Understanding the population structure and biogeography of avian fauna is an important tool for gaining insight into the historical and evolutionary processes leading to the diversification of North American birds. Research into the extensive adaptive radiation by the New World Setophaga warblers of the Parulidae family has been especially useful in illustrating these processes. Through phylogenetic analyses, we investigated the population structure of black-throated gray warblers (Setophaga nigrescens) in the Western United States. Previous analysis describes two distinct groups; a northwestern clade, known as S. n. nigrescens, and a southwestern clade, known as S. n. halseii. To elaborate on this study, we analyzed a larger number of Setophaga nigrescens samples that encompass a wider distribution across the Western US. Using mitochondrial sequences of the ND2 gene, we constructed several phylogenies using 48 S. nigrescens samples and 1 S. graciae sample as the outgroup. Our results support subpopulation structure as indicated by two haplotypes. One haplotype is regularly found in populations west of the Cascades and Sierra Nevada, while the second haplotype is common in the Southwestern US. Admixture appears to be occurring over a wide geographic range extending throughout Northern Arizona, Utah and Nevada, and possibly spanning farther north based on both haplotypes occurring in Washington State East of the Cascades. With a sequence divergence of about 0.8%, a Pleistocene origin seems likely; numerous glaciation cycles during this period may have facilitated this genetic divergence. However, additional samples will be needed to better illustrate the extent of their structure. This will have important implications for the diverse relationships found within the Setophaga genus of the Parulidae family and may benefit future studies involving the evolutionary processes that have led to the diversification of this group and North American birds in general.

One of the most inflammatory topics in animal welfare and wildlife conservation is the issue of feral domestic cats. Wild bird advocates favor lethal eradication programs to protect wildlife from cats, and feral cat advocates support reducing their populations non-lethally through trap-neuter-return programs. Little research has been done regarding the motivations and beliefs of the humans behind this conflict, a gap that this study has sought to remedy. Feral cat and wild bird advocates are as worthy of investigation for potential commonalities as they are for their history of strife. Both groups express a connection to animals which they cannot share much, if any, contact. Most human-animal bond research focuses on traditional pets, and questionnaires routinely use physical closeness as a metric of one's bond to an animal. An online survey was conducted of 3859 adult Americans who identify as advocates for either feral cats or wild birds. Questions included demographics, motivations, political engagement, how the animals make them feel, and what they enjoy or admire about feral cats or wild birds. The groups had statistically significant differences in more areas than they had commonalities. Areas of difference include number of pets, level of emotional attachment, and why they like their focal species. The groups did not have significant differences in subjects such as household size, enjoying feral cat/wild bird activities because they are challenging, and reporting that being a "feral cat person" or "wild bird person" is an important part of their identity. This is the largest study that has been conducted on a human-animal bond topic, as well as the most comprehensive study examining the people behind an important area of policy debate. These results could be useful in deescalating future policy battles and trying to pave a path forward to compromises that both stakeholder groups could accept.

As more technology that utilizes personal electronic devices (PEDs) are being integrated in classrooms, the possibility of cell phone distraction is a real concern amongst many educators. Because of this, we became interested in cell phone use patterns in highly interactive biology classrooms at UW, and what factors influence their use. To answer this, we investigated the impact of in-class polling using PEDs or using clickers (older, standalone devices). We compared cell phone use in two different quarters (same course, same instructor) that either used PEDs or clickers for in-class polling. We also compared the cell phone use in the beginning of quarter vs. the end. In addition, we looked at whether classroom seat location correlates with cell phone use. To assess cell phone use, we directly observed active learning introductory biology lectures. Three to four researchers observed each seat in a designated section of the lecture hall and noted if a cell phone was visible (used as a proxy for use), three to five times during a class session. We used logistic regression and model selection to find a best fit model to determine if polling technology type, seat location or time of quarter (beg. vs end.) can predict cell phone visibility. To our surprise, the results indicated that neither Poll Everywhere nor time of quarter increased the already low cell phone visibility. However, our results also indicated that students that are sitting away from professor (back of classrooms) are more likely to use their cell phone than their peers regardless of polling technology. Taken together, we suggest instructors with highly interactive classrooms should not worry about integrating newer polling technologies. Further, instructors may look into having more TAs or peer facilitators roam around the classroom, especially in the case of large lecture halls to avoid cell phone misuse.

 Functional morphologists examine the anatomy of organisms to elucidate how they are adapted to various habitats and behaviors. These type of studies have also led to intense research and speculation about the specific behaviors associated with the morphologies of now extinct species. Can we predict the hunting behavior of a predator from its skeletal morphology? In this study, we examined both femur morphology and the calcaneus to femur length ratios in extant members of Carnivora, with the goal of finding a link between these traits and a species’ hunting strategy. We categorized hunting strategies from videos and previous accounts by taking note of the presence and timing of each species’ attacks of live prey. To quantify hind limb bone morphology across species with different hunting strategies, we measured the length of the calcaneus and femur, and the minimum bone diameter of the femur. Our sample included 12 extant species from several hunting strategies. We expect to find femurs with a greater minimum diameter in species that have strategies that require greater muscle force during the prey capture period. This type of anatomy would provide the support necessary for attachments of larger running muscles. For femur to calcaneus ratio, we expect to find a lower value in species with longer chase periods in their hunting strategy. This would be due to a greater need for longer strides and contact time to reach the speeds necessary to catch their prey. This study will allow scientists to more accurately predict the hunting behaviors of extinct animals based on measurements that can be easily obtained from an intact fossil.

American Foulbrood (AFB), a disease of honeybee larvae caused by the bacterium Paenibacillus larvae, has global economic significance. AFB spreads through colonies killing the next generation of bees. AFB has traditionally been treated with antibiotics or by burning infected hives and exposed materials. The former method is complicated by antibiotic resistance and bacterial sporulation, while the latter method carries severe financial liability for beekeepers. One alternative treatment is the use of bacteriophages, viruses that infect and destroy bacteria. Bacteriophages are host-specific and co-evolve with their host, unlike antibiotics, thus making resistance and collateral damage a non-issue. Characterizing these phages will be key to future treatments of infected hives. The P. larvae phage Willow, isolated in our lab, is both lysogenic (allow the infected bacterium to survive) and lytic (kill the infected bacterium). Currently, we have confirmed Willow lysogeny in P. larvae strain 3650. This relationship presents a model system for investigation. A comprehensive understanding of the host-pathogen interactions between Willow and P. larvae will aid in the effective targeting of P. larvae in the field. Our laboratory also seeks to determine the relatedness of four P. larvae phages to Willow to further characterize the genes responsible for lysogenic/lytic decision making. In sensitivity assays, lysogens (bacteria with integrated phage) are plated to form a lawn and dilutions of a different phage are spotted onto the plate. An identical wild-type plate is made, and comparison yields plating efficiencies. Plating efficiency determines what degree of protection is offered by the integrated phage. I hypothesize that genetic sequencing will show measurable genetic differences in the putative C1/Cro region of the phages under investigation, and that all genome sequence similarity will correlate directly with established plating efficiencies. Furthermore, I used sequence alignment, product alignment, and dot-plots to illustrate the degree of sequence similarity between phages.

Among the most robust determinants of fitness within the animal kingdom are successful feeding techniques that enable adequate energy acquisition. The need to maintain a steady food supply is especially crucial in mammals who have high metabolic demands in order to maintain a homeostatic internal body temperature. Within the Class Mammalia, the Order Cetacea consists of whales, dolphins, and porpoises, and includes some of the most derived and specialized aquatic carnivores. Of the three Cetacean suborders, Odontoceti retains the ancestral condition of having teeth rather than baleen for filter-feeding as in Mysticeti whales. This allows odontocetes to consume many prey types, ranging from cephalopods to large vertebrates. The aim of this study is to investigate if interspecific differences in bite force and gape size evolved in tandem with the consumption of specific prey types in odontocetes. To achieve this goal, we used skull specimens from the Burke Mammalogy Collection at the University of Washington to take a variety of linear measurements of the cranium and mandible. We used these measurements to estimate gape size and bite force by applying mathematical equations, and then contrasted these values across species that differ in diet. We expect to find that odontocetes evolved cranial adaptations to 1) increase bite force as a means to consume harder prey and 2) increase gape size as a means to consume larger prey. Developing a better understanding of how species maximize energy gain is imperative to determining the factors that drive evolution and species adaptation. This knowledge can also help inform future conservation efforts, improve the general understanding of Odontoceti evolution, and serve as a reference for future studies of mammalian cranial morphology and biomechanics.

Statistics have revealed that males are more susceptible to significant spinal cord injuries than females. Carlos Ayala, MD-PhD student from the Keck Center of Collaborative Neuroscience at Rutgers University, has found preliminary evidence that males have a heightened immune response comparison to females following injury. This immune response involves an increase in inflammation surrounding the injury site, and the release of damaging cytokines that suppress neuronal growth and promote axon demyelination following injury. At the injury site, there is also an aggregation of M1 macrophages, which are known to have inflammatory properties and are involved in the promotion of cell death in the surrounding tissues. Another type of macrophage present are M2 macrophages, which are known to be anti-inflammatory and promote tissue regeneration, but these macrophages appear to be suppressed at the site of injury due to myelin debris and other chemical signals. Recent studies suggest that human umbilical cord blood (hUCB) has anti-inflammatory properties which could be beneficial in decreasing the inflammatory response that occurs in males. In this study, we propose to investigate the use of hUCB derived monocytes to treat spinal cord injury in male rats to determine whether it causes the polarization of monocytes into M1 or M2 macrophages in vivo. Using the classification of monocytes standard of myself, Carlos Ayala, Cameron Wolf, and Johvany Plaisime of Rutgers Univerity, the next step is to determine which monocytes are precursor cells to M1 (inflammatory) and M2 (anti-infammatory) macrophages. Monocytes are a heterogeneous population with cells found at various stages of life. Some of the critera include size of the cell, amount of and form of cytoplasm (smooth vs jagged), density of the cytoplasm, how indented the nucleus is, number of nuclei the cells have, and cell markers that are present for monocyte/macrophage specific cell membrane receptors. If this study is successful, hUCB could be further studied for possible therapeutic applications for the treatment of  spinal cord injury.

It is critically important that eukaryotic cells possess the capacity to undergo intracellular change in response to both internal and external cues. Arabidopsis thaliana F-box (FBX) and 14-3-3 proteins are two distinct protein families that regulate intracellular change and have important roles in regulating responses to environmental stress. FBX proteins are variable substrate adaptors within the Ubiquitin 26S Proteasome System (UPS), a system the selects proteins to be degraded by the 26S proteasome using selective ubiquitylation. 14-3-3 proteins recognize and bind unique phosphorylated residues in client proteins to regulate subcellular localization, inhibit protein interactions, and act as a scaffold to facilitate protein interactions. Thus, these two protein families independently have the ability to drastically alter cell physiology. 14-3-3 proteins have been shown to interact with components of the Ubiquitin 26S Proteasome System in only a few instances, including their interaction with the F-box protein F-BOX STRESS INDUCED 1 (FBS1). However, the biological consequences of this FBS1:14-3-3 interaction are completely unknown. FBS1 belongs to a four-member FBX protein family, along with FBS2-4, and we hypothesize that 14-3-3 proteins more broadly interact to at least regulate this family of four proteins. A Yeast 2-Hybrid assay has been employed to test for interactions between FBS1-4 and five of thirteen different 14-3-3 proteins. Full length and truncated constructs are currently being tested to probe the extent of interactions between these two important protein families. Interaction between multiple members of these two important protein families could point to a more broadly used scheme in regulating intracellular events in plant cells.

The overuse of antibiotics by the health and agriculture industries has resulted in an increase of antibiotic resistance in bacteria, leading to a wide range of untreatable illnesses. The U.S. Department of Health and Human Services Centers for Disease Control and Prevention estimates that at least two million illnesses and 23,000 deaths each year have been caused by antibiotic resistance. Understanding the mechanisms and potential reduction of fitness associated with antibiotic resistance is therefore essential for addressing the ongoing battle with disease-causing bacteria. This study investigates streptomycin resistance in E. coli and explores how resistance may affect the bacteria’s fitness under two stresses, temperature and pH. Mutant strains of E. coli were isolated and exposed to a range of temperatures (30-42°C) and pH levels (4.0-5.0). The results suggest that while antibiotic resistance is a beneficial mutation in the presence of streptomycin, it may impact fitness under environmental stress. Understanding the potential costs of antibiotic resistance could ultimately help us create better models to predict and combat the rapid evolution of drug resistant bacteria.

In the US more than 100 million people are living with diabetes or pre-diabetes. The economic burden caused by these conditions, including medical costs, is approximately $322 billion annually as of 2013. Conventionally, transgenic Escherichia coli has been the primary source of commercial insulin production, a process that requires extensive purification to ensure shelf stability and complete removal of contaminants. This study seeks to establish an alternative mode of insulin production using polyethelyne glycol (PEG) to transform the oyster mushroom, Pleurotus ostreatus, with the human insulin gene. P. ostreatus is a valuable target for genetic transformation due to its lack of endotoxins and fully sequenced genome. P. ostreatus was transformed using PEG with a plasmid containing the human insulin gene and a carboxin resistance gene. Transformed cells were selected using carboxin, extracted, and regenerated on plates composed of yeast extract, malt extract, and glucose (YMG). Integration of the human insulin gene in to the mushroom genome was confirmed through PCR analysis of the transformants. Successful PEG transformation of P.ostreatus offers a new avenue for insulin production, potentially diversifying the market and treatment options for diabetics.

Conventional farming techniques involve large quantities of chemical fertilizers, which often leach into bodies of water causing eutrophication. The influx of excess nutrients from fertilizer results in rapid increase of aquatic algal populations followed by dissolved oxygen depletion. This process creates regions of low oxygen that negatively impact the water quality of many major lakes and coastal regions. To address this problem, the sensitivity of plant growth-promoting bacteria (PGPB) to excess fertilizer was investigated. We hypothesize that the addition of high amounts of fertilizer will result in smaller, less productive plants and diminished rhizosphere colonization of the PGPB, Bacillus subtilis. A modified Kirby-Bauer disk diffusion test was performed as an initial assessment of the effect of varied fertilizer concentrations on B. subtilis. Roots of romaine lettuce seedlings were then inoculated with B. subtilis and grown in soil treated with the same range of fertilizer concentrations. The effects of each treatment on plant growth were determined using total leaf area, quantification of the rhizosphere colonization by B. subtilis, and carbon assimilation measured with a LI-6800 Portable Photosynthesis System. These results are an important step towards establishing guidelines for appropriate application of agricultural fertilizer in order to mitigate the frequency and severity of eutrophication events in aquatic systems.