Sibte Hadi

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Analysis of rpoS and bolA gene expression under various stress-induced environments in planktonic and biofilm phase using 2−ΔΔCT method

Genetic adaptation is one of the key features of Escherichia coli (E. coli) that ensure its survival in different hostile environments. E. coli seems to initiate biofilm development in response to specific environmental cues. A number of properties inherent within bacterial biofilms indicate that their gene expression is different from that of planktonic bacteria. Two of the possible important genes are rpoS and bolA. The rpoS gene has been known as the alternative sigma (σ) factor, which controls the expression of a large number of genes, which are involved in responses to a varied number of stresses, as well as transition to stationary phase from exponential form of growth. Morphogene bolA response to stress environment leads to round morphology of E. coli cells, but little is known about its involvement in biofilms and its development or maintenance. The purpose of this study was to understand and analyse the responses of rpoS and bolA gene to sudden change in the environment. In this study, E. coli K-12 MG1655, rpoS, and bolA mutant strains were used and gene expression was studied. Results show that both genes contribute to the ability to respond and adapt in response to various types of stresses. RpoS response to various stress environments was somehow constant in both the planktonic and biofilm phases, whereas bolA responded well under various stress conditions, in both planktonic and biofilm mode, up to 5–6-fold change in the expression was noticed in the case of pH variation and hydrogen peroxide stress (H2O2) as compared with rpoS.

STR data for the AmpFℓSTR® Identifiler® loci in Kuwaiti population

Allele frequencies for 15 STR loci included in AmpFlSTR Identifiler kit were ascertained in a sample population of 502 unrelated Kuwaiti individuals. Allele frequencies were compared with 6 Caucasian populations using an exact test. This showed that the Kuwaiti population was very similar to the neighboring Iraqi and Saudi populations. As the geographical distance between the populations increased, as expected, more differences were observed. Relevant forensic parameters were also determined.

Increasing the reference populations for the 55 AISNP panel: the need and benefits

Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.

Concordance between the AmpFlSTR MiniFiler and AmpFlSTR Identifiler PCR amplification kits in the Kuwaiti population.

Abstract:  The AmpFℓSTR® MiniFiler™ polymerase chain reaction amplification kit, developed and supplied by Applied Biosystems, complements the AmpFℓSTR® Identifiler® polymerase chain reaction amplification kit (Applied Biosystems, Warrington, U.K.) by improving the success rate when profiling DNA that is degraded or contains inhibitors. Before applying the MiniFiler™ kit to casework, the profiles from 200 unrelated Kuwaitis were compared to Identifiler® profiles. Concordance was observed for 99.875% (1598 of 1600) of the compared STR loci. The two discordant profiles displayed allelic dropout: one at the D13S317 locus due to nonamplification of allele 10 in the MiniFiler™ profile, and one at the D18S51 locus due to nonamplification of allele 18 in the Identifiler® profile.

Use of non-human DNA analysis in forensic science: A mini review

Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.

Functional and health promoting inherent attributes of Enterococcus hirae F2 as a novel probiotic isolated from the digestive tract of the freshwater fish Catla catla

Background Probiotic microorganisms are gaining global importance because of their use in the preparation of a nutraceutical or in the treatment of infections. As per the health industry demand, there is an urgent need for exploring new indigenous probiotic strains with its specific origin due to variation in gut microflora, different food habits and specific host-microbial interactions. The main objective of the present study was to isolate and identify a novel probiotic Enterococcus strain from the gut of Catla catla fish and evaluate its potentiality as a potent probiotic. Methods The whole study was designed with the isolation of novel lactic acid bacterial strain from the gut of Catla catla fish with their biochemical and molecular identifications. The potentiality of the isolated strain as a potent probiotic was carried out according to the parameters described in FAD/WHO guidelines for the evaluation of probiotics in food. Results The isolated strain was confirmed as Enterococcus hirae F2 on the basis of various biochemical and 16s rRNA gene sequencing methods. Enterococcus hirae F2 was able to survive under highly acidic and bile salt concentration with the ability for the production of lipase and Bsh enzyme. It was also able to survive under simulated gastrointestinal conditions with the inhibition ability of various pathogens. The antioxidant potentiality with the cell surface hydrophobicity and cell aggregation ability confirms its potentiality as a potent probiotic. All the results detail the potency of Enterococcus hirae F2 as a novel probiotic for a safer use. Discussion The isolation of Enterococcus hirae with probiotic potential from the gut of fish is a new approach and done for the first time. However, the whole study concluded that the isolated strain might be used as a novel probiotic in the food industry for the production of new probiotic products which imparts health benefits to the host.

Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler(®) PCR amplification kit

Highlights: * GlobalFiler® PCR amplification kit was used to generate a reference dataset for the population of Saudi Arabia. * SE33, D12S391, and D1S1656 in this kit are more informative for the population of Saudi Arabia than any locus in the AmpFlSTR® Identifiler® PCR amplification kit.

Development of PCR internal controls for DNA profiling with the AmpFℓSTR® SGM Plus® amplification kit

Forensic DNA profiling uses a series of commercial kits that co‐amplify several loci in one reaction; the products of the PCR are fluorescently labelled and analysed using CE. Before CE, an aliquot of the PCR is mixed with formamide and an internal lane size standard. Using the SGM Plus amplification kit, we have developed two internal non‐amplified controls of 80 bp and 380 bp that are labelled with ROX fluorescent dye and added to the PCR. Combined with two internal amplification controls of 90 bp and 410 bp, they provide additional controls for the PCR, electrokinetic injection, and CE and also function as an internal size standard.

Commentary on: Vandenberg N, van Oorshcot RAH. The Use of Polilight® in the Detection of Seminal Fluid, Saliva, and Bloodstains and Comparison with Conventional Chemical-Based Screening Tests. J Forensic Sci 2006;51(2):361–70.

Sir: We read the article by Vandenberg and van Oorshcot (1) with interest. The article compares the Phadebas presumptive test for saliva and the Polilight detection method and the authors recommend the use of Polilight for the detection of saliva stains. In this context, we have noted that the method described by Vandenberg and van Oorshcot (1) for the preparation of Phadebas solution is different from the one that we use. Vandenberg et al. state that 0.9 g Phadebas tablets should be dissolved in 100 mL distilled water and then the press test carried out. This is equivalent to four to five tablets only, whereas the manufacturer instructs that 50 tablets be dissolved in 200 mL distilled water (2) before the press test. During our work we follow the manufacturer’s instructions and always obtain clear and noticeable results for a wide range of saliva-stain dilutions within a few minutes. In contrast, when we used the method of Phadebas solution preparation as suggested by Vandenberg and van Oorshcot (1) poor and unclear results were obtained for saliva-stain detection. May we suggest that such results might be due to the procedure they have adopted to prepare the Phadebas solution?