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Bartonella Bacilliformis Hfq Regulates Small Rnas
No full textBartonella bacilliformis is a facultative bacterial intracellular pathogen of the human circulatory system, causing Carrion’s disease. B. bacilliformis is transmitted between human hosts by a sand-fly vector, two markedly distinct backgrounds. As such, it presumably requires a high degree of regulation at the genomic level. Hfq, a common RNA-binding protein of bacteria, is present in B. bacilliforms, and likely plays a key role in post-transcriptional regulation. Hfq is involved in regulating many processes by choreographing small RNA (sRNA) binding to mRNA targets for transcriptional regulation via specific base pairing interactions. To better understand the role of Hfq in B. bacilliformis, the hfq gene was cloned into an expression plasmid to generate a His-tagged Hfq fusion protein. The plasmid was then used to transform E. coli, which was then induced with IPTG, to produce high quantities of the Hfq protein. The cells were lysed and the Hfq protein was purified by affinity chromatography using a NiNTA column with His tag specificity. Recombinant Hfq was used to generate rabbit polyclonal anti-Hfq antibodies, and specificity was verified by western blots. The anti-Hfq antibody will be utilized to co-immunoprecipitate Hfq and its sRNA / mRNA targets from B. bacilliformis lysates. The resulting RNAs will then be used to construct a cDNA library, which in turn will be deep sequenced to generate a list of RNAs that interact with Hfq. Results will directly inform us of the genes that are regulated by Hfq in this potentially life-threatening pathoge
Estimating Forage Quality and Abundance to Better Understand Mule Deer Resource Selection
No full textTo identify the environmental factors limiting growth of herbivore populations, researchers need to understand how benefits (like forage quality and abundance) and costs (like risk of predation) vary across a population’s range, and how individuals select habitat with respect to those resources. For mule deer (Odocoileus hemionus) living in northwest Montana, predicting forage quality and abundance over large extents is difficult, since much of their habitat use occurs within dense conifer forest where remote-sensed metrics (like NDVI) are of limited use. Therefore, we are developing a landscape forage model using field-collected vegetation data to estimate how digestible energy per area varies across 3 mule deer population ranges. Preliminary evidence has shown that forage resource availability varies with landcover-type. With this forage model, and along with previously developed predator resource selection functions (RSFs), we will develop an RSF to assess how mule deer make tradeoffs between nutrition and predation risk. This will allow us to identify the mechanisms driving mule deer resource selection, and will guide more effective management of mule deer populations and habitat in western Montana
Greater Sage-Grouse Response to Bentonite Mining
No full textThe greater sage-grouse has undergone range contraction and population decline because of anthropogenic land surface disturbances; yet, there is little information on the effects of mining on sage-grouse populations. In the Bighorn Basin of Montana and Wyoming, bentonite mining is a growing source of surface disturbance that contributes to loss of sagebrush habitat. We evaluated the response of sage-grouse to active and reclaimed bentonite mining, relative to nesting, brood-rearing, adult breeding, and adult winter habitat, through resource selection and habitat-specific mortality risk analyses, based on female sage-grouse monitored with telemetry from 2011-2015. A greater proportion of our monitored sample was exposed to mining disturbance during winter (65%) than during other seasons (range = 25%-34%). We observed avoidance of all mining disturbance for selection of nesting habitat, adult breeding habitat, and adult winter habitat. Evidence was inconclusive for avoidance of mining for brood-rearing habitat. We also observed increased adult breeding season mortality risk associated with active mining disturbance but observed no effect on nest success. Evidence was inconclusive for increased mortality risk associated with broods and adults during winter. Stakeholders in the Bighorn Basin should be flexible and proactive to minimize the negative effects of bentonite mining on sage-grouse habitat use and demographic rates. Stakeholders should prioritize the conservation of winter habitats because of the influence on a greater proportion of the population and they should strive to perfect mining reclamation to return disturbed sites back to pre-disturbance conditions to minimize long-term effects
New Methods for Monitoring Mountain Goat Populations (Poster)
No full textEstimating the distribution and abundance of wildlife populations is a critical component to the conservation of wild species. Precise estimates of these parameters enable biologists to productively manage and preserve the animal populations they oversee. Methods for monitoring high density species populations are frequently and continuously being improved upon. However, identifying effective methods for monitoring low density species populations (e.g. mountain lions, wolves, mountain goats, and wolverine) has proved challenging due to small population sizes and difficulty of access to low density species habitat. Current approaches for surveying low density species (e.g. aerial surveys, baited camera traps, DNA sampling) often provide insufficient information and application of statistical models to these data can be complex. In this study, and in partnership with Idaho Department of Fish and Game, I will test disparate non-invasive, ground-based methods for monitoring mountain goat (Oreamnos americanus) populations in Idaho, USA. This project will compare and contrast findings from three field and analytical methods: camera trapping techniques, single-observer ground surveys, and double-observer ground surveys. Here, I describe the field methods and statistical models being tested and developed in research project. Additionally, I will present findings from the first field season (June-August 2018) of testing these three methods. By improving occupancy and abundance estimates for mountain goat populations, biologists can begin to make smarter conservation decisions around mountain goat management
Population Demographics, Breeding Ecology and Responses to Grazing of Montana Sagebrush Steppe Songbirds
No full textSagebrush steppe is one of the most threatened ecosystems in North America. Avian adult density estimates are often used to assess conservation actions given the relative ease in collecting data to inform these estimates. However, information on how conservation actions influence life histories such as nest density and nest success are lacking, despite the fact that life histories inform abundance. We investigated songbird adult densities, nest densities, and nest success over multiple breeding seasons in central Montana. Our goal is to understand the relationships among adult abundance, nest density, and nest success, as well as how land management practices, in the form of grazing, influence those patterns. Two grazing systems were compared in our study: a system using a combination of rest and deferment (hereafter restrotation) and traditional grazing. For the purposes of our study, we define rest-rotation grazing as changing the timing of grazing in pastures each year, with some pastures alternately rested every few years. Traditional grazing is defined as grazing a pasture at the same annual season each year or all season. Recently, rest-rotation systems have been used as a conservation management tool by the Natural Resource Conservation Service-Sage Grouse Initiative. Their goal is to encourage private landowners to graze their livestock more sustainably to maintain or improve rangeland productivity, while also benefiting habitat for greater sage-grouse (Centrocercus urophasianus). We explore the effects of rest-rotation compared to traditional grazing on songbird population demographics during the breeding season
The Genetic Structure of American Black Bear Populations in the Southern Rocky Mountains
Get PDFLarge and wide-ranging carnivores typically display genetic connectivity across their distributional range. American black bears (Ursus americanus) are vagile carnivores and habitat generalists. However, they are strongly associated with forested habitats; consequently, habitat patchiness and fragmentation have the potential to drive connectivity and the resultant structure between black bear subpopulations. Our analysis of genetic structure of black bears in the southern Rocky Mountains of Wyoming and Colorado (n = 296) revealed two discrete populations: bears in northern Wyoming were distinct (FST = 0.217) from bears in southern Wyoming and Colorado, despite higher densities of anthropogenic development within Colorado. The differentiation we observed indicates that bears in Wyoming originated from two different clades with structure driven by the pattern of contiguous forest, rather than the simple distance between populations. We posit that forested habitat and competitive interactions with brown bears reinforced patterns of genetic structure resulting from historic colonization. Our work suggests that forested habitat is an important force structuring populations in the southern Rocky Mountains, even for populations of highly vagile carnivores
A Logistic Regression Implementation of the “Abcd” Method for Identifying Malignant Melanoma
No full textThis project investigated a way to more accurately assess the probability that a skin mole is malignant or benign using the ABCD classification system used in healthcare. To determine the probability that a mole was malignant or benign, numerical values were calculated for each classification. The numerical value for A (asymmetry) was calculated by drawing an estimated half-way point through the image and then filling in each half with simple geometric shapes whose areas could be easily calculated in Microsoft Word. Once the area of each half was found, the absolute value of the difference between the area of the two halves was the numerical value assigned to A. For B (border irregularity), the perimeter and area of each mole was put into the formula B=(P)2/(4πT), where T stands for area. C (color) was estimated on a scale of 1-5, where 1 was light, uniform color distribution and 5 was uneven, splotchy, and dark color distribution. For D (diameter), the archive used (ISIC Archive) to obtain the images had the diameter included in the metadata of each image. In total, 45 training images were used, and 5 different test images were used to cross-validate the results obtained. Both a quadratic logistic regression model and linear logistic regression model were used to see how accurate both models were in predicting the probability that a mole was malignant or benign. The results produced showed that the quadratic model was more accurate than the linear; however, both models had a high rate of accurate predictions. The quadratic model accurately predicted 44 out of 45 of the training data sets and 5 out of 5 of the test data sets. The linear model accurately predicted 41 out of 45 of the training data sets and 4 out of 5 of the test data sets
Zic Transcription Factors that Influence Convergent Extension
No full textMy research is focused on a specific time frame during embryonic development called gastrulation, in which intricate cell movements give rise to the ectoderm, mesoderm and endoderm layers of the embryo. The mesoderm layer undergoes movements called convergent extension, which allow cells to intercalate and move inside the embryo. The Zic family of zinc-finger proteins have a crucial role in gastrulation and neurulation. Based on findings from our lab (K. See and Merzdorf, in preparation) and others (Cast et al., 2012), I hypothesize that zic genes are required for convergent extension during gastrulation. Since there are 5 different, but very similar, zic genes, I will test each of these genes for a role in convergent extension during gastrulation. A knockdown method for each of the 5 zic genes in embryos of the model organism Xenopus laevis will be combined with a method called Keller Explants to allow analysis of convergent extension. In my experiments, I have ruled out zic 2 as a regulator of convergent extension. My current hypothesis is that zic3 is the most likely candidate because of its known roles in neural tube formation and other reasons I will explain below. I am also analyzing zic1,4, and 5 for convergent extension regulation
Bioinformatic Analysis of the Flathead Lake Monster Bacteriophage
No full textThe Flathead Lake Monster (FLM) bacteriophage was noted to have an abnormally-long tail upon its discovery. Once its genome was sequenced, this research sought out to identify the 117 FLM gene products using the BLASTp sequence alignment algorithm. This resulted in the discovery of five genes that are considered to be novel to the FLM. A specific gene within the FLM genome called the tape measure gene (TMG) was further analyzed once it was identified based on homology with other phages. Previous literature has suggested that a longer TMG can manifest itself as a longer bacteriophage tail length. This observation led to the hypothesis that a long tail length should yield a correspondingly-long TMG within the FLM. The bioinformatic investigation involved comparing the FLM tail length and FLM tape measure gene length to other phages. The results found that the FLM does not have an abnormally long TMG when compared to how long its tail is, indicating that the FLM is an anomaly when compared to other phages. Future examination of phage mosaicism may yield more information as to why the FLM tail length is abnormally long
Investigating the Binding of Bh3i-1 Derivatives to Anti-Apoptotic Bcl-2 Proteins
No full textCandida albicans is a leading cause of superficial and life threatening fungal disease. The ability to grow as filamentous cells is an important virulence trait for this fungus. Thus, molecules that block filamentous growth may form the basis for a novel approach to controlling infections by C. albicans. We have characterized a small molecule called BH3I-1 that specifically inhibits filamentous growth, but not yeast-form growth. BH3I-1 is not likely to be a good candidate for an anti-fungal drug, as it targets human Bcl-2 proteins and has the potential to induce apoptosis in human cells. The goal of our project is to identify structural derivatives of BH3I-1 that retain anti-fungal activity, but not Bcl-2 binding activity