DNA Copy Number Analysis in Gastrointestinal Stromal Tumors Using Gene Expression Microarrays

We report a method, Expression-Microarray Copy Number Analysis (ECNA) for the detection of copy number changes using Affymetrix Human Genome U133 Plus 2.0 arrays, starting with as little as 5 ng input genomic DNA. An analytical approach was developed using DNA isolated from cell lines containing various X-chromosome numbers, and validated with DNA from cell lines with defined deletions and amplifications in other chromosomal locations. We applied this method to examine the copy number changes in DNA from 5 frozen gastrointestinal stromal tumors (GIST). We detected known copy number aberrations consistent with previously published results using conventional or BAC-array CGH, as well as novel changes in GIST tumors. These changes were concordant with results from Affymetrix 100K human SNP mapping arrays. Gene expression data for these GIST samples had previously been generated on U133A arrays, allowing us to explore correlations between chromosomal copy number and RNA expression levels. One of the novel aberrations identified in the GIST samples, a previously unreported gain on 1q21.1 containing the PEX11B gene, was confirmed in this study by FISH and was also shown to have significant differences in expression pattern when compared to a control sample. In summary, we have demonstrated the use of gene expression microarrays for the detection of genomic copy number aberrations in tumor samples. This method may be used to study copy number changes in other species for which RNA expression arrays are available, e.g. other mammals, plants, etc., and for which SNPs have not yet been mapped

Dirty money: a matter of bacterial survival, adherence, and toxicity

In this study we report the underlying reasons to why bacteria are present on banknotes and coins. Despite the use of credit cards, mobile phone apps, near-field-communication systems, and cryptocurrencies such as bitcoins which are replacing the use of hard currencies, cash exchanges still make up a significant means of exchange for a wide range of purchases. The literature is awash with data that highlights that both coins and banknotes are frequently identified as fomites for a wide range of microorganisms. However, most of these publications fail to provide any insight into the extent to which bacteria adhere and persist on money. We treated the various currencies used in this study as microcosms, and the bacterial loading from human hands as the corresponding microbiome. We show that the substrate from which banknotes are produced have a significant influence on both the survival and adherence of bacteria to banknotes. Smooth, polymer surfaces provide a poor means of adherence and survival, while coarser and more fibrous surfaces provide strong bacterial adherence and an environment to survive on. Coins were found to be strongly inhibitory to bacteria with a relatively rapid decline in survival on almost all coin surfaces tested. The inhibitory influence of coins was demonstrated through the use of antimicrobial disks made from coins. Despite the toxic effects of coins on many bacteria, bacteria do have the ability to adapt to the presence of coins in their environment which goes some way to explain the persistent presence of low levels of bacteria on coins in circulatio

Molecular genetic analysis of the 3p — syndrome

Molecular genetic analysis of five cases of 3p-syndrome (del(3)(qter-p25:)) was performed to investigate the relationship between the molecular pathology and clinical phenotype. Fluorescence in situ hybridization studies and analysis of polymorphic DNA markers from chromosome 3p25-p26 demonstrated that all four informative cases had distal deletions. However, the extent of the deletion was variable: in two patients with the most extensive deletions the deletion breakpoint mapped between RAF1 and D3S1250, in one patient the deletion breakpoint was between D3S1250 and D3S601, and in two patients the deletion commenced telomeric to D3S601 (and telomeric to D3S1317 in one of these). All five patients displayed the classical features of 3p- syndrome (mental retardation, growth retardation, microcephaly, ptosis and micrognathia) demonstrating that loss of sequences centromeric to D3S1317 is not required for expression of the characteristic 3p- syndrome phenotype. The three patients with the most extensive deletions had cardiac septal defects suggesting that a gene involved in normal cardiac development is contained in the interval D3S1250 and D3S18. The PMCA2 gene is contained within this region and deletion of this gene may cause congenital heart defects. At least three patients were deleted for the von Hippel - Lindau (VHL) disease gene although none had yet developed evidence of VHL disease. We conclude that molecular analysis of 3p- syndrome patients enhances the management of affected patients by identifying those at risk for VHL disease, and can be used to elucidate the critical regions for the 3p- syndrome phenotyp

Primary health care delivery models in rural and remote Australia – a systematic review

© 2008 Wakerman et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background One third of all Australians live outside of its major cities. Access to health services and health outcomes are generally poorer in rural and remote areas relative to metropolitan areas. In order to improve access to services, many new programs and models of service delivery have been trialled since the first National Rural Health Strategy in 1994. Inadequate evaluation of these initiatives has resulted in failure to garner knowledge, which would facilitate the establishment of evidence-based service models, sustain and systematise them over time and facilitate transfer of successful programs. This is the first study to systematically review the available published literature describing innovative models of comprehensive primary health care (PHC) in rural and remote Australia since the development of the first National Rural Health Strategy (1993–2006). The study aimed to describe what health service models were reported to work, where they worked and why. Methods A reference group of experts in rural health assisted in the development and implementation of the study. Peer-reviewed publications were identified from the relevant electronic databases. 'Grey' literature was identified pragmatically from works known to the researchers, reference lists and from relevant websites. Data were extracted and synthesised from papers meeting inclusion criteria. Results A total of 5391 abstracts were reviewed. Data were extracted finally from 76 'rural' and 17 'remote' papers. Synthesis of extracted data resulted in a typology of models with five broad groupings: discrete services, integrated services, comprehensive PHC, outreach models and virtual outreach models. Different model types assume prominence with increasing remoteness and decreasing population density. Whilst different models suit different locations, a number of 'environmental enablers' and 'essential service requirements' are common across all model types. Conclusion Synthesised data suggest that, moving away from Australian coastal population centres, sustainable models are able to address diseconomies of scale which result from large distances and small dispersed populations. Based on the service requirements and enablers derived from analysis of reported successful PHC service models, we have developed a conceptual framework that is particularly useful in underpinning the development of sustainable PHC models in rural and remote communities

Somatic cell type specific gene transfer reveals a tumor-promoting function for p21Waf1/Cip1

How proteins participate in tumorigenesis can be obscured by their multifunctional nature. For example, depending on the cellular context, the cdk inhibitors can affect cell proliferation, cell motility, apoptosis, receptor tyrosine kinase signaling, and transcription. Thus, to determine how a protein contributes to tumorigenesis, we need to evaluate which functions are required in the developing tumor. Here we demonstrate that the RCAS/TvA system, originally developed to introduce oncogenes into somatic cells of mice, can be adapted to allow us to define the contribution that different functional domains make to tumor development. Studying the development of growth-factor-induced oligodendroglioma, we identified a critical role for the Cy elements in p21, and we showed that cyclin D1T286A, which accumulates in the nucleus of p21-deficient cells and binds to cdk4, could bypass the requirement for p21 during tumor development. These genetic results suggest that p21 acts through the cyclin D1–cdk4 complex to support tumor growth, and establish the utility of using a somatic cell modeling system for defining the contribution proteins make to tumor development

The evolution of a highly variable sex chromosome in Gehyra purpurascens (Gekkonidae)

A karyotypic survey of the gekkonid lizard Gehyra purpurascens revealed a distinctive sex chromosome system. G-banding showed that the Z Chromosome of males is derived from a tandem fusion of two acrocentric chromosomes of a presumed ancestral Gehyra with 2n=44. Through the application of G-; N- and C-banding, a total of six morphs of the W chromosome were identified. These differ by paracentric and pericentric inversions and, in one case, by a centric shift. The possible reasons for such extensive variation in the W chromosome are considered, and it is suggested that increased mutability of the W chromosome may be a causal factor. In contrast to earlier speculations, this example demonstrates that sex chromosomes can evolve without significant changes in the amount of C-band heterochromatin.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47361/1/412_2004_Article_BF00292447.pd

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead