Fall 2015 Biology Seminar Abstracts

Dec 4, 2015

Kendra Krause '16: Difference in the Decomposition of Humans and Pigs: Search for a Human Specific Marker

Animal remains are found constantly in the environment. Humans make up a portion of the remains found. The decomposing flesh releases particular odors into the air. Cadaver dogs are trained to detect these particular odors; trained using artificial scents. By identifying a human specific marker, the efficiency level will rise and the amount of time it takes to find a body will decrease. The cadaver dogs will not, mistakenly, identify pigs, deer, chickens, or other animals if trained with the human specified marker. I will be presenting the results from a paper by Rosier et al. (2015) who has compared the volatile organic compounds produced by decaying flesh on a variety of animal tissues, including humans. Their work make it possible to develop mobile analytical equipment that will be able to identify human remains in situations that are not accessible to dogs or when trained dogs are unavailable.

Matt Hamilton '15: Antiretroviral Pre-Exposure Prophylaxis (PrEP): A strategy for Reducing the Incidence of HIV

With the United Nations estimating that 2 million new HIV infections occurred in 2014, developing better preventative measures is necessary if HIV is to be contained. One strategy for doing so is a pre-exposure prophylaxis (PrEP) regimen of antiretroviral Truvada, which has proven remarkably effective in preventing new viral infections. Purpose: The PrEP initiative (iPrEX) study was a groundbreaking 2010 study that sought to determine the efficacy of PrEP in reducing incidence, adherence rates, and frequency of adverse reactions. Methods: A placebo controlled, double-blind, multinational cohort of men who have sex with men (n=2499) was followed for an average of 1.2 years. Monthly and quarterly appointments with participants involved HIV testing, drawing of blood samples, pill counts, and collection of self-reported adherence and sexual behavior data. Results: HIV transmission was reduced by 47% in the Truvada group. When the Truvada group individuals with undetectable serum levels of the drug were controlled for, a 98% reduction was seen. Conclusions: This iPrEX study was the first to demonstrate PrEP’s ability to prevent HIV infection in a clinical setting. Open-label study designs like Volk et al. 2015 have shown significant increases in sexual risk behaviors including a 41% decrease in condom use in PrEP users and increased incidence of STIs while still touting a 100% decrease in HIV incidence. Attempts to replicate the success of iPrEX in Sub-Saharan Africa (SSA) have had mixed results; a Kenyan study of heterosexual couples saw a 73% reduction in HIV incidence, while a study of women in SSA discontinued early due to no difference seen in incidence. If PrEP is to be a viable option for preventing HIV infection, issues involving sexual risk behavior and adherence in the populations most at risk for HIV infection must be addressed.

Josephine Kent '16: Paleoecological Investigation of the Impact of Rainbow Trout Predation on Zooplankton Community Structure: a Paired Watershed Approach

Alterations of fish community composition resulting from natural events or intentional fisheries management can significantly alter the zooplankton community structure and the trophic state of lakes. The stocking of rainbow trout (a size-selective, zooplanktivorous species) into Square Lake is an example of a fisheries management practice that has been shown to cause the community structure of the zooplankton to shift from a prevalence of large-bodied grazers (e.g., large Daphnia) to a community dominated by smaller-bodied species that are less effective grazers of algae. Dormant zooplankton eggs (ephippia) can be shed and preserved in the sediment of lakes, displaying a time scale of past zooplankton populations. This study examined the count and size of the Daphnia pulicaria ephippia and remains throughout Square Lake’s history. The experiment was carried out by examining samples from sediment cores obtained from Square Lake and Big Carnelian Lake (Reference Lake), to determine whether changes in zooplankton community composition and Daphnia body size are observed in the paleo-records. Daphnia pulicaria remains in Square Lake sediments were expected to be less abundant in more recently deposited sediments. A decrease in Daphnia pulicaria ephippia size was expected in more recent sediment. The results showed no significant change in the number of Daphnia pulicaria remains but did show a decrease in ephippia size closer to present day. These results suggest that the stocking of Rainbow Trout has an effect on body size of Daphnia pulicaria and therefore impacts the trophic state of Square Lake.

Dec 11, 2015

Alan Blakely '15: Metaproteomic workflow for the identification of microbial proteins from duodenal biopsies

The application of mass spectrometry (MS) to study the proteins in a given sample has opened the door to a vast potential for discovery in the life sciences. Computational methods for the analysis of the resulting spectra are rapidly evolving to accommodate new MS technologies and ever growing datasets and repositories. Metaproteomics, the study of all proteins in a taxonomically diverse sample, offers insights to the role of microbiota present in a given sample as it allows for the identification of microbial species present through finding species-specific peptides, and also provides information about the chemical and functional role such organisms have in the environment of interest. Research is being done to increase the sensitivity and accuracy of metaproteomic experiments through the development of new computational techniques and workflows. Using one such workflow, metaproteomic analysis was conducted on a dataset which had previously only been analysed for human proteins. The dataset consists of spectra obtained from human duodenal biopsies of a group of insulin sensitive subjects and a group of insulin resistant subjects. Microbial peptides were identified from the dataset and the relative abundance of the microbial peptides as they correlate with diabetes was calculated.

Jessica Johnson '15: Bacteriophages as Reservoirs of Antibiotic Genes

Antibiotic resistance in bacteria happens when genes are acquired that confer resistance to different antibiotics. The acquisition of these genes occur by either vertical or horizontal gene transfer. Vertical gene transfer is a result of spontaneous mutation that confers resistance to the bacterium. These mutations are transferred directly during DNA replication to all the bacteria’s progeny. This process is driven by principles of natural selection. Horizontal gene transfer occurs by transformation, transduction, or conjugation. Transformation occurs when parts of DNA are taken up by the bacteria from the external environment. These parts of DNA occur due to the death and lysis of another bacterium. Transduction occurs when bacteriophages transfer DNA between two closely related bacteria. Conjugation is direct cell to cell contact between two bacteria and the transfer of plasmids (small pieces of DNA). Conjugation is the most studied mechanism of horizontal gene transfer. In my presentation I discuss bacteriophages and their role in transfer of antibiotic resistance genes via transduction. The hypothesis explored is “Are bacteriophages reservoirs of antibiotic resistance genes in the environment?” In the study by Colomer-Lluch et al. (2011) when bla genes (blaTEM and bla CTX) from phage DNA were transferred to ampicillin-sensitive gram-negative E. coli bacteria both of the bla genes were detected in the DNA of the resistant clones after transfection. Studies by Mazaheri et al. (2011) show that enterococcal bacteriophages play a role in transfer of antibiotic resistance genes in enterococci as tetracycline and gentamicin resistance were successfully transferred between the same and different enterococcal species. These studies support that phages are reservoirs of resistance genes in the environment.