Fish parasites resolve the paradox of missing coextinctions.

Models of coextinction identify parasites as one of the most menaced ecological groups. The number of host species a parasite uses should strongly affect its risk of coextinction. The naïve expectation is that the lower the number, the higher is the parasite's risk of being left with no hosts. Here we analyse the coextinction risk of 12,141 fish parasite species and find that highly specific parasites are not the most endangered, because they tend to use hosts with low vulnerability to extinction. This unexpected result may explain why the number of documented host-parasite coextinctions is much lower than predicted by theoretical studies. © 2013 Macmillan Publishers Limited. All rights reserved

Nestedness for Dummies (NeD): A User-Friendly Web Interface for Exploratory Nestedness Analysis

Recent theoretical advances in nestedness analysis have led to the introduction of several alternative metrics to overcome most of the problems biasing the use of matrix 'temperature' calculated by Atmar's Nestedness Temperature Calculator. However, all of the currently available programs for nestedness analysis lack the user friendly appeal that has made the Nestedness Temperature Calculator one of the most popular community ecology programs. The software package NeD is an intuitive open source application for nestedness analysis that can be used online or locally under different operating systems. NeD is able to automatically handle different matrix formats, has batch functionalities and produces an output that can be easily copied and pasted to a spreadsheet. In addition to numerical results, NeD provides a graphic representation of the matrix under examination and of the corresponding maximally packed matrix. NeD allows users to select among the most used nestedness metrics, and to combine them with different null models. Integrating easiness of use with the recent theoretical advances in the field, NeD provides researchers not directly involved in theoretical debates with a simple yet robust statistical tool for a more conscious performance of nestedness analysis. NeD can be accessed at http: //purl.oclc.org/ned

Omicidio e lesioni personali da incidenti della strada in stato di ebbrezza e di alterazione psico-fisica. Criticit\ue0 e problematiche. Considerazioni medico-legali

Road traffic crashes are a main cause of physical harm and mortality. That means a heavy burden in terms of short, medium and long-term disability and public costs for society. Among the most relevant cases of severe accidents is driving under the influence of alcohol and psychoactive drugs. That\u2019s the reason of the international strong effort to combating the phenomenon. In Italy the draft law concerning the criminal offence of vehicular homicide and road traffic personal injuries is currently being discussed. Previously the law n. 120/2010 has already changed the regulation in matter of drink-driving and driving under the influence of controlled substances with stiffer penalties for transgressors and (at least some) guidance as to assess the infringement. The draft law suggests that clinical and toxicological evidences of actual driving impairment has to be proved to reach significance in court, nevertheless no standard and effective procedure has being established for detection, at least for what concerns controlled substances. The purpose of this article is to put in evidence, in accordance with a medico-legal perspective, some of the issues that emerge from this complex matter (i.e. the need of a list of the impairing substance under detection, of well-defined legal cut-off values, of a better definition of the problems following the therapeutic use of drugs of abuse and other concerns), issues, those, that are now more troubling whereas the introduction of new crimes and punishments is becoming more concrete

Immunochromatographic Detection of Human Blood: A Forensic Review

Body fluid identification is fundamental in forensic science as it links a specific biological source to a genetic profile, thus providing critical clues for crime scene reconstruction. Blood is one of the most common body fluids found on the crime scene, and several strategies have been developed for its identification in recent decades. Usually, after a preliminary (or presumptive) test to determine the presence of blood (both human and non-human), a confirmatory test is needed to prove that the sample is human blood. Out of the confirmatory tests, immunochromatographic (IC) assays are the most commonly and widely used. This work gives a review of the use of commercial kits specifically developed to detect human hemoglobin or glycophorin A (a surface protein of human red cells) in forensics. Claimed sensitivity varies broadly (ranging from 0.06 to 75 nanoliters of fresh blood), but different values (as low as 0.002 nL) were found during validation procedures. Specificities are high, and the possibility of cross-reaction (with the risk of false-positive results) is so low that it can be considered negligible. False-negative results, however, can be found due to the so-called “hook effect” as well as to the target degradation/modification, which interferes with the Ag-Ab binding. In addition, the chemical compositions of the presumptive test, detergents, and washing can also promote false negative outcomes in peculiar situations. Although IC assays are rapid, inexpensive, specific, and easy to use even on the crime scene, their major limitation is represented by the destructive approach required by this kind of confirmatory test. Since the final goal of the forensic investigation is the genetic typing of a bloodstain, we will describe the strategies developed for IC assays of faint stains as well as the strategies adopted to ensure that exactly the same sample undergoes human blood identification and DNA typing

Performance of the ForenSeqTM DNA Signature Prep kit on highly degraded samples

Next generation sequencing (NGS) is the emerging technology in forensic genomics laboratories. It offers higher resolution to address most problems of human identification, greater efficiency and potential ability to interrogate very challenging forensic casework samples. In this study, a trial set of DNA samples was artificially degraded by progressive aqueous hydrolysis, and analyzed together with the corresponding unmodified DNA sample and control sample 2800 M, to test the performance and reliability of the ForenSeqTM DNA Signature Prep kit using the MiSeq Sequencer (Illumina). The results of replicate tests performed on the unmodified sample (1.0 ng) and on scalar dilutions (1.0, 0.5 and 0.1 ng) of the reference sample 2800 M showed the robustness and the reliability of the NGS approach even from sub-optimal amounts of high quality DNA. The degraded samples showed a very limited number of reads/sample, from 2.9\u201310.2 folds lower than the ones reported for the less concentrated 2800 M DNA dilution (0.1 ng). In addition, it was impossible to assign up to 78.2% of the genotypes in the degraded samples as the software identified the corresponding loci as \u201clow coverage\u201d ( 50x). Amplification artifacts such as allelic imbalances, allele drop outs and a single allele drop in were also scored in the degraded samples. However, the ForenSeqTM DNA Sequencing kit, on the Illumina MiSeq, was able to generate data which led to the correct typing of 5.1\u201344.8% and 10.9\u201358.7% of 58 of the STRs and 92 SNPs, respectively. In all trial samples, the SNP markers showed higher chances to be typed correctly compared to the STRs. This NGS approach showed very promising results in terms of ability to recover genetic information from heavily degraded DNA samples for which the conventional PCR/CE approach gave no results. The frequency of genetic mistyping was very low, reaching the value of 1.4% for only one of the degraded samples. However, these results suggest that further validation studies and a definition of interpretation criteria for NGS data are needed before implementation of this technique in forensic genetics

The Baron Pasquale Revoltella's Will in the Forensic Genetics Era

In this article, we describe multiple analytical strategies that were first developed for forensic purposes, on a set of three bone samples collected in 2011. We analyzed a single bone sample (patella) collected from the artificially mummified body of the Baron Pasquale Revoltella (1795-1869), as well two femurs which allegedly belonged to the Baron's mother (Domenica Privato Revoltella, 1775-1830). Likely due to the artificial mummification procedures, the inner part of the Baron's patella allowed the extraction of high-quality DNA yields, which were successfully used for PCR-CE and PCR-MPS typing of autosomal, Y-specific, and mitochondrial markers. The samples extracted from the trabecular inner part of the two femurs yielded no typing results by using the SNP identity panel, whereas the samples extracted from the compact cortical part of the same bone samples allowed genetic typing, even by the employment of PCR-CE technology. Altogether, 10/15 STR markers, 80/90 identity SNP markers, and HVR1, HVR2, and HVR3 regions of the mtDNA were successfully typed from the Baron's mother's remains by the combined use of PCR-CE and PCR-MPS technologies. The kinship analysis showed a likelihood ratio of at least 9.1 × 106 (corresponding to a probability of maternity of 99.9999999%), and thus confirmed the identity of the skeletal remains as those of the Baron's mother. This casework represented a challenging trial for testing forensic protocols on aged bones samples. It highlighted the importance of accurately sampling from the long bones, and that DNA degradation is not blocked by freezing at -80 °C

Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples

Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1–5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field

The role of single nucleotide polymorphisms related to iron homeostasis in mesothelioma susceptibility after asbestos exposure: a genetic study on autoptic samples

Asbestos-related diseases still represent a major public health problem all over the world. Among them, malignant mesothelioma (MM) is a poor-prognosis cancer, arising from the serosal lining of the pleura, pericardium and peritoneum, triggered by asbestos exposure. Literature data suggest the key role of iron metabolism in the coating process leading to the formation of asbestos bodies, considered to be both protective and harmful. Two sample sets of individuals were taken into consideration, both residing in Broni or neighboring cities (Northwestern Italy) where an asbestos cement factory was active between 1932 and 1993. The present study aims to compare the frequency of six SNPs involved in iron trafficking, previously found to be related to protection/predisposition to MM after asbestos exposure, between 48 male subjects with documented asbestos exposure who died of MM and 48 male subjects who were exposed to asbestos but did not develop MM or other neoplastic respiratory diseases (Non-Mesothelioma Asbestos Exposed - NMAE). The same analysis was performed on 76 healthy male controls. The allelic and genotypic frequencies of a sub-group of 107 healthy Italian individuals contained in the 1000 genomes database were considered for comparison. PCR-multiplex amplification followed by SNaPshot mini-sequencing reaction was used. The findings presented in this study show that the allelic and genotypic frequencies for six SNP markers involved in iron metabolism/homeostasis and the modulation of tumor microenvironment are not significantly different between the two sample sets of MM and NMAE. Therefore, the SNPs here considered do not seem to be useful markers for individual susceptibility to mesothelioma. This finding is not in agreement with previous literature

Pitfalls in the Genetic Identification of Human Remains

DNA technology is an irreplaceable tool for the identification of human remains, but the reliability of the ante mortem reference data remains a serious concern. We present here two cases where misleading conclusions could be achieved by using only the genetic profile of the missing person\u2019s father such as reference sample. Nevertheless, when appropriate reference DNA samples (e.g., the maternal samples) became available, certain identifications were achieved as shown by the probability of maternity (> 99.999%). Thus, all these data together show that extra-pair paternity was found by the way, in both cases. Precautions to avoid misleading conclusions are addressed