Current Genomics

ISSN: 1389-2029

Current Genomics
Volume 7, Number 7, November 2006

Contents


Expression Microarray Proteomics and the Search for Cancer Biomarkers Pp. 399-426
F.E. Ahmed
[Abstract]


High-Precision Genome Surgery in Human Stem Cells Pp. 427-433
R. Zhou and P. Dröge
[Abstract]


Intercellular Genomic (Chromosomal) Variations Resulting in Somatic Mosaicism: Mechanisms and Consequences Pp. 435-446
I.Y. Iourov, S.G. Vorsanova and Y.B. Yurov
[Abstract]


Bioinformatic Analyses of Gram-Negative Bacterial OstA Outer Membrane Assembly Homologues Pp. 447-461
K.-Y. Hu and M.H. Saier, Jr.
[Abstract]

Supplementary Tables S1-S3
Supplementary Figures S1-S2


Epistatic Control of Human Obesity as Revealed by Linkage Disequilibrium Mapping: A Report from the NHLBI-Sponsored WISE Study Pp. 463-468
H. Li, R. Wu, M. Lin, S.G. Terra, C.J. Pepine, S.P. McGorray, B.D. Johnson and J.A. Johnson
[Abstract]




Abstracts


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Expression Microarray Proteomics and the Search for Cancer Biomarkers
F.E. Ahmed

Protein microarrays allow the simultaneous determination of a variety of parameters in parallel from minute amounts of sample, which allows for a high throughput analysis of translated gene functions. This article provides a wide and updated coverage of topics such as the complexity of this technology as compared to the gene expression technology, classification of protein microarrays, surface chemistry, detection methods, capture agents, experimental design, data analysis, standards, databases and interactions. The role of protein microarrays for the identification of cancer biomarkers in tissue and serum has also been elucidated. There are currently no guidelines on how to standardize these assays for biomarker discovery. Issues of sensitivity, specificity, difficulty in maintaining the native state of the protein upon surface immobilization, and limitations of the current arrays represent challenges that need to be overcome, and should be understood by those who are employing this parallel multiplexed technology in order to be able to achieve high throughput applications and minimize the occurrence of false positive and negative results.


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High-Precision Genome Surgery in Human Stem Cells
R. Zhou and P. Dröge

The great potential of human embryonic and adult stem cells in regenerative medicine, gene therapy, drug discovery, and basic research is widely recognized. Many future applications depend on our ability to manipulate stem cell genomes with exogenous DNA in a safe and controllable way. Foreign DNA which carries, for example, a therapeutically active gene, a key regulatory gene involved in cell differentiation, or encodes for small interfering RNA may be inserted into or excised from stem cell genomes. Here, we review current progress and technical challenges in this field of genetic modification with a focus on controlled gene insertion into and ablation from stem cell genomes mediated by site-specific or homologous DNA recombination.


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Intercellular Genomic (Chromosomal) Variations Resulting in Somatic Mosaicism: Mechanisms and Consequences
I.Y. Iourov, S.G. Vorsanova and Y.B. Yurov

Large-scale variations of the human genome can be produced by losses or gains of whole chromosomes (aneuploidy). In contrast to DNA sequences variations at subchromosomal level (single nucleotide polymorphisms, short tandem repeat variations) or interindividual subtle chromosome region changes (deletions, duplications, large-scale copy-number variants, fragile sites), aneuploidy simultaneously involves hundreds or even thousands of genes and, therefore, dramatically affects functional genome activity. Aneuploidy originates from either meiotic or mitotic chromosome instability and, in some instances, manifests as somatic chromosomal mosaicism. Although the real incidence of mosaic aneuploidy in somatic human tissues remains to be determined, one can suppose an overlooked fraction of cells with unshared genomes due to large-scale genomic alterations among 10¹⁴ cells forming the human body. Intercellular differences in chromosome number can be considered an overlooked type of structural and functional genome variations, which produce genetic mosaicism. This review refers to somatic chromosomal mosaicism and aims to describe its mechanisms and consequences. Moreover, the effect of somatic chromosomal mosaicism on both interindividual and intercellular diversity as well as human diseases is discussed. Finally, since the identification of these genomic variations faces numerous difficulties, we found pertinent to describe available approaches towards the detection of chromosomal mosaicism in human somatic tissues.


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Bioinformatic Analyses of Gram-Negative Bacterial OstA Outer Membrane Assembly Homologues
K.-Y. Hu and M.H. Saier, Jr.

OstA (Imp) homologues have been shown to play a role in outer membrane biogenesis. Bioinformatic analyses of these proteins in organisms with fully sequenced genomes reveal that these proteins occur only in bacteria with two membranes. Two OstA types were identified, large OstAs (L; 812 ± 94 residues) and small OstAs (S; 181 ± 25 residues). S possesses only the OstA domain while L has this domain plus a larger nonhomologous OstA-C domain. Bacteria lacking both S and L proteins were primarily restricted to reduced genome size pathogens and symbionts. Several of these bacteria appear to also have incomplete sets of genes required for the biosynthesis of typical Gram-negative bacterial lipopolysaccharide (LPS). Phylogenetic analyses of both S and L homologues showed that they generally follow the phylogenies of the 16S rRNAs from the same organisms with few exceptions. They may comprise two orthologous sets of proteins that together facilitate a single unified function. While most organisms possess a single L and a single S, those lacking S but possessing L are more numerous than those lacking L but possessing S. Based on our findings and those of others, we suggest that (1) the L and S proteins are nonessential for outer membrane assembly, (2) they normally act together in macromolecular insertion, (3) they are important for proper LPS assembly in the outer leaflet of the outer membrane, (4) they function specifically to export LPS to the outer leaflet, and (5) L provides a primary function while S provides an important auxiliary function.

Supplementary Tables S1-S3
Supplementary Figures S1-S2


[Back to top]
Epistatic Control of Human Obesity as Revealed by Linkage Disequilibrium Mapping: A Report from the NHLBI-Sponsored WISE Study
H. Li, R. Wu, M. Lin, S.G. Terra, C.J. Pepine, S.P. McGorray, B.D. Johnson and J.A. Johnson

Obesity is a major risk factor for type II diabetes, hypertension, cardiovascular disease and certain forms of cancers. Obesity is a complex, multifactorial disorder, influenced by a network of genes, as well as diet, age, ethnicity, gender and exercise. Single nucleotide polymorphisms (SNPs) genotyped in six candidate genes for lipolysis and thermogenesis in human adipose tissue were used to identify and estimate epistatic quantitative trait loci (QTL) predisposing to human obesity based on linkage disequilibrium analysis for 105 black women and 538 white women drawn from the Women's Ischemia Syndrome Evaluation (WISE) study. A few pairs of epistatic QTL were found to affect different aspects of human obesity, including body weight, body mass index, waist and hip circumstances and their ratio, based on association studies of SNPs from different candidate genes. For example, two QTL associated with the β₁-adrenergic receptor and G_s protein alpha subunit, respectively, trigger significant additive x additive, additive x dominant, dominant x additive and dominant x dominant epistatic effects on body weight in the black population. It appeared that more obesity QTL interactions occur in black than white populations, supporting the view that obesity genes may originate from Africa. Results from this study provide fundamental information about the genetic architecture of human obesity and the evolutionary mechanisms of population differentiation.