Mini-STRs em genética forense

A análise do ADN baseada nos STRs (Short Tandem Repeats) tem provado ser uma ferramenta extremamente útil em estudos forenses. A aplicação dos multiplex de STRs resulta em perfis genéticos completos, para a maior parte das amostras, desde que contenham uma quantidade apreciável de ADN. Contudo, em amostras com ADN degradado, a análise tornase mais complicada, uma vez que os STRs com maior peso molecular (acima dos 250 pb), podem não ser amplificados nestas condições. Como a metodologia de Mini-STRs não estava, ainda, implementada nos Laboratórios Forenses portugueses, o objectivo principal deste estudo consistiu na aplicação de um multiplex, designado por Mini-SGM, que contém os marcadores TH01, FGA, D18S51, D16S359, D2S1338 e a Amelogenina, para implementação na prática forense, tendo os resultados sido comparados com a metodologia de rotina. O trabalho experimental teve início com um estudo populacional, que compreendeu uma amostra de 110 indivíduos de origem portuguesa, não relacionados e uma amostra de 52 indivíduos, não relacionados, oriundos de Cabo Verde, encontrando-se, ambas as populações, em Equilíbrio de Hardy-Weinberg, excepto para o locus D18S51, na população portuguesa e o locus D2S1338 na população de origem africana. Em relação aos parâmetros estatísticos forenses, este estudo demonstrou que o poder de discriminação varia entre 0,903 e 0,959, para a população portuguesa, e entre 0,908 e 0,958, para a população de Cabo Verde. Após o estudo populacional, foram analisados 39 casos forenses, devidamente anonimizados, da casuística do Serviço de Genética e Biologia Forense da Delegação de Lisboa do INML, com diferentes tipos de vestígios biológicos, como sangue, ossos, pulmão, coração, tecidos embrionários, tecidos inclusos em parafina, fígado, rim e dentes, de modo a ilustrar a utilidade desta nova metodologia nos casos forenses. No estudo de amostras degradadas, o uso da metodologia de rotina pode,

Identification of infectious agents in onychomycoses by PCR-terminal restriction fragment length polymorphism.

A fast and reliable assay for the identification of dermatophyte fungi and nondermatophyte fungi (NDF) in onychomycosis is essential, since NDF are especially difficult to cure using standard treatment. Diagnosis is usually based on both direct microscopic examination of nail scrapings and macroscopic and microscopic identification of the infectious fungus in culture assays. In the last decade, PCR assays have been developed for the direct detection of fungi in nail samples. In this study, we describe a PCR-terminal restriction fragment length polymorphism (TRFLP) assay to directly and routinely identify the infecting fungi in nails. Fungal DNA was easily extracted using a commercial kit after dissolving nail fragments in an Na(2)S solution. Trichophyton spp., as well as 12 NDF, could be unambiguously identified by the specific restriction fragment size of 5'-end-labeled amplified 28S DNA. This assay enables the distinction of different fungal infectious agents and their identification in mixed infections. Infectious agents could be identified in 74% (162/219) of cases in which the culture results were negative. The PCR-TRFLP assay described here is simple and reliable. Furthermore, it has the possibility to be automated and thus routinely applied to the rapid diagnosis of a large number of clinical specimens in dermatology laboratories.

Characterization of a new clinical yeast species, Candida tunisiensis sp. nov., isolated from a strain collection from Tunisian hospitals.

From a collection of yeast isolates isolated from patients in Tunisian hospitals between September 2006 and July 2010, the yeast strain JEY63 (CBS 12513), isolated from a 50-year-old male that suffered from oral thrush, could not be identified to the species level using conventional methods used in clinical laboratories. These methods include matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), germ tube formation, and the use of CHROMagar Candida and metabolic galleries. Sequence analysis of the nuclear rRNA (18S rRNA, 5.8S rRNA, and 26S rRNA) and internal transcribed spacer regions (ITS1 and ITS2) indicated that the ribosomal DNA sequences of this species were not yet reported. Multiple gene phylogenic analyses suggested that this isolate clustered at the base of the Dipodascaceae (Saccharomycetales, Saccharomycetes, and Ascomycota). JEY63 was named Candida tunisiensis sp. nov. according to several phenotypic criteria and its geographical origin. C. tunisiensis was able to grow at 42°C and does not form chlamydospores and hyphae but could grow as yeast and pseudohyphal forms. C. tunisiensis exhibited most probably a haploid genome with an estimated size of 10 Mb on at least three chromosomes. Using European Committee for Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) Candida albicans susceptibility breakpoints as a reference, C. tunisiensis was resistant to fluconazole (MIC = 8 μg/ml), voriconazole (MIC = 0.5 μg/ml), itraconazole (MIC = 16 μg/ml), and amphotericin B (MIC = 4 μg/ml) but still susceptible to posaconazole (MIC = 0.008 μg/ml) and caspofungin (MIC = 0.5 μg/ml). In conclusion, MALDI-TOF MS permitted the early selection of an unusual isolate, which was still unreported in molecular databases but could not be unambiguously classified based on phylogenetic approaches.

Insects associated with exposed decomposing bodies in the Colombian Andean Coffee Region

In Colombia, mainly classic forensic medicine methods were used to clarify crimes until 2004. However, other disciplines, including forensic entomology, started to be considered only after the New Accusatory System introduction in Bogotá and the Coffee Region in 2005. In order to provide tools for obtaining evidentiary material elements in judicial trials, it is presented here the succession of insects throughout the decomposition process of an exposed carcass of Sus scrofa Linnaeus 1758 (Suidae) and the Occurrence Matrix of colonizing species. This process was evaluated under ambient conditions in the Andean rural area of the city of Pereira, in the Mundo Nuevo district, located in a pre-montane Wet Forest area, from October to November 2006. A sampling period of 27 days and 3198 individuals were collected. We found these colonizing species in the following stages of decomposition: Lucilia eximia (Wiedemann, 1819) fresh; Hemilucilia semidiaphana (Rondani, 1850), Oxelytrum discicolle (Brullé, 1840), and Cochliomyia macellaria (Fabricius 1775) bloated; Chrysomya albiceps (Wiedemann 1819), Compsomyiops verena (Walker, 1849), Ophyra aenescens (Wiedemann, 1830) and Musca domestica Linnaeus, 1758 active; Fannia sp. advanced and Stearibia nigriceps (Meigen, 1826) remains. This study provides support tools to define the Post Mortem Interval that may be used by experts from government institutions and laboratories officially accredited.

First nationwide study on driving under the influence of drugs in Switzerland.

In Switzerland, a two-tier system based on impairment by any psychoactive substances which affect the capacity to drive safely and zero tolerance for certain illicit drugs came into force on 1 January 2005. According to the new legislation, the offender is sanctioned if Delta(9)-tetrahydrocannabinol THC is >or=1.5ng/ml or amphetamine, methamphetamine, 3,4-methylenedioxymethamphetamine (MDMA), 3,4-methylenedioxyethylamphetamine (MDEA), cocaine, free morphine are >or=15ng/ml in whole blood (confidence interval+/-30%). For all other psychoactive substances, impairment must be proven in applying the so-called "three pillars expertise". At the same time the legal blood alcohol concentration (BAC) limit for driving was lowered from 0.80 to 0.50g/kg. The purpose of this study was to analyze the prevalence of drugs in the first year after the introduction of the revision of the Swiss Traffic Law in the population of drivers suspected of driving under the influence of drugs (DUID). A database was developed to collect the data from all DUID cases submitted by the police or the Justice to the eight Swiss authorized laboratories between January and December 2005. Data collected were anonymous and included the age, gender, date and time of the event, the type of vehicle, the circumstances, the sampling time and the results of all the performed toxicological analyses. The focus was explicitly on DUID; cases of drivers who were suspected to be under the influence of ethanol only were not considered. The final study population included 4794 DUID offenders (4243 males, 543 females). The mean age of all drivers was 31+/-12 years (range 14-92 years). One or more psychoactive drugs were detected in 89% of all analyzed blood samples. In 11% (N=530) of the samples, neither alcohol nor drugs were present. The most frequently encountered drugs in whole blood were cannabinoids (48% of total number of cases), ethanol (35%), cocaine (25%), opiates (10%), amphetamines (7%), benzodiazepines (6%) and methadone (5%). Other medicinal drugs such as antidepressants and benzodiazepine-like were detected less frequently. Poly-drug use was prevalent but it may be underestimated because the laboratories do not always analyze all drugs in a blood sample. This first Swiss study points out that DUID is a serious problem on the roads in Switzerland. Further investigations will show if this situation has changed in the following years.

Clinical microbiologists facing an anthrax alert.

Microbiological war and terrorist attacks are made to weaken populations by transmitting pathogenic and epidemic microorganisms. These bacteria or viruses are often difficult to diagnose. Anthrax alerts following September 2001 showed that most clinical microbiology laboratories were not adequately prepared, using obsolete diagnostic methods or being too slow to use accurate tools when facing a major threat. Following this period, most microbiology laboratories were prepared for bioterrorism alerts, in order to provide accurate and rapid results, although such events are rare and unexpected. In this review, we describe the organization and preparedness of our clinical microbiology laboratory regarding bioterrorism risk, although its main task is to perform routine diagnostic microbiology tests. To illustrate the difficulties, we briefly describe an anthrax alert.

Human growth hormone doping in sport.

BACKGROUND AND OBJECTIVES: Recombinant human growth hormone (rhGH) has been on the list of forbidden substances since availability of its recombinant form improved in the early 1990s. Although its effectiveness in enhancing physical performance is still unproved, the compound is likely used for its potential anabolic effect on the muscle growth, and also in combination with other products (androgens, erythropoietin, etc.). The degree of similarity between the endogenous and the recombinant forms, the pulsatile secretion and marked interindividual variability makes detection of doping difficult. Two approaches proposed to overcome this problem are: the indirect method, which measures a combination of several factors in the biological cascade affected by administration of GH; and the direct method, which measures the difference between the circulating and the recombinant (represented by the unique 22 kD molecule) forms of GH. This article gives an overview of what is presently known about hGH in relation to sport. The available methods of detection are also evaluated. METHODS: Review of the literature on GH in relation to exercise, and its adverse effects and methods of detection when used for doping. RESULTS AND CONCLUSION: The main effects of exercise on hGH production and the use and effects of rhGH in athletes are discussed. Difficulties encountered by laboratories to prove misuse of this substance by both indirect and direct analyses are emphasised. The direct method currently seems to have the best reliability, even though the time window of detection is too short. hGH doping is a major challenge in the fight against doping. The effect of exercise on hGH and its short half-life are still presenting difficulties during doping analysis. To date the most promising method appears to be the direct approach utilising immunoassays.

Atypical EPO profiles in anti-doping analyses

Résumé : Erythropoietin (EPO) is a glycoprotein hormone endogenously produced by the kidney, whose main physiological role is the stimulation of erythropoiesis. Since the beginning of the nineties, recombinant human EPO (rhEPO), a potent anti-anaemia treatment drug, has been manufactured by pharmaceutical industries. However, the erythropoiesis stimulating power of rhEPO was rapidly misused by unscrupulous athletes in order to improve their performances in endurance sports. Endogenous EPO has the same amino-acid backbone as most of recombinant forms; the molecules however differ through their respective glycosylation patterns. This difference constitutes the basis of the usual EPO screening test (IEF) developed in 2000 and still currently used in all anti-doping laboratories of the world. Nowadays, 3 EPO generations have been commercialized. The fight against EPO abuse is a continuous challenge for anti-doping laboratories. The diversity of recombinant EPO forms and the continuous development of new ones considerably confuse the identification of EPO doping. Several facets of this fight were investigated in this work. One of the limiting aspects of doping agents screening is the availability of positive samples. Therefore, 2nd and 3rd generation EPOS, namely NESP and C.E.R.A., were injected to healthy subjects in the frame of pilot clinical studies. These latter allowed to review the current EPO identification criteria defined by the World Anti-Doping Agency (WADA) in the case of NESP and to validate and implement a new assay targeting C.E.R.A. in human serum. Both studies resulted in the determination of the respective detection windows of NESP and C.E.R.A. in biological fluids. Following that, Dynepo, a 1st generation EPO presenting similarities with the endogenous form, was also in the centre of a similar clinical study. Our work aimed to overcome the actual identification criteria, which are not adapted to Dynpeo, and to propose an alternative pattern classification method based on the discriminant analysis of IEF EPO profiles. This method might be validated for other EPO forms in the future. The detection window of this molecule was also determined. Under particular conditions, confounding effects can complicate the identification of EPO in biological matrices. For example, athletes having performed a strenuous physical effort can excrete modified isoforms of endogenous EPO, making it very similar to some recombinant forms. Such phenomena, called effort urines, were reproduced under controlled conditions and, after characterization of effort EPO, an urinary biochemical marker was proposed to unequivocally identify effort urines. It also happens that EPO analyses fail to detect endogenous levels of EPO. Such profiles were thoroughly investigated and potential causes identified. Natural reasons relying on urine properties and test specificity were underlined, but the possible addition of adulterant agents in urine samples was also considered. Therefore, a simple biochemical assay targeting the suspected substances was set up. Our work was based on the characterization of atypical EPO profiles from different origins. Therefore, 3 EPO molecules representing the 3 generations of the drug and 2 confounding effects confusing the results interpretation were studied. These studies resulted in tangible applications for the laboratory, the best example of which being the C.E.R.A. assay, but also in scientific findings allowing to improve our comprehension of EPO doping in sport.

MGMT promoter methylation in malignant gliomas: ready for personalized medicine?

The DNA repair enzyme O(6)-methylguanine-DNA methyltransferase (MGMT) antagonizes the genotoxic effects of alkylating agents. MGMT promoter methylation is the key mechanism of MGMT gene silencing and predicts a favorable outcome in patients with glioblastoma who are exposed to alkylating agent chemotherapy. This biomarker is on the verge of entering clinical decision-making and is currently used to stratify or even select glioblastoma patients for clinical trials. In other subtypes of glioma, such as anaplastic gliomas, the relevance of MGMT promoter methylation might extend beyond the prediction of chemosensitivity, and could reflect a distinct molecular profile. Here, we review the most commonly used assays for evaluation of MGMT status, outline the prerequisites for standardized tests, and evaluate reasons for difficulties in reproducibility. We critically discuss the prognostic and predictive value of MGMT silencing, reviewing trials in which patients with different types of glioma were treated with various chemotherapy schedules, either up-front or at recurrence. Standardization of MGMT testing requires comparison of different technologies across laboratories and prospectively validated cut-off values for prognostic or predictive effects. Moreover, future clinical trials will need to determine, for each subtype of glioma, the degree to which MGMT promoter methylation is predictive or prognostic, and whether testing should become routine clinical practice.

Characterization and Application of Educational Virtual Environments for Science Teaching in Secondary School

This work describes the characteristics of a representative set of seven different virtual laboratories (VLs) aimed for science teaching in secondary school. For this purpose, a 27-item evaluation model that facilitates the characterization of the VLs was prepared. The model takes into account the gaming features, the overall usability, and also the potential to induce scientific literacy. Five of the seven VLs were then tested with two larger and highly heterogenic groups of students, and in two different contexts – biotechnology and physics, respectively. It is described how the VLs were received by the students, taking into account both their motivation and their self-reported learning outcome. In some cases, students’ approach to work with the VLs was recorded digitally, and analyzed qualitatively. In general, the students enjoyed the VL activities, and claimed that they learned from them. Yet, more investigation is required to address the effectiveness of these tools for significant learning.

Iowa Influenza Surveillance Network Final Report 2006-2008

The Iowa Influenza Surveillance Network (IISN) tracks the overall activity, age groups impacted, outbreaks, type and strain, and severity of seasonal influenza. In the 2006-2007 season the network had more than 90 reporting sites that included physicians, clinics, hospitals, schools and long term care facilities (Appendix A). Other non-network reporters who contributed influenza data included medical clinics, hospitals, laboratories, local public health departments and neighboring state health departments. 010203040506070424548495051521234567891011121314MMWR weekNumber of cases2006-20072005-2006 The 2006-2007 influenza season in Iowa began earlier than any previously recorded data indicates, however, the season’s peak occurred much later in the season. In addition to early cases, this season was also unusual in that all three anticipated strains (AH1N1, AH3N2, and B) were reported by the first of December (Appendix B). The first laboratory-confirmed case in the 2005-2006 season was identified December 5, 2005; the first case for the 2006-2007 season was on November 2, 2006. The predominant strain for 2005-2006 was influenza AH3, but for 2006-2007 both influenza AH1 and B dominated influenza infections. However improvements in influenza specimen submission to the University Hygienic Laboratory may have also played a role in early detection and overall case detection. In summary, all influenza activity indicators show a peak between the MMWR weeks 5 and 9 (i.e. February 14- March 4). Children from five years to eight years of age were impacted more than other age groups. There were few influenza hospitalizations and fatalities in all age groups.

Indirect hydrogen monitoring by chemi-ionisation following an associative ionisation pathway after metastable helium atoms production by electron impact ionisation: Protonation and deuteration of carrier gas

Gas chromatography (GC) is an analytical tool very useful to investigate the composition of gaseous mixtures. However, hydrogen (H2) detection after a GC separation is only possible with a Thermal Conductivity Detector (TCD), a Helium Ionisation Detector (HID) or expensive Atomic Emission Detector (AED). Recently, indirect H2 detection by GC coupled to mass spectrometry (MS) was demonstrated but the mechanism of carrier gas protonation remained unclear. With electron impact as ionisation source of MS and helium (He) as GC carrier gas, H2 is not ionised according the expected Penning ionisation neither according to the Associative ionisation. Rearrangement ionisation (RI) was found to be the main channel for H2 and D2 ionisation under GC-MS conditions used in most of laboratories using GC-MS, leading to the formation of [He−H]+ and [He−D]+ ions.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications.

Recent developments in the use of isotope ratio mass spectrometry in sports drug testing.

According to the annual report of the World Anti-Doping Agency, steroids are the most frequently detected class of doping agents. Detecting the misuse of endogenously occurring steroids, i.e. steroids such as testosterone that are produced naturally by humans, is one of the most challenging issues in doping control analysis. The established thresholds for urinary concentrations or concentration ratios such as the testosterone/epitestosterone quotient are sometimes inconclusive owing to the large biological variation in these parameters.For more than 15 years, doping control laboratories focused on the carbon isotope ratios of endogenous steroids to distinguish between naturally elevated steroid profile parameters and illicit administration of steroids. A variety of different methods has been developed throughout the last decade and the number of different steroids under investigation by isotope ratio mass spectrometry has recently grown considerably. Besides norandrosterone, boldenone was found to occur endogenously in rare cases and the misuse of corticosteroids or epitestosterone can now be detected with the aid of carbon isotope ratios as well. In addition, steroids excreted as sulfoconjugates were investigated, and the first results regarding hydrogen isotope ratios recently became available.All of these will be presented in detail within this review together with some considerations on validation issues and on identification of parameters influencing steroidal isotope ratios in urine.