Current Genomics - Volume 7, Issue 3, 2006

The pathogenesis of inflammatory bowel disease is only partially understood; various environmental and host (e.g. genetic-, epithelial-, immune and non-immune) factors are involved. It is a multifactorial polygenic disease with probable genetic heterogeneity. Much of the recent emphasis in inflammatory bowel disease genetics research has been directed at the evaluation of candidate disease susceptibility genes within inflammatory bowel disease linkage intervals. Such studies have elucidated associations of numerous gene variants (e.g. NOD2/CARD15, SLC22A4/A5 and DLG5) with inflammatory bowel disease, but most of these require further replication and functional validation. Some genes are associated with inflammatory bowel disease itself, while others increase the risk of ulcerative colitis or Crohn's disease or are associated with disease location and/or behaviour. Recently, some new data also indicated at a possible role for genetics in predicting therapeutic success (e.g. response to infliximab or steroids). Genetic information acquired in recent years helps in understanding the pathogenesis of inflammatory bowel disease and identifying a number of potential targets for therapeutic intervention. In the future, genetics may also help in more accurate diagnosis and prediction of disease course and response to therapy in inflammatory bowel disease.

With operon predictions based on conservation of gene order and 330 Prokaryotic genomes available, I am able to show that in most of the genomes analyzed about 70% of the genes in operons are separated by distances of -20 to 30 base pairs. Most of the differences in this tendency might be related to the appearance of signals inside the operons. However, a closer look at the extreme exceptions confirms that annotation problems are partly responsible for inter-genic distance distributions that deviate from that of operons in Escherichia coli K12. I also argue that the inter-genic distances of adjacent genes in different transcription units (transcription unit boundaries or TUBs) should be expected to be more variable than those for genes in the same operon. Using phylogenetic profiles I show that predictions adjusted on a per genome basis might help increase the accuracy of operon predictions. Improvements in automated annotation might be necessary to fully evaluate the overall tendencies of genes in operons towards short inter-genic distances, and to better understand differences in regulatory complexity across Prokaryotes.

In Gram-negative pathogens, β-lactamase production remains the most important contributing factor to β- lactam resistance. β-lactamases are bacterial enzymes that inactivate β-lactam antibiotics by hydrolysis, which results in ineffective compounds. The three major groups usually referred to as the "newer β-lactamases" are plasmid-mediated AmpC enzymes, extended-spectrum β-lactamases (ESBLs) and carbapenem-hydrolyzing enzymes (including metallo-β- lactamases [MBLs]). Molecular methods that include simple and multiplex PCR, real-time PCR, DNA sequencing and various hybridization-based techniques are used widely in research and reference laboratories for the detection of organisms producing newer β-lactamases. The routine screening in clinical diagnostic laboratories of organisms producing TEM, SHV and OXA types of ESBLs using genotypic methods remains problematic, while the detection of CTX-Ms, plasmid-mediated AmpCs and MBLs shows clinical usefulness. Molecular methods have advantages over phenotypic tests by accurately detecting resistant genes in a rapid fashion and by defining the precise genetic basis of the resistance mechanism providing important information valuable to the early introduction of infection control practices. Molecular assays have the potential to complement conventional phenotypic susceptibility techniques and impact directly on patient care.

Gene therapy has advanced rapidly over the last few decades due to the development of viral and plasmid vectors for gene delivery and strategies for the direct alteration of DNA/RNA species. Gene replacement using modified viral vectors and plasmids has yielded the greatest levels of therapeutic protein expression in muscle to date, however there are issues with immune mediated response to transgene and viral proteins, hindering sustained expression. New efforts have been made to make viral delivery of genes safer and sustainable, these include the development of hybrid vectors and "gutted" helper dependant vectors. Non-viral methods of gene delivery and repair provide an alternative to viral based methods. Major concerns with nonviral approaches include the effective distribution and integration of therapeutic molecules throughout the muscle. However, a number of methods have been developed to overcome these obstacles. These include electroporation, vascular injection and occlusion, myotoxins promoting muscle regeneration, muscle specific promoters and the use of pharmacological agents to enhance DNA delivery for gene delivery or gene repair. A number of non-viral plasmid based protocols for gene delivery to muscle have reached the clinical trial stage and show great promise. This review discusses recent advances in viral and non-viral based therapies for muscle diseases, the issues faced by these technologies and current efforts to overcome these obstacles.

Hypodontia, the congenital agenesis of one or few permanent teeth is among the most common alterations in human dentition. Pax9 and Msx1 genes have critical roles in craniofacial development. Mutations in these genes cause severe tooth agenesis in humans and mice. The aim of the present work was to study the association of the CA repeat in the first intron of MSX1 gene and the C-160T polymorphism in the promoter region of PAX9 gene and hypodontia in humans, with emphasis on third molar agenesis. DNA extracted from buccal epithelial cells was amplified by the Polymerase Chain Reaction. Denaturing Gel Electrophoresis, DNA sequencing and PCR-RLFP were employed on the investigation of the polymorphisms. The 169 bp allele of MSX1-CA repeat was the most prevalent in both groups. Borderline associations were found for MSX1 gene. The 169-bp allele was more frequent in individuals with hypodontia (OR=1.9; 95% CI= 1.0 - 3.6; p=0.05) and 169/175 genotype was less prevalent in individuals with hypodontia (OR=0.4; 95% CI=0.2 - 0.9; p=0.05). The CC genotype of the PAX9 C-160T polymorphism was found at a significant higher frequency in individuals with hypodontia (p=0.0009). A separated analysis of individuals with third molar agenesis also revealed a positive association with the CC genotype (p=0.0007).

DNA microarray analysis has emerged as a leading technology to enhance our understanding of gene regulation and function in cellular mechanism controls on a genomic scale. This technology has advanced to unravel the genetic machinery of biological rhythms by collecting massive gene expression data during a time course. In this article, we have proposed a two-step procedure for clustering periodic patterns of gene expression in terms of different transcriptional profiles. In step 1, a least squares approach was used to estimate the coefficients that determine periodic gene expression profiles based on Fourier series approximation. In step 2, the estimated Fourier coefficients were employed to cluster genes into different expression patterns with a traditional clustering analysis and mixture model-based maximum likelihood method implemented with the EM algorithm. Applying our procedure to a case study published in Spellman et al. (1998), 632 cell-cycle regulated genes measured at a multitude of different time points were sorted into five distinct groups. The advantages of this procedure lie in the biological relevance of results obtained and the construction of a general framework within which the interplay between gene expression and development can be tested.