Analysis of Alternative Storage Conditions for DNA Recovery from Field Samples

As ecologists increasingly employ molecular methods, they find that tried and true preservation solutions (e.g. ethanol or formalin) may not be optimal when samples are targeted for genetic analyses. Before traveling to remote sample sites, researchers need to consider which preservation methods are likely to yield the largest quantity and highest quality of DNA based on their travel times and field conditions. They also need to consider whether they will have access to preservatives at remote sites and whether those preservatives can be safely transported. To determine which preservation methods would most reliably preserve tissue for genetic analysis under a range of field conditions, we examined total DNA recovery from female fruit flies (Drosophila melanogaster) individually held in various solutions (70% ethanol; 2% SDS, 100 mM EDTA; 1% SDS, 50 mM EDTA; 0.66% SDS, 33 mM EDTA; Zymo© lysis buffer; Zymo Xpedition© lysis buffer) at three different temperatures (22oC, 4oC and -20oC) for varying lengths of time (1 day, 4 weeks, and 8 weeks). We predicted that insects held in Zymo Xpedition© buffer would yield the overall highest DNA recovery since this buffer was designed for field collected animal tissue. We also predicted that variation in DNA recovery from insects held in different solutions would increase with preservation time and holding temperature. Although we observed significant differences in total DNA recovery from some of our samples, no trends were identified. Preliminary band quality analyses of PCR products utilizing stored DNA as template for amplification of the mCOI gene generally indicated decline in product quality as storage time increased. Future work will focus on better quantifying stored DNA quality and examining the relationship between total DNA recovered and overall DNA quality

Anti-proliferative Effects of Common Plant Extracts on Tumor Cells in Vitro

In 2018, the World Health Organization identified cancer as responsible for 1 in 6 deaths globally, encouraging the exploration of creative forms of cancer treatment. Our research interests include identifying anti-proliferative plant extracts and illuminating mechanisms of growth inhibition. In this study we measured the effects of Vitis vinifera (grapeseed), Juniperus communis (juniper berry), and Curcuma longa (turmeric) extracts on the proliferation of several normal and tumorigenic cell strains and lines (HFF-S2, HeLa, HepG2, MDA MB 231, and RAW 264.7). We performed dose response CyQUANT assays to analyze the effects on cell growth. We are using DNA analysis, recovery experiments, and DAPI staining to investigate whether our extracts induce apoptosis in these cells. Our results showed dose-dependent inhibition of cell growth in vitro with all three extracts but not with extracts from other plants. The results of this study suggest the potential for further study of components of grapeseed, juniper berry, and turmeric extracts as potential chemo preventive agents

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

Genomic diversity of bacteriophages infecting Microbacterium spp.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics

Extremely low gestational age and very low birthweight for gestational age are risk factors for autism spectrum disorder in a large cohort study of 10-year-old children born at 23-27 weeks’ gestation

No prospective cohort study of high-risk children has used rigorous exposure assessment and optimal diagnostic procedures to examine the perinatal antecedents of autism spectrum disorder (ASD), separately among those with and without cognitive impairment

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching