PCR-based rapid genotyping of Stenotrophomonas maltophilia isolates

<p>Abstract</p> <p>Background</p> <p>All bacterial genomes contain repetitive sequences which are members of specific DNA families. Such repeats may occur as single units, or found clustered in multiple copies in a head-to-tail configuration at specific loci. The number of clustered units per locus is a strain-defining parameter. Assessing the length variability of clusters of repeats is a versatile typing methodology known as multilocus variable number of tandem repeat analysis (MLVA).</p> <p>Results</p> <p><it>Stenotrophomonas maltophilia </it>is an environmental bacterium increasingly involved in nosocomial infections and resistant to most antibiotics. The availability of the whole DNA sequence of the <it>S. maltophilia </it>strain K279a allowed us to set up fast and accurate PCR-based diagnostic protocols based on the measurement of length variations of <it>loci </it>carrying a variable number of short palindromic repeats marking the <it>S. maltophilia </it>genome. On the basis of the amplimers size, it was possible to deduce the number of repeats present at 12 different <it>loci </it>in a collection of <it>S. maltophilia </it>isolates, and therefore label each of them with a digit. PCR-negative regions were labelled 0. Co-amplification of two pairs of <it>loci </it>provided a 4-digit code sufficient for immediate subtyping. By increasing the number of <it>loci </it>analyzed, it should be possible to assign a more specific digit profile to isolates. In general, MLVA data match genotyping data obtained by PFGE (pulsed-field gel electrophoresis). However, some isolates exhibiting the same PCR profiles at all <it>loci </it>display distinct PFGE patterns.</p> <p>Conclusion</p> <p>The utilization of the present protocol allows to type several <it>S. maltophilia </it>isolates in hours. The results are immediately interpretable without the need for sophisticated softwares. The data can be easily reproducible, and compared among different laboratories.</p

Can Bibliographic Pointers for Known Biological Data Be Found Automatically? Protein Interactions as a Case Study

The Dictionary of Interacting Proteins (DIP) (Xenarios et al., 2000) is a large repository of protein interactions: its March 2000 release included 2379 protein pairs whose interactions have been detected by experimental methods. Even if many of these correspond to poorly characterized proteins, the result of massive yeast two-hybrid screenings, as many as 851 correspond to interactions detected using direct biochemical methods

Does low and oscillatory wall shear stress correlate spatially with early atherosclerosis? A systematic review

Low and oscillatory wall shear stress is widely assumed to play a key role in the initiation and development of atherosclerosis. Indeed, some studies have relied on the low shear theory when developing diagnostic and treatment strategies for cardiovascular disease. We wished to ascertain if this consensus is justified by published data. We performed a systematic review of papers that compare the localization of atherosclerotic lesions with the distribution of haemodynamic indicators calculated using computational fluid dynamics. The review showed that although many articles claim their results conform to the theory, it has been interpreted in different ways: a range of metrics has been used to characterize the distribution of disease, and they have been compared with a range of haemodynamic factors. Several studies, including all of those making systematic point-by-point comparisons of shear and disease, failed to find the expected relation. The various pre- and post-processing techniques used by different groups have reduced the range of shears over which correlations were sought, and in some cases are mutually incompatible. Finally, only a subset of the known patterns of disease has been investigated. The evidence for the low/oscillatory shear theory is less robust than commonly assumed. Longitudinal studies starting from the healthy state, or the collection of average flow metrics derived from large numbers of healthy vessels, both in conjunction with point-by-point comparisons using appropriate statistical techniques, will be necessary to improve our understanding of the relation between blood flow and atherogenesis

Lysine demethylases KDM6A and UTY: the X and Y of histone demethylation

Histone demethylases remove transcriptional repressive marks from histones in the nucleus. KDM6A (also known as UTX) is a lysine demethylase which acts on the trimethylated lysine at position 27 in histone 3. The KDM6A gene is located on the X chromosome but escapes X inactivation even though it is not located in the pseudoautosomal region. There is a homologue of KDM6A on the Y chromosome, known as UTY. UTY was thought to have lost its demethylase activity and to represent a non-functional remnant of the ancestral KDM6A gene. However, results with knockout mice suggest that the gene is expressed and the protein performs some function within the cell. Female mice with homozygous deletion of Kdm6a do not survive, but hemizygous males are viable, attributed to the presence of the Uty gene. KDM6A is mutated in the human condition Kabuki syndrome type 2 (OMIM 300867) and in many cases of cancer. The amino acid sequence of KDM6A has been conserved across animal phyla, although it is only found on the X chromosome in eutherian mammals. In this review, we reanalyse existing data from various sources (protein sequence comparison, evolutionary genetics, transcription factor binding and gene expression analysis) to determine the function, expression and evolution of KDM6A and UTY and show that UTY has a functional role similar to KDM6A in metabolism and development

Meeting the review family : exploring review types and associated information retrieval requirements

Background and objectives The last decade has witnessed increased recognition of the value of literature reviews for advancing understanding and decision making. This has been accompanied by an expansion in the range of methodological approaches and types of review. However, there remains uncertainty over definitions and search requirements beyond those for the ‘traditional’ systematic review. This study aims to characterise health related reviews by type and to provide recommendations on appropriate methods of information retrieval based on the available guidance. Methods A list of review types was generated from published typologies and categorised into ‘families’ based on their common features. Guidance on information retrieval for each review type was identified by searching pubmed, medline and Google Scholar, supplemented by scrutinising websites of review producing organisations. Results Forty‐eight review types were identified and categorised into seven families. Published guidance reveals increasing specification of methods for information retrieval; however, much of it remains generic with many review types lacking explicit requirements for the identification of evidence. Conclusions Defining review types and utilising appropriate search methods remain challenging. By familiarising themselves with a range of review methodologies and associated search methods, information specialists will be better equipped to select suitable approaches for future projects

Taking stock of 10 years of published research on the ASHA programme: Examining India’s national community health worker programme from a health systems perspective

Background: As India’s accredited social health activist (ASHA) community health worker (CHW) programme enters its second decade, we take stock of the research undertaken and whether it examines the health systems interfaces required to sustain the programme at scale. Methods: We systematically searched three databases for articles on ASHAs published between 2005 and 2016. Articles that met the inclusion criteria underwent analysis using an inductive CHW–health systems interface framework. Results: A total of 122 academic articles were identified (56 quantitative, 29 mixed methods, 28 qualitative, and 9 commentary or synthesis); 44 articles reported on special interventions and 78 on the routine ASHA program. Findings on special interventions were overwhelmingly positive, with few negative or mixed results. In contrast, 55% of articles on the routine ASHA programme showed mixed findings and 23% negative, with few indicating overall positive findings, reflecting broader system constraints. Over half the articles had a health system perspective, including almost all those on general ASHA work, but only a third of those with a health condition focus. The most extensively researched health systems topics were ASHA performance, training and capacity-building, with very little research done on programme financing and reporting, ASHA grievance redressal or peer communication. Research tended to be descriptive, with fewer influence, explanatory or exploratory articles, and no predictive or emancipatory studies. Indian institutions and authors led and partnered on most of the research, wrote all the critical commentaries, and published more studies with negative results. Conclusion: Published work on ASHAs highlights a range of small-scale innovations, but also showcases the challenges faced by a programme at massive scale, situated in the broader health system. As the programme continues to evolve, critical comparative research that constructively feeds back into programme reforms is needed, particularly related to governance, intersectoral linkages, ASHA solidarity, and community capacity to provide support and oversight