Biology Commons^™

Characterizing The Requirements For The Matricellular Protein, Dccn, In Nervous System Function, Elizabeth L. Catudio Garrett

Graduate Student Theses, Dissertations, & Professional Papers

The brain is organized as a complex network of specialized neurons that communicate via a combination of electrical and chemical signals. Our brains function to generate movement, control organ function, or direct complex behaviors; all of which requires the ability to regulate the flow of communication between circuits and networks. Work in this thesis addresses two areas of neuron communication: first, how does the release of more than one neurotransmitter from a single neuron impact behavior, and second, are matricellular proteins (MCPs) key contributors to synaptic transmission and neuron function? The conserved CCN family of MCPs have a …

Heat For The Masses: Thermal Ecology Of The Western Tent Caterpillar, Victoria Dahlhoff

Graduate Student Theses, Dissertations, & Professional Papers

A unique feature of some gregarious, colonial insects is their ability to create external structures that alter environmental conditions for the entire (often family) group. A combination of physical alteration of local microhabitats and behavioral thermoregulation allows many of these animals to actively control their body temperatures, which allows them to regulate energy use and metabolism in variable thermal environments. Here I describe mechanisms of microhabitat modification and thermal regulation in the western tent caterpillar, Malacosoma californicum pluviale. Tent caterpillars build communal silk tents, whose temperatures can rise substantially above ambient air temperature. I experimentally manipulated colony sizes and examined …

A Csra-Binding, Trans-Acting Srna Of Coxiella Burnetii Is Necessary For Optimal Intracellular Growth And Vacuole Formation During Early Infection Of Host Cells, Shaun Wachter, Matteo Bonazzi, Kyle Shifflett, Abraham S. Moses, Rahul Raghavan, Michael F. Minnick

Biological Sciences Faculty Publications

Coxiella burnetii is an obligate intracellular gammaproteobacterium and zoonotic agent of Q fever. We previously identified 15 small noncoding RNAs (sRNAs) of C. burnetii. One of them, CbsR12 (Coxiella burnetii small RNA 12), is highly transcribed during axenic growth and becomes more prominent during infection of cultured mammalian cells. Secondary structure predictions of CbsR12 revealed four putative CsrA-binding sites in stem loops with consensus AGGA/ANGGA motifs. We subsequently determined that CbsR12 binds to recombinant C. burnetii CsrA-2, but not CsrA-1, proteins in vitro. Moreover, through a combination of in vitro and cell culture assays, we identified several in trans mRNA …

Diverse Conditions Support Near-Zero Growth In Yeast: Implications For The Study Of Cell Lifespan, Jordan Gulli, Emily Cook, Eugene Kroll, Adam Rosebrock, Amy Caudy, Frank Rosenzweig

Biological Sciences Faculty Publications

Baker’s yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including met-azoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes …

Structure, Function, And Dynamics Of The Gα Binding Domain Of Ric-8a, Baisen Zeng, Tung-Chung Mou, Tzanko I. Doukov, Andrea Steiner, Wenxi Yu, Makaia Papasergi-Scott, Gregory G. Tall, Franz Hagn, Stephen Sprang

Biological Sciences Faculty Publications

Ric-8A is a 530-amino acid cytoplasmic molecular chaperone and guanine nucleotide exchange factor (GEF) for i, q, and 12/13 classes of heterortrimeric G protein alpha subunits (Gα). We report the 2.2-Å crystal structure of the Ric-8A Gα-binding domain with GEF activity, residues 1-452, and is phosphorylated at Ser435 and Thr440. Residues 1-429 adopt a superhelical fold comprised of Armadillo (ARM) and HEAT repeats, and the C terminus is disordered. One of the phosphorylated residues potentially binds to a basic cluster in an ARM motif. Amino acid sequence conservation and published hydrogen-deuterium exchange data indicate repeats 3 through 6 to be …

Musineon Glaucescens (Apiaceae), A New Species From Central Montana, U.S.A., Peter Lesica

Biological Sciences Faculty Publications

Musineon glaucesens is described as a new species from two populations in the Big Belt Mountains of Montana, U.S.A. It appears to be most closely allied to the small genus Musineon which is endemic to western North America. It occurs just outside the range of M. vaginatum but differs from that species by its larger fruits, more widely lobed and glaucous leaves, and talus-slope habitat.

De Novo Origins Of Multicellularity In Response To Predation, Matthew D. Herron, Joshua M. Borin, Jacob C. Boswell, Jillian Walker, I. Chen Kimberly Chen, Charles A. Knox, Margrethe Boyd, Frank Rosenzweig, William C. Ratcliff

Biological Sciences Faculty Publications

The transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation …

Canis Lupus (Gray Wolf) Pup Survival In Yellowstone National Park, Anne Marie Jehle

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The aim of this study was to describe gray wolf (Canis lupus) pup survival rates throughout the summer months in Yellowstone National Park. Understanding pup survival has implications for trends in pack and population age structure, cooperative breeding ecology and other breeding tendencies, social hierarchies, and population fitness, among other elements of species-specific population ecology. A general understanding of trends in pup survival is also relevant to state and federal land that allow gray wolf harvest. Understanding such trends and survival ecology gives managers and biologists the opportunity to evaluate gray wolf populations at a more comprehensive level and implement …

Spatiotemporal Dynamics Of Nitrogen And Carbon Biogeochemistry In A Wetland-Stream Sequence, Patrick E. Hurley

Graduate Student Theses, Dissertations, & Professional Papers

Studies of aquatic ecosystems often segregate streams from the influential ponds, lakes, and wetland zones that act as important transitions between terrestrial and fluvial systems. Across the aquatic landscape, these zones interact to form linked ecosystems that function as discrete nutrient processing domains, shifting biogeochemical signals due to spatial and temporal variability in hydrologic and biologic controls. Using a mass-balance approach, we profiled nutrient dynamics along a 23-km wetland-stream sequence over three seasons. Hydrologic, morphologic, and biologic conditions, as well as landscape attributes, were quantified to determine potential controls on biogeochemical cycling in a tributary of the Upper Clark Fork …

Population And Breeding Ecology Of Sagebrush Steppe Songbirds, Kayla Ann Ruth

Graduate Student Theses, Dissertations, & Professional Papers

Sagebrush steppe is one of the most threatened ecosystems in North America. Domestic livestock grazing is the dominant land use of sagebrush steppe across the west. Rest-rotation grazing systems can be a conservation management tool, most recently, by the Natural Resource Conservation Service - Sage Grouse Initiative (SGI). The goal of SGI is to encourage private landowners to use a livestock grazing regime that maintains or improves habitat for greater sage-grouse (Centrocercus urophasianus), as well as improve rangeland productivity. Songbirds are biological indicators that can assess the health of sagebrush steppe. Avian adult density estimates are often used …

Methods For Estimating Mountain Goat Occupancy And Abundance, Molly Mcdevitt

Graduate Student Theses, Dissertations, & Professional Papers

Abundance and occupancy are two parameters of central interest to the field of ecology. Furthermore, accurate (both precise and unbiased) estimates are key pieces to the puzzle of effective wildlife management decision-making. While there exist a variety of sampling techniques and statistical models for effectively estimating population parameters for frequently encountered and large mammals, methods for sampling unmarked and rare species are few and far between. The first step to acquiring usable parameter estimates is through the use of sampling theory and incorporation of probabilistic sampling designs to collect count-data and occurrence-data. Often, it is assumed that probabilistic sampling designs …

Atypical Activation Of The G Protein Gα By The Oncogenic Mutation Q209p, Marcin Maziarz, Anthony Leyme, Arthur Marivin, Alex Luebbers, Prachi P. Patel, Zhe Chen, Stephen R. Sprang, Mikel Garcia-Marcos

Biological Sciences Faculty Publications

The causative role of G protein-coupled receptor (GPCR) pathway mutations in uveal melanoma (UM) has been well-established. Nearly all UMs bear an activating mutation in a GPCR pathway mediated by G proteins of the G family, driving tumor initiation and possibly metastatic progression. Thus, targeting this pathway holds therapeutic promise for managing UM. However, direct targeting of oncogenic Gα mutants, present in ∼90% of UMs, is complicated by the belief that these mutants structurally resemble active Gα WT. This notion is solidly founded on previous studies characterizing Gα mutants in which a conserved catalytic glutamine (Gln-209 in Gα) is replaced …

Genetics Of A De Novo Origin Of Undifferentiated Multicellularity, Matthew D. Herron, William C. Ratcliff, Jacob Boswell, Frank Rosenzweig

Biological Sciences Faculty Publications

The evolution of multicellularity was a major transition in evolution and set the stage for unprecedented increases in complexity, especially in land plants and animals. Here, we explore the genetics underlying a de novo origin of multicellularity in a microbial evolution experiment carried out on the green alga Chlamydomonas reinhardtii. We show that large-scale changes in gene expression underlie the transition to a multicellular life cycle. Among these, changes to genes involved in cell cycle and reproductive processes were overrepresented, as were changes to C. reinhardtii-specific and volvocine-specific genes. These results suggest that the genetic basis for the experimental evolution …

Streamlined Preparation Of Genomic Dna In Agarose Plugs For Pulsed-Field Gel Electrophoresis, Linda D. Hicks, Charlotte M. Van Der Graaf, Jacob Childress, Emily Cook, Karen Schmidt, Frank Rosenzweig, Eugene Kroll

Biological Sciences Faculty Publications

Genome analysis using pulsed-field gel electrophoresis (PFGE) has been used in applications ranging from typing bacterial strains to radiobiology to cancer research. While methods for running PFGE have been significantly improved since its invention, the method for preparing chromosomal DNA itself has remained essentially unchanged. This limits the applicability of PFGE, especially when analyses require many samples. We have streamlined sample preparation for routine applications of PFGE through the use of deep-well 48-well plates. Besides saving time, our protocol has the added advantage of reducing the volume of expensive reagents. Our improved protocol enables us to reduce throughput time and …

Analysis Of Motility In Multicellular Chlamydomonas Reinhardtii Evolved Under Predation, Margrethe Boyd, Frank Rosenzweig, Matthew D. Herron

Biological Sciences Faculty Publications

The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular alga Chlamydomonas reinhardtii has never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve in C. reinhardtii in response to predation or to settling rate-based selection. Structures …

Deciphering The Origin, Evolution, And Physiological Function Of The Subtelomeric Arylalcohol Dehydrogenase Gene Family In The Yeast Saccharomyces Cerevisiae, Dong Dong Yang, Gustavo M. De Billerbeck, Jin Jing Zhang, Frank Rosenzweig, Jean Marie Francois

Biological Sciences Faculty Publications

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5' sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr73 …

Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick

Biological Sciences Faculty Publications

Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited.

Results: We describe two MITE families discovered during research on small non-coding …

Crystal Structure Of The Major Quadruplex Formed In The Promoter Region Of The Human C-Myc Oncogene, Sascha Stump, Tung-Chung Mou, Stephen R. Sprang, Nicholas R. Natale, Howard D. Beall

Biological Sciences Faculty Publications

The c-MYC oncogene mediates multiple tumor cell survival pathways and is dysregulated or overexpressed in the majority of human cancers. The NHE III1 region of the c-MYC promoter forms a DNA quadruplex. Stabilization of this structure with small molecules has been shown to reduce expression of c-MYC, and targeting the c-MYC quadruplex has become an emerging strategy for development of antitumor compounds. Previous solution NMR studies of the c-MYC quadruplex have assigned the major conformer and topology of this important target, however, regions outside the G-quartet core were not as well-defined. Here, we report a high-resolution crystal structure (2.35 Å) …

Colonization Of And Adaptation To Tidal Marshes In The Savannah Sparrow (Passerculus Sandwichensis), Phred M. Benham

Graduate Student Theses, Dissertations, & Professional Papers

Intraspecific patterns of geographic variation reflect a dynamic history of colonization and divergence in response to spatially varying selective pressures. Analysis of this phenotypic variation has long stimulated biological thought, yet many outstanding questions remain regarding the ecological and evolutionary mechanisms driving patterns of geographic variation. In my dissertation, I collected data on demographic history, physiological traits contributing to salinity tolerance, and acclimation responses to different salinities to elucidate the mechanisms shaping colonization and adaptive divergence in tidal marsh populations of Savannah Sparrows (Passerculus sandwichensis). Specifically, I addressed two main questions related to adaptive divergence in this species: (1) how …

Conflicting Hydraulic Effects Of Xylem Pit Structure Relate To The Growth-Longevity Tradeoff In A Conifer Species, Beth Roskilly

Graduate Student Theses, Dissertations, & Professional Papers

Consistent with a ubiquitous life history tradeoff, trees exhibit a negative relationship between growth and longevity among and within species. However, the mechanistic basis of this life history tradeoff is not well understood. In addition to tradeoffs among multiple traits based on resource allocation conflicts, life history tradeoffs may arise from tradeoffs based on single traits under opposing selection. While a myriad of factors likely contribute to the growth-longevity tradeoff in trees, we hypothesized that conflicting functional effects of xylem structural traits contribute to the growth-longevity tradeoff. We tested this hypothesis by examining the extent to which xylem morphological traits …

Avian Community Responses To Bison Grazing In North American Intermountain Grasslands, Danielle A. Fagre

Graduate Student Theses, Dissertations, & Professional Papers

Grassland and shrubland songbird species are a guild of conservation concern in North America. Many of these species have experienced severe population declines, due to habitat loss and land use change. This makes the conservation and management of remaining habitat of crucial importance for this guild. Grazing by large herbivores is an ecosystem process in grassland systems, and in North America, one of the major historic grazers was the Plains bison (Bison bison). Bison are considered ecosystem engineers, because they modify habitat to be more or less suitable for other species, such as grassland and shrubland songbirds. Bison …

Life On The Edge: Risk Of Predation Drives Selection Of Habitat And Survival Of Neonates In Endangered Sierra Nevada Bighorn Sheep, Shannon Forshee

Graduate Student Theses, Dissertations, & Professional Papers

Long-term viability of endangered populations requires development of effective management strategies that target the population vital rate with the highest potential to influence population trajectories. When adult survival is high and stable, juvenile recruitment is the vital rate with the greatest potential to improve population trajectories. For my thesis I examined how lactating Sierra Nevada Bighorn sheep (Ovis Canadensis sierra) balance forage and predation risk during the neonatal period. I first identified resource selection strategies employed by lactating females to promote survival of neonates and then determined the primary factors affecting survival of neonates. I found lactating females selected for …

Accommodating Mixed-Severity Fire To Restore And Maintain Ecosystem Integrity With A Focus On The Sierra Nevada Of California, Usa, Dominick A. Dellasala, Richard L. Hutto, Chad T. Hanson, Monica L. Bond, Timothy Ingalsbee, Dennis C. Odion, William L. Baker

Biological Sciences Faculty Publications

Existing fire policy encourages the maintenance of ecosystem integrity in fire management, yet this is difficult to implement on lands managed for competing economic, human safety, and air quality concerns. We discuss a fire management approach in the mid-elevations of the Sierra Nevada, California, USA, that may exemplify similar challenges in other fire-adapted regions of the western USA. We also discuss how managing for pyrodiversity through mixed-severity fires can promote ecosystem integrity in Sierran mixed conifer and ponderosa pine (Pinus ponderosa Laws) forests. To illustrate, we show how coarse-filter (landscape-level) and complementary fine-filter (species-level) approaches can enhance forest management …

Reply To Marques Et Al. (2017): How To Best Handle Potential Detectability Bias, Richard L. Hutto

Biological Sciences Faculty Publications

Marques et al. (2017) write in response to a communications paper in which I (Hutto 2016) question whether a model-based approach is the only way to deal with the detectability problem inherent in bird survey work. The model-based approach to dealing with potential detectability bias is widely viewed as the operational gold standard, and I welcome the comments from experts in this field. The authors did uncover some errors on my part, which I address below, but they also misrepresented my most important points, so I am glad to have the opportunity to respond here. [1st paragraph]

Analysis Of The Caenorhabditis Elegans Innate Immune Response To Coxiella Burnetii, James M. Battisti, Lance A. Watson, Myo T. Naung, Adam M. Drobish, Ekaterina Voronina, Michael F. Minnick

Biological Sciences Faculty Publications

The nematode Caenorhabditis elegans is well established as a system for characterization and discovery of molecular mechanisms mediating microbe-specific inducible innate immune responses to human pathogens. Coxiella burnetii is an obligate intracellular bacterium that causes a flu-like syndrome in humans (Q fever), as well as abortions in domesticated livestock, worldwide. Initially, when wild type C. elegans (N2 strain) was exposed to mCherry-expressing C. burnetii (CCB) a number of overt pathological manifestations resulted, including intestinal distension, deformed anal region and a decreased lifespan. However, nematodes fed autoclave-killed CCB did not exhibit these symptoms. Although vertebrates detect C. burnetii via TLRs, pathologies …

Factors Influencing Mountain Lion Kill Rates Across Three Ecosystems In The Americas, Steven Cross

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Kill rate, defined as the number of prey killed per predator per unit time, is a key component to understanding predator-prey dynamics. A multitude of factors may affect kill rates, including, variation in age, sex, weight, or presence of offspring of either predator or prey species (intraspecific variation) and events such as the theft of a kill made by another animal (kleptoparasitism). These factors may influence the time a predator spends locating prey (search time) and the pursuing, killing, and consumption of prey (handling time). The sum of search time and handling time may be measured as the time between …

Examining Drivers Of Phenotypic Variation In The Perennial Herb Showy Milkweed (Asclepias Speciosa)., Kira I. Sussman

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Many plant species show variation in phenotypic traits, such as traits related to growth and defense against herbivores, across environmental gradients. Differences in phenotypic traits can be due to selection, leading to local adaptation, or due to the random process of genetic drift. To examine the driver of phenotypic variation, I conducted a Qst (a measure of phenotypic variation among populations) vs. Fst (a measure of genetic variation among populations) analysis for 13 populations of A. speciosa grown in a common garden, using five growth and defense traits and seven microsatellite markers. I found relatively low differentiation at the neutral …

Responding To Soil Fungal Communities: A Look At Interactions Between Arbuscular Mycorrhizal Fungi And The Common Yellow Monkeyflower, Mariah Mcintosh

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The obligate fungal mutualists arbuscular mycorrhizal fungi (AMF) colonize the roots approximately 80% of vascular plants, generally thought to provide mineral nutrition, pathogen protection, or drought resistance to plants in exchange for photosynthetic carbon. Because of the ecological and evolutionary significance of these interactions, much work has been done to understand this symbiosis at the community level. However, much remains to be understood about how AMF affect plant fitness on an individual level. In this study, we took advantage of the tractability of the emerging model species Mimulus guttatus, the common yellow monkeyflower, to identify genetic differences in how …

¬Multilocus Phylogeny Of The Lichen Family Megasporaceae, Tim B. Wheeler

Graduate Student Theses, Dissertations, & Professional Papers

The lichen symbiosis is one of the oldest studied mutualisms; in fact, Frank and De Bary coined the term "symbiosis" while studying lichens (Frank, 1877; De Bary 1879). The widespread, stable association between the mycobiont and photobiont in lichens offers an ideal system for the study of co-evolution. The recent application of molecular data to lichens has begun to unveil the complexities involved in these associations (Upreti et al. 2015, Spribille et al. 2016). Lichenized fungi make up a huge fraction of fungal diversity (Nash 2008), yet very little is known of their genetic diversity. Fungal taxonomy is notoriously difficult …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …