Genomics

Traditionally man has looked to nature to provide cures for diseases. This approach still exists today in the form of ‘bio-prospecting’ for therapeutically-active compounds in venoms. For example, the venoms of many reptiles offer a spectacular laboratory of bioactive molecules, including peptides and proteins. In the last 10–15 years, there...

We designed a targeted-array called GOLD (Gain or Loss Detection) Chip consisting of 900 FISH-mapped non-overlapping BAC clones spanning the whole genome to enhance the coverage of 66 unique human genomic regions involved in well known micro-deletion/microduplication syndromes. The array has a 10 Mb backbone to guarantee the detection of...

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...

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:...

Mitochondria are subcellular organelles that provide energy for a variety of basic cellular processes in eukaryotic cells. Mitochondria maintain their own genomes and many of their endosymbiont genes are encoded by nuclear genomes. The crosstalk between the mitochondrial and nuclear genomes ensures mitochondrial biogenesis, dynamics and maintenance. Mitochondrial proteins are...

In this report, we compared the success rate of classification of coding sequences (CDS) vs. introns by Codon Structure Factor (CSF) and by a method that we called Universal Feature Method (UFM). UFM is based on the scoring of purine bias (Rrr) and stop codon frequency. We show that the...

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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....

Pathological grade is a useful prognostic factor for stratifying breast cancer patients into favorable (low-grade, well-differentiated tumors) and less favorable (high-grade, poorly-differentiated tumors) outcome groups. Under the current system of tumor grading, however, a large proportion of tumors are characterized as intermediate-grade, making determination of optimal treatments difficult. In an...

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...

In this report, we revisited simple features that allow the classification of coding sequences (CDS) from non-coding DNA. The spectrum of codon usage of our sequence sample is large and suggests that these features are universal. The features that we investigated combine (i) the stop codon distribution, (ii) the product...

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...

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

Laura Kennedy1, J. Keith Vass1, D. Ross Haggart1, Steve Moore1, Michael E. Burczynski2, Dan Crowther1 and Gino Miele1 1Translational Medicine Research Collaboration Laboratory, Sir James Black Centre, University of Dundee, Dundee, DD1 5EH, U.K. 2Biomarker Laboratory, Wyeth Research, Collegeville, U.S.A. Abstract Peripheral blood as a surrogate tissue...

Arnaud Le Rouzic1 and José M. Álvarez-Castro2 1Center for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway. 2Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. Abstract Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Evidence of cardiotoxicity in the preclinical testing of drugs will often lead to compound attrition. The standard method for identifying cardiotoxic compounds involves histopathological analysis of tissue sections, a resource intensive process. In an effort to reduce attrition and capture safety endpoints early within the drug discovery paradigm, a more...

Li-Xuan Qin Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, U.S.A. Abstract Background: MicroRNAs are believed to play an important role in gene expression regulation. They have been shown to be involved in cell cycle regulation and cancer. MicroRNA expression profiling became...

Yunfeng Shan1,2 and Xiu-Qing Li1 1Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada,850 Lincoln Rd, P.O. Box 20280, Fredericton, New Brunswick, E3B 4Z7, Canada. 2Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada. Abstract Genomes and genes diversify during evolution; however, it...

Zhenling Yao1, Eric P. Hoffman3, Svetlana Ghimbovschi3, Debra C. DuBois1,2, Richard R. Almon1,2 and William J. Jusko1 1Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, 2Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York. 3Children’s National Research Center, Washington D.C. Abstract...

Hsiao-Wei Chen†,1,2, Hsuan-Cheng Huang†,3, Yi-Shing Lin4, King-Jen Chang5, Wen-Hung Kuo5, Hsiao-Lin Hwa6, Fon-Jou Hsieh1,6,9 and Hsueh-Fen Juan1,7,8,9 1Department of Life Science, National Taiwan University, Taipei 106, Taiwan. 2Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan. 3Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan. 4Welgene Biotech....

Introductory Editorial by Dr Gustavo Caetano-Anolles, Institute for Genomic Biology and Department of Crop Sciences, University of Illinois, Urbana, IL, U.S.A.

Anasuya Hazra1,3, Debra C. DuBois1,2, Richard R. Almon1,2, Grayson H. Snyder2 and William J. Jusko1 1Department of Pharmaceutical Sciences. 2Department of Biological Sciences, University at Buffalo, NY 14260, 3Clinical Pharmacology (Infectious Diseases), Pfizer Inc, New London, CT 06380, U.S.A. Abstract Corticosteroids (CS) regulate many enzymes at both...

RiLee H. Robeson1, Andrew M. Siegel1 and Travis Dunckley1 1Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004. Abstract Technology for high-throughout scanning of the human genome and its encoded proteins have rapidly developed to allow systematic analyses of human disease. Application of these technologies...

Gary Guishan Xiao1, Robert R. Recker1 and Hong-Wen Deng2 1Osteoporosis Research Center, Departments of Medicine and Biomedical Sciences, Creighton University, 601 N 30th ST, Suite 6730, Omaha, NE 68131; 2Departments of Orthopedic Surgery and Basic Medical Sciences, University of Missouri—Kansas City, 2411 Holmes Street. Room M3-C03, City, Missouri, ...

Goberdhan P. Dimri Department of Medicine, ENH Research Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Evanston, IL 60201. Abstract: I would like to welcome breast cancer research community to the fi rst editorial of our newest journal “Breast...