Current Genomics - Volume 7, Issue 2, 2006

Genomic DNA from WBCs is widely often used for PCR. Although kits for DNA isolation are in common use, there is scarce information about their performance and about the PCR quality of the genomic DNA obtained. Hence, three different kits, QIAamp blood mini kit, High Pure PCR Template Preparation Kit and the Puregene DNA isolation kit were evaluated on these aspects. Genomic DNA was isolated from whole blood samples with WBC counts ranging from 0.5 to 20*109 WBC/L. The WBC count was used to calculate the amount of genomic DNA. The actual amount of genomic DNA isolated, was determined spectrophotometrically. The DNA extraction efficiency was obtained by dividing the actual amount of DNA by the calculated amount yielded. PCR quality was analysed by measuring Cycle threshold (Ct) values with a quantitative real-time PCR β-globin assay. The extraction efficiency of the three DNA isolation kits was 20% to 40%. Spectrophotometrically determined DNA concentrations correlated inversely with Ct values, regardless of the DNA isolation kit applied, whereas the strongest correlation was obtained for the Puregene DNA isolation kit. WBC counts also correlated inversely with Ct values and here the strongest correlation was found for the QIAamp blood mini kit. In conclusion, the overall performance of the DNA isolation kits was quite comparable (DNA recoveries of 20-40%), albeit the QIAamp blood mini kit yielded the most reproducible extraction efficiencies and lowest Ct values within every WBC count category.

Determining gene functions from genomic sequences is a central goal of bioinformatics. Traditionally computational approaches to this problem are based on the detection of genes with homologous sequences. With the completion of fully sequenced genomes alternative approaches have become feasible. One such method is that of phylogenetic profiles. In this method a gene is described by its phylogenetic profile, i.e. a string that encodes the presence or absence of a homologous gene in other genomes. This string is then used to search for other genes with similar profiles. In this paper we briefly review the field, including extensions to the original method. We also discuss variations on this theme including inverse phylogenetic profiles and non-exact profiles using phylogenetic trees. In conclusion our work indicates that phylogenetic profiles might be useful for some, but not all functional annotations. Functional annotation of genomes remains an important problem in genomics when no close homologs exist.

Functional divergence after gene duplications is a fundamental issue for functional innovations in many organisms. As gene family proliferation (gene duplication) may have provided the raw materials for the origin of new genes, the details of how duplicate genes have preserved through functional divergence remain largely unknown. In this review paper, we discuss some recent developments about this important issue, with special references to the implication for functional genomics. With a combination of large-scale genome sequencing and powerful computational analysis, we show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The software DIVERGE can be obtained form http://xgu.gdcb.iastate.edu.

How organismal complexity is achieved is a fundamental biological issue. The surprising revelation that complex eukaryotes have fewer than expected genes presents an important challenge for deciphering how organisms achieve complexity. The genome size and the gene number do not necessarily correlate in a consistent manner with the perceived organismal complexity. In this review, we focus on known molecular mechanisms that increase genetic complexity at the molecular and functional levels, and discuss features that have likely contributed to organismal complexity.

Gene expression profiling using microarrays and SAGE is a widely used technology to elucidate important aspects of epithelial ovarian cancer (EOC) in order to improve the clinical management of this disease: Despite the high degree of morphological heterogeneity, epithelial ovarian cancer gene expression profiling reflects morphology and biological behaviour. Based on multiple studies, gene expression profiling results can be used to stratify the four different subtypes of EOC, namely serous papillary, mucinous, endometrioid, and clear cell carcinoma, but some overlapping gene expression was also noted. An aneuploid DNA content is a frequent phenomenon in EOC as well as in other solid tumours. However, when differential RNA expression and the DNA copy number as measured by comparative genomic hybridisation (CGH) were compared, the level of concordance was not significant in most studies. The reason for this will mostly lie in the low resolving power of currently used CGH methods and might improve with a wider access to arrayCGH. Several novel candidate markers for the early detection of EOC have been identified by gene expression profiling and examples that have been validated by ELISA on the protein level in serum from EOC patients and healthy controls are discussed. The information from gene expression profiling experiments is now being overlaid with additional information from Gene Ontology, protein-protein interaction and signal transduction pathway databases in order to discover novel therapeutic pathways and targets. Genes involved in cell cycle regulation, the extracellular matrix, and in immunological responses are relevant to epithelial ovarian cancer biology and particular genes might have the potential to be exploited as therapeutic targets for small molecules, biologicals, and immunologicals. We hope to accomplish that the scope of the review which includes a discussion of the recently published papers and the implications of the results for the clinical management of EOC is of help to researchers and clinicians in the field.

Far from serving as an inert skeletal scaffold, bone is a dynamic tissue that cycles through tightly coordinated cycles of developmental growth and regeneration. Bone growth, which determines the overall growth of vertebrates, is well-characterized histologically and increasingly understood at the molecular level. Positional cloning strategies applied to diseases of simple Mendelian inheritance have revealed genes important in the proper formation of bone. Functional studies of these genes, aided considerably by insights provided by studies of orthologs in various model systems, have led to significant advances in our understanding of the pathways of mammalian bone morphogenesis. One such disorder, hereditary multiple exostoses, is caused by members of the EXT tumor suppressor gene family. Progress on the molecular dissection of this disorder, with emphasis on the interplay of genomic, model system, and clinical studies, is reviewed herein. We are now challenged to re-direct the biochemical pathway of chondrogenesis/osteogenesis defined by the EXT genes toward therapeutic control of bone growth and malignancy.