Diagnostic testing for Legionnaires’ disease

Legionnaires’ disease is commonly diagnosed clinically using a urinary antigen test. The urinary antigen test is highly accurate for L. pneumophila serogroup 1, however other diagnostic tests should also be utilized in conjunction with the urinary antigen as many other Legionella species and serogroups are pathogenic. Culturing of patient specimens remains the gold standard for diagnosis of Legionnaires’ disease. Selective media, BYCE with the addition of antibiotics, allows for a high sensitivity and specificity. Culturing can identify all species and serogroups of Legionella. A major benefit of culturing is that it provides the recovery of a patient isolate, which can be used to find an environmental match. Other diagnostic tests, including DFA and molecular tests such as PCR and LAMP, are useful tests to supplement culturing. Molecular tests provide much more rapid results in comparison to culture, however these tests should not be a primary diagnostic tool given their lower sensitivity and specificity in comparison to culturing. It is recommended that all laboratories develop the ability to culture patient specimens in-house with the selective media.     

Mysids in toxicity testing — a review

The use of mysid shrimp, particularly the genusMysidopsis, along with specific testing procedures, has become accepted in aquatic toxicology. Investigators have developed methodologies for both culture and testing of these organisms. Acute and chronic (life cycle) toxicity tests in addition to dredge spoil and effluent tests with mysids are now becoming common. Attempts have been made to use mysids as test organisms in behavioral, physiological, nutritional, and food-chain studies. In general,Mysidopsis spp. have been shown to be as sensitive or more sensitive to toxic substances than other marine species tested. The ease of handling and culture, relative sensitivity to toxicants, short life cycle, small size and direct larval development make these organisms desirable for research purposes. Continued research using mysid species will probably demonstrate even greater usefulness of these organisms in assessment of pollutant impacts on estuarine or marine communities.     

Barriers to HIV testing in Côte d'Ivoire: the role of individual characteristics and testing modalities

Background

Expanding HIV testing requires a better understanding of barriers to its uptake. We investigated barriers to HIV testing in Côte d''Ivoire, taking into account test circumstances (client vs. provider-initiated).

Methods

We used data from the 2005 nationally representative Demographic and Health Survey conducted in Côte d''Ivoire. Socio-demographic characteristics, sexual behaviour and knowledge and attitudes toward HIV/AIDS associated with recent (<2 years) HIV testing were identified using gender-specific univariate and multivariate logistic regressions. Among women, differential effects of barriers to testing according to test circumstance (whether they have been offered for a prenatal test or not) were assessed through interaction tests.

Results

Recent HIV testing was reported by 6.1% of men and 9.5% of women (including 4.6% as part of antenatal care). Among men, having a low socioeconomic status, having a low HIV-related knowledge level and being employed [compared to those inactive: adjusted Odds Ratio (aOR) 0.46; 95% confidence interval (CI) 0.25–0.87] were associated with lower proportions of recent HIV testing. Among women without a prenatal HIV testing offer, living outside the capital (aOR 0.38; CI 0.19–0.77) and reporting a unique lifetime sexual partner constituted additional barriers to HIV testing. By contrast, among women recently offered to be tested in prenatal care, none of these variables was found to be associated with recent HIV testing.

Conclusions

Various dimensions of individuals'' characteristics constituted significant barriers to HIV testing in Côte d''Ivoire in 2005, with gender specificities. Such barriers are substantially reduced when testing was proposed in the framework of antenatal care. This suggests that provider-initiated testing strategies may help overcome individual barriers to HIV testing.     

Insurance and genetic testing: where are we now?

Basic research will spur development of genetic tests that are capable of presymptomatic prediction of disease, disability, and premature death in presently asymptomatic individuals. Concerns have been expressed about potential harms related to the use of genetic test results, especially loss of confidentiality, eugenics, and discrimination. Existing laws and administrative policies may not be sufficient to assure that genetic information is used fairly. To provide factual information and conceptual principles upon which sound social policy can be based, the Human Genome Initiative established an Ethical, Legal, and Social Issues Program. Among the first areas to be identified as a priority for study was insurance. This paper provides a review of life, health, and disability insurance systems, including basic principles, risk classification, and market and regulatory issues, and examines the potential impact of genetic information on the insurance industry.     

GeneTools – application for functional annotation and statistical hypothesis testing

Background  

Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.     

Computational design and experimental testing of the fastest-folding β-sheet protein

One of the most important and elusive goals of molecular biology is the formulation of a detailed, atomic-level understanding of the process of protein folding. Fast-folding proteins with low free-energy barriers have proved to be particularly productive objects of investigation in this context, but the design of fast-folding proteins was previously driven largely by experiment. Dramatic advances in the attainable length of molecular dynamics simulations have allowed us to characterize in atomic-level detail the folding mechanism of the fast-folding all-β WW domain FiP35. In the work reported here, we applied the biophysical insights gained from these studies to computationally design an even faster-folding variant of FiP35 containing only naturally occurring amino acids. The increased stability and high folding rate predicted by our simulations were subsequently validated by temperature-jump experiments. The experimentally measured folding time was 4.3 μs at 80 °C—about three times faster than the fastest previously known protein with β-sheet content and in good agreement with our prediction. These results provide a compelling demonstration of the potential utility of very long molecular dynamics simulations in redesigning proteins well beyond their evolved stability and folding speed.     

Unleashing the force of cladistics? Metazoan phylogenetics and hypothesis testing

The accumulation of multiple phylogenetic hypotheses for theMetazoa invites an evaluation of current progress in the field.I discuss three case studies from the recent literature to assesshow cladistic analyses of metazoan morphology have contributedto our understanding of animal evolution. The first case studyon cleavage cross patterns examines whether a decade of unanimouscharacter scoring across different cladistic studies can beconsidered a reliable indicator of accumulated wisdom. The tworemaining case studies illustrate how the unique strength ofcladistic analyses to arbitrate between competing hypothesescan be crippled when insufficient attention is directed towardsthe construction of the data matrix. The second case study discussesa recent morphological cladistic analysis aimed at providinginsight into the evolution of larval ciliary bands (prototrochs)in the Spiralia, and the third case study evaluates how foursubsequent morphological cladistic analyses have contributedto our understanding of the phylogenetic placement of a problematicum,the Myzostomida. I conclude that current phylogenetic analysesof the Metazoa have not fully exploited the power of cladisticsto test available alternative hypotheses. If our goal is togenerate genuine progress in understanding rather than stochasticvariation of opinions through time, we have to shift our attentionfrom using cladistics as an easy tool to generate "novel" hypothesesof metazoan relationships, towards employing cladistics morecritically as an effective instrument to test the relative meritof available multiple alternative hypotheses.     

Swab or biopsy samples for bioburden testing of allograft musculoskeletal tissue?

Swab and biopsy samples of allograft musculoskeletal tissue are most commonly collected by tissue banks for bacterial and fungal bioburden testing. An in vitro study was performed using the National Committee for Clinical Laboratory Standards standard ‘Quality control of microbiological transport systems’ (2003) to validate and evaluate the recovery of six challenge organisms from swab and biopsy samples of allograft musculoskeletal tissue. On average, 8.4 to >100 and 7.2 to >100 % of the inoculum was recovered from swab and biopsy samples respectively. A retrospective review of donor episodes was also performed, consisting of paired swab and biopsy samples received in this laboratory during the period 2001–2012. Samples of allograft femoral heads were collected from living donors during hip operations. From the 3,859 donor episodes received, 21 paired swab and biopsy samples each recovered an isolate, 247 swab samples only and 79 biopsy samples only were culture positive. Low numbers of challenge organisms were recovered from inoculated swab and biopsy samples in the in vitro study and validated their use for bioburden testing of allograft musculoskeletal tissue. Skin commensals were the most common group of organisms isolated during a 12-year retrospective review of paired swab and biopsy samples from living donor allograft femoral heads. Paired swab and biopsy samples are a suitable representative sample of allograft musculoskeletal tissue for bioburden testing.     

Should antifungal treatments be based upon results of antifungal susceptibility testing?

The development of reliable procedures for detecting resistance in vitro to antifungal agents and the increase in the prevalence of mycoses due to organisms with intrinsic or secondary resistance have reinforced the clinical relevance of antifungal susceptibility testing. A matter is currently in the limelight: can antifungal agents indications be based on susceptibility testing results? The present paper reviews the reliability of susceptibility testing procedures available at the moment, their capability for predicting therapeutic failure, and their clinical usefulness.     

Diffusion of genetic testing in oncology: what criteria for regulation?

Does gene testing indicate a switch from an histopathological to a molecular approach of human diseases ? Disease management in oncology is already improved by gene testing, at least for some specific cancers. It is however necessary to distinguish the analysis of genes specific to the tumour which gives clues about the fate of the tumours, from those unique to the patients, which gives clues about the future of the person. For the latter so-called germline mutations, wide scale gene-default screening would put pressure on resource allocation from the health care systems of developed countries. Currently the cost of detecting of 700 genes in the whole French population would exceed the whole health budget of the country for the next 10 years. Even if we can anticipate a dramatic decrease in the unit cost of these genetic tests in the future, their diffusion should not be controlled exclusively by technological and market forces. In this paper, we propose to discuss four main parameters for regulating these genetic tests, using as an archetypal example their application to cancer prevention and treatment: (1) which specific cancer disease is targeted by the test (prevalence, incidence, likelihood of cure with current therapeutics, number of years of life potentially saved...); (2) what are the characteristics of the genes tested and which level of evidence is required about the predictive value of the test; (3) what are the size and characteristics of the population who will be offered the test, and (4) which process and public control are necessary before market approval of the test and reimbursement of related expenditures by health care insurance schemes.     

Can mutation theories of carcinogenesis set priorities for carcinogen testing programs?

The recent activity in designing, validating and implementing short-term tests for carcinogens has been spurred by the fairly convincing correlation between the carcinogenicity and mutagenicity of chemicals and by the assumption that mutations are somehow involved in neoplastic transformation. Moreover, it has been tacitly assumed that the mutagenic capacity alone of compounds would induce regulatory agencies to pass rules for their removal from man's environment, and would lead the public to avoid them. The actual response, however, is quite different. Government departments shy away from making any decisions on the basis of in vitro test systems, the public at large is becoming irritated by daily announcements that many of their cherished habits could adversely affect their health, and industries feel threatened and may reduce their search for new beneficial chemicals. The reluctance to accept wholeheartedly the mutagenicity tests for the detection of carcinogens is partly due to the uncertainty about the involvement of mutations in the formation of benign and malignant tumors. Following the initial rapid advances in the detection of environmental chemicals with carcinogenic and mutagenic properties, we seem to have arrived at the cross roads: we must now set new priorities for future research, and must make an unbiased assessment of the actual hazard of a compound to man and the human population.     

Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis

A number of observations have led researchers to postulate that, despite being replication‐defective, human endogenous retroviruses (HERVs) may have retained the potential to cause or contribute to disease. However, mechanisms of HERV pathogenicity might differ substantially from those of modern infectious retroviruses or of the infectious precursors of HERVs. Therefore, novel pathways of HERV involvement in disease pathogenesis should be investigated. Recent technological advances in sequencing and bioinformatics are making this task increasingly feasible. The accumulating knowledge of HERV biology may also facilitate the definition and general acceptance of criteria that establish HERV pathogenicity. Here, we explore possible mechanisms whereby HERVs may cause disease and examine the evidence that either has been or should be obtained in order to decisively address the pathogenic potential of HERVs.