Evaluation of DNA Extraction Efficiencies of Promega’s DNA IQ™ Methods and Casework Extraction Kit for Low Template Samples

Biological evidence from crime scene samples frequently contain low levels of DNA, such as the most predominant form of evidence, which is DNA deposited by handling objects or “touch evidence”. To maximize the DNA yield recovered from theses challenging samples, forensic laboratories must optimize the extraction methods utilized to isolate and purify DNA for downstream short tandem repeat (STR) amplifications. Currently, the Virginia Department of Forensic Science (VADFS) uses a DNA IQ™ System (DNA IQ) extraction method for isolation of DNA from most forensic samples. This extraction procedure, which combines DNA IQ™ lysis buffer and Dithiothreitol (DTT), has been validated for nearly every forensic casework sample other than sexual assault samples requiring differential extraction, hair roots, and bone. In 2004, VADFS created an in-house proteinase K buffer (IQP) to be utilized in conjunction with the DNA IQ™ System for hair, concentrated bloodstains, and other difficult samples believed to contain low quantities of DNA. The IQP extraction method was implemented at VADFS for lower template samples but also to digest hemoglobin found in concentrated bloodstains, as undigested proteins from these sample types had been observed to competitively bind to the DNA IQ™ resin, thus occluding it from binding DNA. In this study, the current methods utilized by VADFS for the extraction and purification of DNA with the DNA IQ™ System were evaluated against Promega Corporation’s Casework Extraction Kit (CEK). Similar to IQP, the CEK contains a proteinase K treatment step prior to DNA purification using the DNA IQ™ System. DNA yields and STR profiles obtained from a variety of low-template samples including diluted blood and saliva, environmental samples, hair, cigarette butts, and touch DNA samples were compared across these three extraction procedures. This research found that all three extraction methods produced comparable results for the extraction of anagen/catagen hair roots and cigarette butts. The in-house proteinase K extraction method provided significantly lower DNA yields and percent profiles for diluted blood and saliva samples, environmental samples, and touch samples, when compared to the CEK and the DNA IQ extraction methods. The Casework Extraction Kit demonstrated higher DNA yields and percent profiles for diluted blood and saliva samples when compared to DNA IQ and IQP methods. The CEK also yielded higher average DNA concentrations for the degraded bloodstain samples, however, the DNA IQ method produced consistent STR profiles with those extracted using the CEK. The DNA IQ and CEK extraction methods demonstrated overall superior performance over the IQP method for extraction of DNA from touch samples. The results of this study provide confirmation that the utilization of the DNA IQ extraction method for isolation of DNA from challenging casework samples is comparable to, and sometimes outperforms, the Casework Extraction Kit and should therefore be maintained as the primary DNA extraction method when purifying samples using the DNA IQ™ System

Survey of Congenital Heart Surgeons’ Preferences for Antimicrobial Prophylaxis for Pediatric Cardiac Surgery Patients

Patients with congenital heart defects are a unique population with generally immature immune systems. Fragility in the postoperative period may contribute to surgical site infections (SSIs), a life threatening complication for this population. The need for postoperative antimicrobial prophylaxis for these patients is a standard of care that is indisputable. When choosing an antimicrobial regimen for surgical prophylaxis, consideration should be given to balancing the prevention of nosocomial infections, avoiding emergence of bacterial resistance, and minimizing drug toxicities and cost

Peacing it together : why peace education is an integral aspect of development for post-conflict societies

121 leaves : col. map ; 29 cm.Includes abstract and appendix.Includes bibliographical references (leaves 108-117).Peace education, a relatively new prevention strategy, is based on teaching curriculum designed to address the immediate needs of children living in a post-conflict society. Children are provided with the tools and techniques to help manage conflict and hatred in their own lives - redefining the notion that conflict is an inevitable part of life while fostering the understanding that conflicts need not be dealt with using violence or hatred. The success of peace education programs is evidenced in the Education for Peace (EFP) program in Bosnia-Herzegovina (BiH). While the characteristics of this program are culturally specific, it provides hope for other post-conflict societies. There are underlying ideals stemming from this program that establish a foundation that can be replicated in other developing countries emerging from conflict. Although peace education has been critiqued and largely overlooked, this thesis has demonstrated how peace education is an effective tool in helping to reduce the prevalence of conflict

High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing

Small RNA cloning and sequencing is uniquely positioned as a genome-wide approach to quantify miRNAs with single-nucleotide resolution. However, significant biases introduced by RNA ligation in current protocols lead to inaccurate miRNA quantification by 1000-fold. Here we report an RNA cloning method that achieves over 95% efficiency for both 5′ and 3′ ligations. It achieves accurate quantification of synthetic miRNAs with less than two-fold deviation from the anticipated value and over a dynamic range of four orders of magnitude. Taken together, this high-efficiency RNA cloning method permits accurate genome-wide miRNA profiling from total RNAs

Study Title-Based Framing Effects on Reports of Sexual Violence Factors in College Students

Objective: There are many methodological issues in studying sexual violence, including potential framing effects. Framing effects refer to how researchers communicate the purpose of a study to participants, such as, how the study is advertised or explained. The aim of the current study was to investigate if framing effects were associated with differences in participants’ self-reported experiences of sexual violence and related correlates. Methods: College students (N = 782) were recruited to participate in one of four identical studies that differed in the title: “Questionnaires about Alcohol,” “Questionnaires about Crime,” “Questionnaires about Health,” or “Questionnaires about Sexual Assault.” Participants chose one of the four studies and completed measures of sexual violence as well as attitudinal and behavioral measures in randomized order. Results: We found significantly more reports of childhood sexual abuse (33.6% vs. 18.5%), rape (33.9% vs. 21.1%), higher frequency of victimization (M = 11.35 vs. 5.44), and greater acknowledged rape for bisexual people (46.2% vs. 0.0%) in the Sexual Assault condition compared to other conditions. There were no differences in sexual violence perpetration or attitudinal or behavioral measures. Conclusion: These results revealed that framing effects, based on the study title, affect outcomes in sexual victimization research. Rape was reported 1.6x more in the “Sexual Assault” condition than in the “Health” condition. It is unclear whether these framing effects reflect self-selection bias or framing related increased reports in the Sexual Assault condition, suppression of reports in other conditions, or a combination thereof

Cardenolide, Potassium, and Pyrethroid Insecticide Combinations Reduce Growth and Survival of Monarch Butterfly Caterpillars (Lepidoptera: Nymphalidae)

The monarch butterfly, Danaus plexippus L., has evolved to be insensitive to milkweed cardenolides via genetic modifications of Na+/K+-ATPase. There is concern for insecticide exposures near agriculture, with little information on monarch caterpillar toxicology. It is unclear how cardenolide insensitivity may affect the sensitivity of monarch caterpillars to pyrethroid insecticides. Additionally, potassium fertilizers may affect monarch caterpillar physiology and cardenolide sequestration. Here, we investigated the growth, survival, and development of caterpillars exposed to the cardenolide ouabain, bifenthrin, and potassium chloride (KCl) alone and in combination. Caterpillars were either exposed to (1) ouabain from third- to fifth-instar stage, (2) KCl at fifth-instar stage, (3) KCl and bifenthrin at fifth-instar stage, or (4) combinations of ouabain at third-instar stage + KCl + bifenthrin at fifth-instar stage. Caterpillar weight, diet consumption, frass, and survival were recorded for the duration of the experiments. It was observed that 1–3 mg ouabain/g diet increased body weight and diet consumption, whereas 50 mg KCl/g diet decreased body weight and diet consumption. Caterpillars feeding on KCl and treated with 0.2 μg/μl bifenthrin consumed significantly less diet compared to individuals provided untreated diet. However, there was no effect on survival or body weight. Combinations of KCl + ouabain did not significantly affect caterpillar survival or body weight following treatment with 0.1 μg/μl bifenthrin. At the concentrations tested, there were no effects observed for bifenthrin sensitivity with increasing cardenolide or KCl concentrations. Further studies are warranted to understand how milkweed-specific cardenolides, at increasing concentrations, and agrochemical inputs can affect monarch caterpillar physiology near agricultural landscapes

Assessing the permeability of landscape features to animal movement: Using genetic structure to infer functional connectivity

Human-altered environments often challenge native species with a complex spatial distribution of resources. Hostile landscape features can inhibit animal movement (i.e., genetic exchange), while other landscape attributes facilitate gene flow. The genetic attributes of organisms inhabiting such complex environments can reveal the legacy of their movements through the landscape. Thus, by evaluating landscape attributes within the context of genetic connectivity of organisms within the landscape, we can elucidate how a species has coped with the enhanced complexity of human altered environments. In this research, we utilized genetic data from eastern chipmunks (Tamias striatus ) in conjunction with spatially explicit habitat attribute data to evaluate the realized permeability of various landscape elements in a fragmented agricultural ecosystem. To accomplish this we 1) used logistic regression to evaluate whether land cover attributes were most often associated with the matrix between or habitat within genetically identified populations across the landscape, and 2) utilized spatially explicit habitat attribute data to predict genetically-derived Bayesian probabilities of population membership of individual chipmunks in an agricultural ecosystem. Consistency between the results of the two approaches with regard to facilitators and inhibitors of gene flow in the landscape indicate that this is a promising new way to utilize both landscape and genetic data to gain a deeper understanding of human-altered ecosystems. © 2015 Anderson et al

Genus expansion for real Wishart matrices

We present an exact formula for moments and cumulants of several real compound Wishart matrices in terms of an Euler characteristic expansion, similar to the genus expansion for complex random matrices. We consider their asymptotic values in the large matrix limit: as in a genus expansion, the terms which survive in the large matrix limit are those with the greatest Euler characteristic, that is, either spheres or collections of spheres. This topological construction motivates an algebraic expression for the moments and cumulants in terms of the symmetric group. We examine the combinatorial properties distinguishing the leading order terms. By considering higher cumulants, we give a central limit-type theorem for the asymptotic distribution around the expected value