Genomics

Peroxisomes are membrane bound cytoplasmic organelles that are involved in lipid metabolism and other biological functions. In rat and mouse, profound xenobiotic-induced peroxisome proliferation has been reported, with a marked increase in number and size of peroxisomes in liver parenchymal cells and induction of lipid metabolising enzymes, in particular cytochrome...

Oligonucleotide arrays are increasingly used in comparative genomic hybridization (CGH) to detect genomic copy number variation (CNV). The design of these arrays usually prefers uniquely mapped probes but routinely includes multiply mapped probes within a genome to maintain the high coverage and resolution. These duplicated probes could cause several limitations:...

Glycogen synthase kinase 3β (GSK3β) was discovered as a major factor in glucose homeostasis. GSK3β is a pivotal regulator of glycogen synthesis by altering the activity of glycogen synthase and perturbation in this process have been linked to at least some sub-entities of insulin resistance and diabetes mellitus. However, GSK3β...

Introductory Editorial by Dr Shiva M. Singh, Professor Molecular Genetics and Distinguished University Professor, The University of Western Ontario, London, Ontario and Canada N6A 5B7

Microarrays are becoming a widely used tool to study gene expression evolution. A recent paper by Wang and Rekaya describes a comprehensive study of gene expression evolution by microarray. The work provides a perspective to study gene expression evolution in terms of functional enrichment and promoter conservation. It was found...

Hereditary inclusion body myopathy type 2 (HIBM2) is a myopathy characterized by progressive muscle weakness with early adult onset. The disease is the result of a recessive mutation in the Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase gene (GNE), which results in reduced enzyme function and sialic acid levels. A majority of individuals with...

In order to investigate the possible mechanisms for eve stripe formation of Drosophila embryo, a spatio-temporal gene/ protein interaction network model is proposed to mimic dynamic behaviors of protein synthesis, protein decay, mRNA decay, protein diffusion, transcription regulations and autoregulation to analyze the interplay of genes and proteins at different...

Microarray measurements of mRNA abundances is a standard tool for evaluation of transcriptional activity in functional genomics. The methodology underlying these measurements assumes existence of a direct link between transcription levels, that is, gene-specific mRNA copy numbers present in the cell, and transcription rates, that is, the numbers of gene-specific...

Hepatocyte growth factor receptor tyrosine kinase substrate (HRS) is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2) gene product, and this interaction may be important for Merlin’s tumor suppressor activity. Understanding the evolution, origin,...

Fibroblast growth factor 23 (FGF23) has recently been identified as a critical regulatory factor in phosphate (P) metabolism. Although the exact molecular mechanism of FGF23 synthesis through sensing the concentration of P is yet to be determined, experimental and clinical data indicate the influential role of FGF23 in P and...

Gene fusion is a hallmark of cancer development with the mechanisms underlying their genesis emerging. The Staege and Max paper together with another recent paper have provided a comprehensive first view on current TET-ETS translocation studies. This significance, the trigering of gene fusion and beyond will be discussed in this...

Epigenetics is the study of the transmission of cell memory through mitosis or meiosis that is not based on the DNA sequence. At the molecular level the epigenetic memory of a cell is embedded in DNA methylation, histone post-translational modifications, RNA interference and histone isoform variation. There is a tight...

Efficient nutrient assimilation into useful animal-derived products is the ultimate requirement for successful animal production. Infection in young growing animals can decrease energy and nutrient use required for growth rate by redirection of nutrients to support immune defense processes. Bovine leukemia virus (BLV) infection is prevalent in several regions of...

Introductory Editorial by Dr Christian Bronner, CNRS UMR7175, University Louis Pasteur, Faculty of Pharmacy, Illkirch, France.

We compare the results of three different assembler programs, Celera, Phrap and Mira2, for the same set of about a hundred thousand Sanger reads derived from an unknown bacterial genome. In difference to previous assembly comparisons we do not focus on speed of computation and numbers of assembled contigs but...

More than half a century after the discovery of the molecular basis of Sickle Cell Disease (SCD), the causes of the phenotypic heterogeneity of the disease remain unclear. This heterogeneity manifests with different clinical outcomes such as stroke, vaso-occlusive episodes, acute chest syndrome, avascular necrosis, leg ulcers, priapism and retinopathy....

To investigate the general radiation-resistant mechanisms of bacteria, bioinformatic method was employed to predict highly expressed genes for four radiation-resistant bacteria, i.e. Deinococcus geothermalis (D. geo), Deinococcus radiodurans (D. rad), Kineococcus radiotolerans (K. rad) and Rubrobacter xylanophilus (R. xyl). It is revealed that most of the three reference gene sets,...

Aim: To assess the possible relationship between serum alpha-1 antitrypsin (AAT) levels and anti-neutrophil cytoplasmic antibodies (ANCA) in autistic children with severe GI disease and to test the hypothesis that there is an association between low serum AAT levels, the presence of ANCA and inflammatory GI disease seen in some...

Amphibian defensive skin secretions and reptile venoms are rich sources of bioactive peptides with potential pharmacological/pharmaceutical applications. As amphibian and reptile populations are in rapid global decline, our research group has been developing analytical methods that permit generation of robust molecular data from non-invasive skin secretion samples and venom samples....

Background: Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs1042725, within the HMGA2 locus and height as a consequence of a genome wide association (GWA) study of this trait in adults; this observation was also reported in children aged 7–11 years old. Objective: We examined in our Caucasian...

Aim: To assess serum Anti-Neutrophil cytoplasmic Antibody (ANCA—PR3 and MPO) and Anti-Saccharomyces Cerevisiæ Antibody (ASCA) levels in autistic children with severe gastrointestinal (GI) disease and to test the hypothesis that there is generalized autoimmunity in a subpopulation of autistic children with severe GI disease and that this autoimmunity is associated...

Objective: To better understand the effects of simvastatin (SS) on the expression and secretion of two chemokines, CXCL10 and CX3CL1, by osteoblasts, and to test whether inhibition of isoprenoid intermediates of cholesterol biosynthesis were involved in the effects of SS. Methods: Human osteoblasts were incubated in the presence or absence of...

Aim: To assess both ant-PR3 and anti-MPO IgG anti-neutrophil cytoplasmic antibodies (ANCA), in autistic children with gastrointestinal symptoms and controls, and to test the hypothesis that there is an association between the presence of these antibodies and inflammatory GI disease seen in many autistic children. Subjects and Methods: ELISA’s were used...

Background: Microbial translocation has been recognized as an important factor in monocyte activation and contributing to AIDS pathogenesis with elevated plasma lipopolysaccharide (LPS) levels, as a marker for microbial translocation, seen in advanced HIV disease. Therefore, the current study was undertaken to assess monocyte activation in vitro by LPS...

It is now broadly accepted that white adipose tissue disorders, such as obesity, are associated with a chronic low-grade inflammation predisposing to the development of insulin-resistance, type 2 diabetes and cardiovascular complications. In obesity, accumulation of visceral adipose tissue, rather than subcutaneous adipose tissue, is regarded as the most critical...

Introductory Editorial by Dr Darren R Flower, The Jenner Institute, University of Oxford, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headley Way, Headington, Oxford, U.K.

Genomic islands interspersed in the chromosome of P. aeruginosa led to inter- and intraclonal diversity. Recently, a particular clone of P. aeruginosa called clone C was isolated from cystic fibrosis (CF) patients, clinical and non-clinical habitats throughout Europe and in Canada. P. aeruginosa clone C strains harbour up to several...

Traditionally, antibody-based assays, such as enzyme immunoassay (EIA), enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA), are the primary tool for the targeted quantification of a specific protein. An antibody-based assay can be run at high-throughput and has extraordinary sensitivity and specificity. In the cases where antibody-based assays exist, the process...

This short note highlights a procedure to distinguish the residues having similar masses, oxidized methionine and phenylalanine containing peptides using MALDI TOF/TOF. The isotope intensities give a preliminary recognition of peptides containing oxidized methionine. In the peptides with partial oxidation of methionine a mass difference of 16 Da can be...

Proteomic discoveries are usually made using database searches for identification of proteins in a given protein sample derived from cells or tissues. High throughput searches leave a number of peptides not analyzed for a variety of reasons, such as posttranslational modification or a mutation that results changes in the peptide...

A Met residue is located adjacent to phosphorylation site 1 in the sequences of mitochondrial pyruvate dehydrogenase E1α subunits. When synthetic peptides including site 1 were treated with H2O2, the Met residue was oxidized to methionine sulfoxide (MetSO), and the peptides were no longer phosphorylated by E1α-kinase. Isolated mitochondria were...

G. Aravindhan1, R. Sathish Kumar2, K. Subha1, T.K.Subazini1, Alpana Dey3, Krishna Kant3 and G. Ramesh Kumar11Bioinformatics Division, AU-KBC Research Centre, MIT Campus, Anna University, Chennai—600 044, India. 2NRCFOSS, AU-KBC Research Centre, MIT Campus, Anna University, Chennai—600 044, India. 3Ministry of Communications and Information Technology, DT, New Delhi-110 003, India.AbstractAIM-BLAST, AJAX...

The myelodysplastic syndromes (MDS) are clonal stem cell disorders, characterized by ineffective and dysplastic hematopoiesis. The genetic and epigenetic pathways that determine disease stage and progression are largely unknown. In the current study we used gene expression microarray methodology to examine the gene expression differences between normal hematopoietic cells and...

In the review, the nature of protein multifunctionality is analyzed. In the first part of the review the principles of structural/functional organization of protein are discussed. In the second part, the main mechanisms involved in development of multiple functions on a single gene product(s) are analyzed. The last part represents...

Sirtuins are NAD+-dependent histone deacetylases (Class III HDACs). Recently, Sirtuins have been shown to play important roles, both direct and indirect, in transcriptional regulation. This transcriptional control, through incorporation of Sirtuins into transcription complexes and deacetylation of histones locally at gene promoters, or direct interaction with specific transcription factors, is...

In the last two decades there has been considerable progress in our understanding of the role of sphingolipids in controlling signal transduction processes, particularly in the mechanisms leading to regulation of cell growth and death. Ceramide is a well-characterized sphingolipid metabolite and second messenger that can be produced by cancer...

Gene associated with retinoid-interferon-β-induced mortality (GRIM)—19, was originally identifi ed as a critical regulatory protein necessary for Interferon-β-Retinoic acid-induced cell death. Overexpression of GRIM-19 activates cell death and its suppression or inactivation promotes cell growth. GRIM-19 targets multiple proteins/pathways for exerting growth control and cell death. However, GRIM-19 is also...

A great amount of literature has demonstrated a connection between obesity, visceral fat and the metabolic disorders such as hyperglycemia, hypertension, and hyperlipidemia. Lately, there has been an increased interest in understanding if cancer is related to obesity and visceral fat accumulation. The prevalence of both obesity and cancer are...