Arati Iyengar

Development of internal amplification controls for DNA profiling with the AmpFℓSTR(®) SGM Plus(®) kit.

DNA extracted from forensic samples can be degraded and also contain co‐extracted contaminants that inhibit PCR. The effects of DNA degradation and PCR inhibition are often indistinguishable when examining a DNA profile. Two internal amplification controls (IACs) were developed to improve quality control of PCR using the AmpFℓSTR® SGM Plus® kit. The co‐amplification of these controls with DNA samples was used to monitor amplification efficiency and detect PCR inhibitors. IAC fragments of 90 and 410 bp (IAC90 and IAC410) were generated from the plasmid pBR322 using tailed primers and then amplified with ROX‐labelled primers. Co‐amplification of IAC90 and IAC410 was performed with varying amounts of template DNA, degraded DNA and DNA contaminated with humic acid, heme and indigo dye. Both IAC90 and IAC410 were successfully amplified with human DNA without significantly affecting the quality of the DNA profile, even with DNA amounts lower than 0.5 ng. In the presence of inhibitors, the IAC90 signal was still present after all human DNA loci fail to amplify; in contrast, the IAC410 signal was reduced or absent at low levels of inhibition. Amplification of the two IACs provided an internal PCR control and allowed partial profiles caused by inhibition to be distinguished from degraded DNA profiles.

Phylogenetic Evidence for a Case of Misleading Rather than Mislabeling in Caviar in the United Kingdom

Sturgeons and paddlefish are freshwater fish which are highly valued for their caviar. Despite the fact that every single species of sturgeon and paddlefish is listed under CITES, there are reports of illegal trade in caviar where products are deliberately mislabeled. Three samples of caviar purchased in the United Kingdom were investigated for accurate CITES labeling using COI and cyt b sequencing. Initial species identification was carried out using BLAST followed by phylogenetic analyses using both maximum parsimony and maximum likelihood methods. Results showed no evidence for mislabeling with respect to CITES labels in any of the three samples, but we observed clear evidence for a case of misleading the customer in one sample.

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.

SkydancerPlex: A novel STR multiplex validated for forensic use in the hen harrier (Circus cyaneus).

The hen harrier (Circus cyaneus) is a bird of prey which is heavily persecuted in the UK because it preys on the game bird red grouse (Lagopus lagopus scoticus). To help investigations into illegal killings of hen harrier, a STR multiplex kit containing eight short tandem repeat (STR) markers and a chromohelicase DNA binding protein 1 (CHD 1) sexing marker was developed. The multiplex kit was tested for species specificity, sensitivity, robustness, precision, accuracy and stability. Full profiles were obtained with as little as 0.25 ng of template DNA. Concurrent development of an allelic ladder to ensure reliable and accurate allele designation across laboratories makes the SkydancerPlex the first forensic DNA profiling system in a species of wildlife to be fully validated according to SWGDAM and ISFG recommendations. An average profile frequency of 3.67 × 10(-8), a PID estimate of 5.3 × 10(-9) and a PID-SIB estimate of 9.7 × 10(-4) make the SkydancerPlex an extremely powerful kit for individualisation.

FMLP-, thapsigargin-, and H2O2-evoked changes in intracellular free calcium concentration in lymphocytes and neutrophils of type 2 diabetic patients

Type 2 diabetic (T2DM) patients are immune-compromised having a higher susceptibility to infections and long-term complications in different parts of the body contributing to increased morbidity and mortality. A derangement in the homeostasis of intracellular free calcium concentration [Ca2+]i is known to be associated with several diseases in the body including T2DM. Both neutrophils and lymphocytes play active protective roles in host immune response to infection showing impairment in microbicidal functions including phagocytosis and chemotaxis which are calcium-dependent processes. This study evaluated the process of [Ca2+]i mobilization from both neutrophils and lymphocytes taken from blood of both T2DM patients and healthy age-matched control subjects investigating the effect of N-formyl-methionyl-leucyl-phenylalanine (fMLP), thapsigargin (TG), and hydrogen peroxide (H2O2) on [Ca2+]i homeostasis. This study employed isolated peripheral blood neutrophils and lymphocytes from 24 T2DM patients and 24 healthy volunteers. Either neutrophils or lymphocytes were stimulated separately with fMLP, TG, or H2O2. Induced changes in [Ca2+] in both neutrophils and lymphocytes were evaluated using spectrofluorometric methods. Stimulation of human neutrophils and lymphocytes with fMLP, TG, or H2O2 in the presence of [Ca2+]o resulted in significant decreases in [Ca2+]i mobilization from T2DM patients compared with healthy controls. These data indicate that neutrophils and lymphocytes from T2DM patients are less responsive to calcium mobilizing agents compared with granulocytes from healthy controls and this is possibly due to the hyperglycemia. The results suggest that agonist-evoked decrease in [Ca2+]i in immune cells might be one of the possible mechanisms of impaired immunity in diabetic patients.

Reliable and Robust Molecular Sexing of the Hen Harrier (Circus cyaneus) Using PCR-RFLP Analysis of the CHD 1 Gene†

The hen harrier (Circus cyaneus) is a bird of prey that is persecuted in the United Kingdom, and there is a need for a DNA‐based individual identification and sexing system for the use in forensic investigations. This study reports a new set of PCR primers for the chromo‐helicase‐DNA‐binding protein 1 gene, which allows sexing using PCR‐RFLP. Instead of exonic primers that amplify across a large intron, this set consists of a primer within the intron, enabling reduction in amplicon sizes from 356 to 212 bp and 565 to 219 bp in W and Z chromosomes. DNA degradation and dilution experiments demonstrate that this set is significantly more robust than one that amplifies across the intron, and sequencing of the intronic primer‐binding region across several individuals shows that it is highly conserved. While our objective is to incorporate this primer set into an STR‐based individualization kit, it may in the meantime prove useful in forensic or conservation studies.

Sequence data of six unusual alleles at SE33 and D1S1656 STR Loci

When profiling a reference dataset of 500 DNA samples for the population of Saudi Arabia, using the GlobalFiler® PCR amplification kit, six unusual alleles were detected. At the SE33 locus, four novel alleles were found: 2, 14.3, 20.3, and 38; two alleles at the D1S1656 locus: 7 and 8 had been previously reported, but no published sequence data was available. The D1S1656 alleles were sequenced using ForenSeq™ DNA Signature Prep with the MiSeq FGx System (Illumina, USA). As the SE33 is not reported by available Massively Parallel Sequencing (MPS) systems, samples that exhibited the unreported alleles were sequenced using BigDye™ Terminator v3.1 Cycle Sequencing Kit. Here we present the sequence and structure of the previously uncharacterized alleles.