with or without autism. The existence of disruption in SLC6A8 paralogous gene associated with idiopathic autism suggests that this gene may ...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Subcellular Localization and RNA Interference of an RNA Methyltransferase Gene from Silkworm, Bombyx MoriEmail this article to a colleague.
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RNA methylation, which is a form of posttranscriptional modification, is catalyzed by S-adenosyl-L-methionone-dependent RNA methyltransterases (RNA MTases). We have identified a novel silkworm gene, BmRNAMTase, containing a 369-bp open reading frame that encodes a putative protein containing 122 amino acid residues and having a molecular weight of 13.88 kd. We expressed a recombinant His-tagged BmRNAMTase in E. coli BL21 (DE3), purified the fusion protein by metal-chelation affinity chromatography, and injected a New Zealand rabbit with the purified protein to generate anti-BmRNAMTase polyclonal antibodies. Immunohistochem...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Genome-Based Construction
of the Metabolic Pathways of
Orientia tsutsugamushi
and Comparative Analysis within the
Rickettsiales OrderEmail this article to a colleague.
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Orientia
tsutsugamushi, the causative agent of
scrub typhus, is an obligate intracellular
bacterium that belongs to the order of
Rickettsiales. Recently, we have reported that
O. tsutsugamushi has a unique
genomic structure, consisting of highly
repetitive sequences, and suggested that it may
provide valuable insight into the evolution of
intracellular bacteria. Here, we have used
genomic information to construct the major
metabolic pathways of
O. tsutsugamushi and performed a
comparative analys...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Protein Coding Gene Nucleotide Substitution Pattern in the Apicomplexan Protozoa Cryptosporidium parvum and Cryptosporidium hominisEmail this article to a colleague.
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Cryptosporidium parvum and C. hominis are related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes in C. parvum and C. hominis. Genome-wide calculation of the ratio of nonsynonymous versus synonymous nucleotide substitutions (dN/dS) was performed to detect the impact of positive and purifying selection. Of 2465 pairs of orthologous genes, a total of 27 (1.1%) showed a high ratio of nonsynonymous s...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Global Transcriptional Analysis of Yeast Cell Death Induced by Mutation of Sister Chromatid CohesinEmail this article to a colleague.
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Cohesin is a protein complex that regulates sister chromatid cohesin during cell division. Malfunction in chromatid cohesin results in chromosome missegregation and aneuploidy. Here, we report that mutations of MCD1 and PDS5, two major components of cohesin in budding yeast, cause apoptotic cell death, which is characterized by externalization of phosphatidylserine at cytoplasmic membrane, chromatin condensation and fragmentation, and ROS production. Microarray analysis suggests that the cell death caused by mutation of MCD1 or PDS5 is due to the internal stress response, contrasting to the environmental or external stress...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Tandemly Arrayed Genes in Vertebrate GenomesEmail this article to a colleague.
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Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important
physiological and biochemical functions. Here we performed a survey
of these genes in 11 available vertebrate genomes. TAGs account for
an average of about 14% of all genes in these vertebrate genomes, and
about 25% of all duplications. The majority of TAGs (72–94%) have
parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes
in parallel transcription orientation. The majority of tandem arrays
have only two me...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial GenomesEmail this article to a colleague.
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Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of o...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding RegionsEmail this article to a colleague.
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In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant ana...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102Email this article to a colleague.
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Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in pa...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Evolutionary Conservation Levels of Subunits of Histone-Modifying Protein Complexes in FungiEmail this article to a colleague.
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In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and d...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Evidence of Extensive Homologous Recombination in the Core Genome of RickettsiaEmail this article to a colleague.
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In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome of Rickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently during Rickettsia evolution. 28% of Rickettsia core genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
MicroRNA Profiling and Head and Neck CancerEmail this article to a colleague.
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Head and neck/oral cancer (HNOC) is a devastating disease. Despite advances in diagnosis and treatment, mortality rates have not improved significantly over the past three decades. Improvement in patient survival requires a better understanding of the disease progression so that HNOC can be detected early in the disease process and targeted therapeutic interventions can be deployed. Accumulating evidence suggests that microRNAs play important roles in many human cancers. They are pivotal regulators of diverse cellular processes including proliferation, differentiation, apoptosis, survival, motility, and morphogenesis. Micr...
Source: Comparative and Functional Genomics - June 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Evidence of Extensive Homologous Recombination in the Core Genome of RickettsiaEmail this article to a colleague.
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In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome of Rickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently during Rickettsia evolution. 28% of Rickettsia core genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall...
Source: Comparative and Functional Genomics - May 27, 2009 Category: Genetics & Stem Cells Source Type: journals
Evolutionary Conservation Levels of Subunits of Histone-Modifying Protein Complexes in FungiEmail this article to a colleague.
Save this article to My Clippings.
Discuss or comment on this article.
In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and d...
Source: Comparative and Functional Genomics - May 20, 2009 Category: Genetics & Stem Cells Source Type: journals
Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102Email this article to a colleague.
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Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in pa...
Source: Comparative and Functional Genomics - April 24, 2009 Category: Genetics & Stem Cells Source Type: journals
A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding RegionsEmail this article to a colleague.
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In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant ana...
Source: Comparative and Functional Genomics - April 10, 2009 Category: Genetics & Stem Cells Source Type: journals
Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial GenomesEmail this article to a colleague.
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Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of o...
Source: Comparative and Functional Genomics - December 3, 2008 Category: Genetics & Stem Cells Source Type: journals
Tandemly Arrayed Genes in Vertebrate GenomesEmail this article to a colleague.
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Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important
physiological and biochemical functions. Here we performed a survey
of these genes in 11 available vertebrate genomes. TAGs account for
an average of about 14% of all genes in these vertebrate genomes, and
about 25% of all duplications. The majority of TAGs (72–94%) have
parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes
in parallel transcription orientation. The majority of tandem arrays
have only two me...
Source: Comparative and Functional Genomics - September 21, 2008 Category: Genetics & Stem Cells Source Type: journals
