Multiplex short tandem repeat amplification of low template DNA samples with the addition of proofreading enzymes

Abstract:  With <100 pg of template DNA, routine short tandem repeat (STR) analysis often fails, resulting in no or partial profiles and increased stochastic effects. To overcome this, some have investigated preamplification methods that include the addition of proofreading enzymes to the PCR cocktail. This project sought to determine whether adding proofreading polymerases directly in the STR amplification mixture would improve the reaction when little template DNA is available. Platinum Taq High Fidelity and GeneAmp High Fidelity were tested in Profiler Plus? STR reactions alone and in combination with AmpliTaq^® Gold. All reactions included the additional step of a post‐PCR purification step. With both pristine low template DNA and casework samples, the addition of these polymerases resulted in comparable or no improvement in the STR amplification signal. Further, stochastic effects and artifacts were observed equally across all enzyme conditions. Based on these studies, the addition of these proofreading enzymes to a multiplex STR amplification is not recommended for low template DNA work.     

Predestination and Hierarchy: Vallabh��c��rya��s Discourse on the Distinctions Between Blessed, Rule-Bound, Worldly, and Wayward Souls (the Pu??iprav��hamary��d��bheda)

The Pu??iprav??hamary??d??bheda (PPM) by Vallabh??c??rya (1479?C1531?) is a brief work (25 verses) written in Sanskrit in about the year 1500, which is accompanied by four Sanskrit commentaries and one Hindi (Brajbh????) commentary. The most important and authoritative commentary is by Puru?ottama, written about two centuries after the original text. The article contains a translation of the PPM with long extracts from the commentaries, particularly the one composed by Puru?ottama. After an introduction placing the PPM??s doctrine of the hierarchy of embodied souls (j??vas) and their eligibility to obtain states of devotion (bhakti) in a wider context of Vai??ava sectarian and philosophical schools, the text is presented along with the translation and notes to the text (including extracts from the commentaries). The article concludes with reflections on the PPM??s doctrine of predestination, comparing it with those of other Indian religious sects and within the wider context of predestination in Western religions, where these discussions have been ongoing for more than 1500 years. An extensive bibliography is included at the end.     

Perceptions of Safety in Intimate Relationships: Group Differences Based on Gender and Setting

Intimate partner violence continues to be prevalent, resulting in negative consequences for the individuals involved and for society as a whole. Perceptions of safety in relationships where intimate partner violence is present is an understudied topic in the literature. The Safety Assessment of Future Events Scale (SAFE) was developed to assess respondents’ perceptions of safety in their intimate relationship. The purpose of this study was to examine whether group differences existed on respondents’ SAFE scores. 428 participants from community and clinic samples completed the SAFE and other measures contained in a southwest university’s marriage and family therapy clinic intake packet. ANCOVA was used to control for gender and setting in determining if group differences existed on the SAFE based on measures assessing interpersonal violence, relational adjustment, intrapersonal symptoms, and PTSD symptoms. Results indicated group differences based on gender, interpersonal violence victimization, and relational adjustment.     

A theory of entangled political economy, with application to TARP and NRA

The recent financial crisis has provoked a raft of contending claims as to whether the cause of the crisis is better attributed to market failure or political failure. Such claims are predicated on a presumption that markets and polities are meaningfully separate entities. To the contrary, we argue that contemporary arrangements create an entangled political economy that renders theorizing based on separation often misleading. Within this alternative framework of entangled political economy, we illuminate both the recent Troubled Assets Relief Program (TARP) and the New Deal??s National Recovery Administration (NRA).     

Interpretation of ante-mortem stature estimates in South Africans

We developed a simple method for animal species identification of humans, dogs and cats, using a multiplex single-base primer extension reaction in the cytochrome b gene. Using this method, three points of a single nucleotide in the cytochrome b gene were examined in these species using primers of different lengths. Our method was found to be able to successfully identify humans (26 samples), dogs (21 samples) and cats (9 samples), and no differences were found among the samples from each animal species in this study. The amount of template DNA required was over 0.01 ng for humans and dogs, and over 0.1 ng for cats. The present method was able to identify animal species from hair shaft (2 cm) and forensic casework samples (blood stains and hair shafts), and is thus a useful tool for animal species (human, dog and cat) identification in forensic science.     

Significance of additional RFLP single locus probes analysis after STR based determination of sibship

Autosomal STR typing alone seems to be no sufficient tool for resolving deficiency cases (e.g. cases of questioned paternity or half-sibships). Therefore, we investigated whether the additional analysis of RFLP single locus probes can improve the solution of such complicated kinship cases. We analyzed 207 children and men from 101 families using the AmpFlSTRIdentifiler multiplex PCR kit and three RFLP single locus probes. A comparison between each child and all unrelated men resulted in 11,023 man / child pairs. Less than three excluding STRs were found in 125 child / unrelated man pairs (1.13%). Additional analysis of RFLP results reduced the number of ambiguous cases to 35. Half-sibling pairs were simulated using STR results from 20 cases with high paternity probabilities (group 1) and relatively low paternity probabilities (group 2). Using a commercially available computer program we calculated probabilities for 778 half-sibling pairs. In 35 pairs (4.49%) half-sibling probabilities over 90.0% could be calculated. Additional investigation of RFLP single locus probes did not lead to a more reliable evaluation of these results. The combined investigation of autosomal STRs and RFLP single locus probes can satisfactorily solve deficient paternities but does not contribute to the solution of questioned half-sibships.