Correcting Forensic DNA Errors

DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National Institutes of Standards and Technology (NIST) study of 109 North American crime laboratories in this journal demonstrates this most clearly. This latest study supports earlier work that shows common methods such as the Combined Probability of Inclusion (CPI) have wrongly included innocent people as contributors to DNA mixtures.The 2016 President’s Council of Advisors on Science and Technology report concluded,“In summary, the interpretation of complex DNA mixtures with the CPI statistic has been an inadequately specified—and thus inappropriately subjective—method. As such, the method is clearly not foundationally valid.” The adoption of probabilistic genotyping by many laboratories will certainly prevent some of these errors from occurring in the future,but the same laboratories that produced past errors can also now review old cases with their new software—without additional bench work. It is critical that laboratories adopt procedures and policies to do this

When DNA Won\u27t Work

Within the criminal justice system, DNA (deoxyribonucleic acid) evidence has often been heralded as the gold standard of forensic science. In a 2009 U.S. Supreme Court decision, Chief Justice Roberts wrote that DNA testing has an unparalleled ability both to exonerate the wrongly convicted and to identify the guilty. It has the potential to significantly improve both the criminal justice system and police investigative practices. The phrases “unparalleled ability” and “significantly improve” reflect the high standard that DNA has attained in both forensic science and the entire criminal justice system. Forensic DNA technology has a major advantage over other forensic science fields because of its reliance on statistics and its historical development from medical science, which relies on double-blind testing, error analysis, and rigorous peer review. These factors distinguish DNA analysis from other forms of forensic analysis such as fingerprinting, ballistics, trace evidence, forensic anthropology (bones), handwriting analysis, and others. But every analytical field has its limits, and can be misappropriated. This article summarizes some of the key areas where the use of forensic DNA can be improved and includes proposed remedies

Device with Magnetoplastic and/or Magnetoelastic Thin-Film Transducer and Pick-Up Coil for Harvesting Energy

A magnetoplastic and/or magnetoelastic material transduces linear motion, delivered to it by a mechanical counection, into a change of magnetic field, via twin boundary deformation. A bias magnetic field assures a net change of magnetization during the deformation, and a coil, coaxial with the magnetoplastic/ elastic material, couples the magnetic field change to an electrical output. The bias magnetic field or a device that produces strain in a reverse direction resets the magnetomechanical transducer to its initial state. Microgenerators using the magnetoplastic/elastic material may be connected in series or parallel, combined with solar cells, and used to capture energy from passive motion such as random, cyclic or vibrational motion

Dynamic Passivation with BSA Overcomes LTCC Mediated Inhibition of PCR

The increasing use of low temperature co-fired ceramic (LTCC) for the fabrication of biological microfluidic devices necessitates further research on LTCC biocompatibility. In this study we explore the inhibitory effect of DuPont\u27s 951 LTCC on Polymerase Chain Reaction (PCR), and demonstrate a novel mechanism to increase biocompatibility between LTCC and PCR with the addition of a common passivation substance, bovine serum albumin (BSA). We show that DuPont\u27s 951 LTCC binds negatively charged proteins including BSA and ovalbumin (OVA). This is a significant discovery as proteins (enzymes) are an essential component of most biological reactions, and a frequent addition to microfluidic devices. A proposed model for LTCC inhibition of PCR by enzyme adsorption is presented

Morphology and Phylogeny of a New Woodruffiid Ciliate, \u3cem\u3eEtoschophrya inornata\u3c/em\u3e sp. n. (Ciliophora, Colpodea, Platyophryida), with an Account on Evolution of Platyophryids

We studied the morphology, morphometry, resting cysts and molecular phylogeny of a new woodruffiid ciliate, Etoschophrya inornata, from ephemeral puddles and two lacustrine habitats in Idaho, North-west USA. Up to now, the genus Etoschophrya has included a single species, Etoschophrya oscillatoriophaga, from which our new form is distinguished by (i) the absence of interkinetal cortical granules and, consequently, the absence of extrusible red material in methyl green-pyronin stains, (ii) usually ≥5 adoral membranelles vs. usually four, (iii) greater length and length/width ratio, (iv) prominent cortical furrows vs. inconspicuous and (v) adaptation to non-saline semi-terrestrial and lacustrine habitats in the Nearctic vs. highly saline alkaline Afrotropic soil habitats. Resting cysts have two distinct membranes and a thick hyaline mucous pericyst layer. However, only one membrane persists in older cysts. Like its congener, Etoschophrya inornata feeds exclusively on filamentous cyanobacteria. The 18S rRNA gene sequence places this species in a strongly supported clade with Kuklikophrya ougandae basal to the other platyophryids. We include a morphologic cladistic analysis of platyophryid ciliates and present a hypothetical scenario for the evolution of the platyophryid oral structures

The Y-STR Genetic Diversity of an Idaho Basque Population, with Comparison to European Basques and US Caucasians

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity for the immigrant Basque sample is within 0.4% of the haplotype diversity of the European Basques (0.9903); thus the power of discrimination is similar for each population. The Idaho Basque population has less diversity in 9 out of 16 loci (considering DYS385a/b together) and 3% less diversity across all loci, compared to the European Basque population. A multi-dimensional scaling analysis (MDS) was created using pairwise RST values to compare the Idaho Basques to other populations. Based upon RST and FST measures, no significant differentiation was found between the Idaho and source European Basque population

What’s in the Water?: Detecting Chlamydia and Gonorrhea in Treasure Valley Wastewater

Wastewater-based epidemiology (WBE) gained prominence as a reliable method for predicting SARS-CoV-2 outbreaks and trends during the COVID-19 pandemic. We modified the technique to detect Chlamydia (C. trachomatis) and Gonorrhea (N. gonorrhoeae) in wastewater sourced from four wastewater facilities in the Treasure Valley (West, Lander, Meridian, and Nampa) using variations of two extraction methods, the AllPrep PowerViral DNA/RNA Mini Kit and paper filtration (0.22µm and 0.45µm). Both pathogens were detected in samples from both Boise, Idaho facilities (West and Lander) on three of the six days tested (N. gonorrhoeae 6/14/23, and C. trachomatis and N. gonorrhoeae 6/19/23 and 6/28/23). Neither pathogen was detected in samples from the Meridian and Nampa facilities. Pathogens were detected in 25% of all treatment facilities sampled. The 0.22µm filter paper produced positive results in 3 of 4 tests (75%), while the 0.45µm paper did not produce any positive results. Surprisingly, Nanotrap A, designed for viral detection, was more effective in detecting the bacteria than Nanotrap B, designed for bacterial detection (50% vs 33%)

Nullomer Derived Anticancer Peptides (NulloPs): Differential Lethal Effects on Normal and Cancer Cells \u3cem\u3ein vitro\u3c/em\u3e

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control PolyArgNulloP, 124R (RRRRRWFMHW), was also included. The lethal effects of 9R and 9S1R are mediated by mitochondrial impairment as demonstrated by increased ROS production, ATP depletion, cell growth inhibition, and ultimately cell death. These effects increase over time for cancer cells with a concomitant drop in IC-50 for breast and prostate cancer cells. This is in sharp contrast to the effects in normal cells, which show a decreased sensitivity to the NulloPs over time

Safeguarding Forensic DNA Reference Samples with Nullomer Barcodes

Unintended transfer of biological material containing DNA is a concern to all laboratories conducting PCR analysis. While forensic laboratories have protocols in place to reduce the possibility of contaminating casework samples, there is no way to detect when a reference sample is mislabeled as evidence, or contaminates a forensic sample. Thus there is public concern regarding the safeguarding of DNA submitted to crime labs. We demonstrate a method of introducing an internal amplification control to reference samples, in the form of a nullomer barcode which is based upon sequences absent or rare from publically accessible DNA databases. The detection of this barcode would indicate that the source of analyzed DNA was from a reference sample provided by an individual, and not from an evidence sample. We demonstrate that the nullomers can be added directly to collection devices (FTA paper) to allow tagging during the process of sample collection. We show that such nullomer oligonucleotides can be added to existing forensic typing and quantification kits, without affecting genotyping or quantification results. Finally, we show that even when diluted a million-fold and spilled on a knife, the nullomer tags can be clearly detected. These tags support the National Research Council of the National Academy recommendation that “Quality control procedures should be designed to identify mistakes, fraud, and bias” in forensic science (National Academy of Sciences, 2009)

Case Report: Coincidental Inclusion in a 17-Locus Y-STR Mixture, Wrongful Conviction and Exoneration

We report the case of a suspect (Suspect-3) who was convicted (and later exonerated) of participating in the multiple-attacker rape of two women. The forensic evidence against him was his inclusion in a 17-marker Y-STR mixture isolated from semen on one victim’s clothing. The DNA inclusion produced a match statistic with a combined probability of inclusion of 1 in 741, and a Likelihood Ratio of 3296. While the defense team was told that Suspect-3 was included in the semen DNA mixture, they were not told that all of the Y-STR alleles could also be explained by just the other two accused attackers’ haplotypes. Suspect-3 was subsequently freed after the Taiwan Association for Innocence requested re-examination of the incriminating mixed DNA sample. The Criminal Investigation Bureau was then able to exclude him using an extended set of Y-STR markers (23 loci), leading to his exoneration