Phase Diagram of alpha-Helical and beta-Sheet Forming Peptides

The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of unfolded or natively folded proteins, and amyloid fibrils. Here we use a coarse-grained protein model that enables us to perform Monte Carlo simulations for determining the phase diagram of natively folded alpha-helical and unfolded beta-sheet forming peptides. The simulations reveal the existence of various metastable peptide phases. The liquidlike phases are metastable with respect to the fibrillar phases, and there is a hierarchy of metastability

Forensic identification of urine samples: a comparison between nuclear and mitochondrial DNA markers

Urine samples from 20 male volunteers of European Caucasian origin were stored at 4°C over a 4-month period in order to compare the identification potential of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) markers. The amount of nDNA recovered from urines dramatically declined over time. Consequently, nDNA likelihood ratios (LRs) greater than 1,000 were obtained for 100, 70 and 55% of the urines analysed after 6, 60 and 120 days, respectively. For the mtDNA, HVI and HVII sequences were obtained for all samples tested, whatever the period considered. Nevertheless, the highest mtDNA LR of 435 was relatively low compared to its nDNA equivalent. Indeed, LRs obtained with only three nDNA loci could easily exceed this value and are quite easier to obtain. Overall, the joint use of nDNA and mtDNA markers enabled the 20 urine samples to be identified, even after the 4-month perio

Forensic evaluation of the QIAshredder/QIAamp DNA extraction procedure.

The potential to recover genetic profiles from evidence samples has substantially increased since robust and sensitive amplification kits are commercially available. Nevertheless, even the best amplification kits cannot succeed when the extracted DNA is of poor quality. In this study we compared the efficiency of silica (QIAamp DNA Mini Kit), Chelex and Phenol-Chloroform (PC) based protocols to recover DNA from different categories of samples (blood and saliva on cotton swabs, muscles, cigarette butts, saliva on foods and epidermal cells on clothes). The efficiency of the QIAamp system was improved when samples were treated with QIAshredder homogenizing columns. Overall, conventional Chelex or PC protocols allowed to recover conclusive SGM Plus profiles for 61% of the samples considered in this study. Contrastingly, 82% of them were successfully genotyped after being treated with a combination of QIAshredder and QIAamp systems. Our results further suggested that the QIAshredder/QIAamp protocol was particularly helpful to analyze evidence samples with few DNA and/or that were collected on substrates containing PCR inhibitors

Consensus profiles and databasing of casework samples amplified with 34 PCR cycles: an empirical approach

Forensic laboratories commonly have to analyze samples that contain minute amounts of DNA (Low Copy Number DNA). LCN samples can be amplified with increased numbers of PCR cycles, but stochastic variations of their profiles are generally observed. Here, we compare some characteristics of the AmplSTR SGM Plus profiles from casework samples amplified with 28 and 34 cycles in order to evaluate the interpretation guidelines used in our laboratory to genotype LCN samples. A first striking result was that 60% of the 563 casework samples considered yielded DNA concentrations <200 pg/µl DNA and were considered as LCN. Conclusive profiles were recovered for 142 of them (42%). At the end, 142 profiles amplified with 28 cycles and 119 profiles amplified with 34 cycles were sent to the Swiss data base. Respectively, 43.66% and 43.70% of them made a hit. This suggests that reliable LCN profiles can be obtained when using an adapted strategy