Biology Commons^™

Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase, Kohei Homma, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but …

Role Of Vapbc Toxin–Antitoxin Loci In The Thermal Stress Response Of Sulfolobus Solfataricus, Charlotte R. Cooper, Amanda J. Daugherty, Sabrina Tachdjian, Paul H. Blum, Robert M. Kelly

School of Biological Sciences: Faculty Publications

TA (toxin–antitoxin) loci are ubiquitous in prokaryotic microorganisms, including archaea, yet

their physiological function is largely unknown. For example, preliminary reports have suggested

that TA loci are microbial stress-response elements, although it was recently shown that knocking

out all known chromosomally located TA loci in Escherichia coli did not have an impact on

survival under certain types of stress. The hyperthermophilic crenarchaeon Sulfolobus solfataricus

encodes at least 26 vapBC (where vap is virulence-associated protein) family TA loci in its

genome. VapCs are PIN (PilT N-terminus) domain proteins with putative ribonuclease activity,

while VapBs are proteolytically labile proteins, which purportedly function …

Evolution And Pleiotropy Of Trithorax Function In Arabidopsis, Zoya Avramova

School of Biological Sciences: Faculty Publications

The SET domain-containing genes of the TRITHORAX family encode epigenetic factors that maintain the expression of targeted genes. Trithorax homologs have been found in both animals and plants. Since these are thought to have evolved multicellularity independently, common mechanisms of epigenetic regulation must be evolutionarily ancient and derived from a common ancestor. In addition, each lineage has evolved unique mechanisms to expand the original repertoire of epigenetic functions. Phylogenetic analysis of SET domain proteins has outlined some intriguing evolutionary trends. In plants, epigenetic gene silencing mechanisms have been aggressively pursued. In contrast, studies of epigenetic mechanisms maintaining active gene expression …

Interactive Effects Of Time, Co2, N, And Diversity On Total Belowground Carbon Allocation And Ecosystem Carbon Storage In A Grassland Community, E. Carol Adair, Peter B. Reich, Sarah E. Hobbie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Predicting if ecosystems will mitigate or exacerbate rising CO2 requires understanding how elevated CO₂ will interact with coincident changes in diversity and nitrogen (N) availability to affect ecosystem carbon (C) storage. Yet achieving such understanding has been hampered by the difficulty of quantifying belowground C pools and fluxes. Thus, we used mass balance calculations to quantify the effects of diversity, CO₂, and N on both the total amount of C allocated belowground by plants (total belowground C allocation, TBCA) and ecosystem C storage in a periodically burned, 8-year Minnesota grassland biodiversity, CO₂, and N experiment …

Caenorhabditis Elegans Genomic Response To Soil Bacteria Predicts Environment-Specific Genetic Effects On Life History Traits, Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, Bryanua C. Carr, Michael A. Herman

School of Biological Sciences: Faculty Publications

With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential expression is predictive of functional importance has yet to be tested. Here we have addressed this expectation by employing Caenorhabditis elegans as a model for the interaction of native soil nematode taxa and …

The Nuclear Receptor Nhr-25 Cooperates With The Wnt/Β-Catenin Asymmetry Pathway To Control Differentiation Of The T Seam Cell In C. Elegans, Martina Hajduskova, Marek Jindra, Michael A. Herman, Masako Asahina

School of Biological Sciences: Faculty Publications

Asymmetric cell divisions produce new cell types during animal development. Studies in Caenorhabditis elegans have identified major signal-transduction pathways that determine the polarity of cell divisions. How these relatively few conserved pathways interact and what modulates them to ensure the diversity of multiple tissue types is an open question. The Wnt/β-catenin asymmetry pathway governs polarity of the epidermal T seam cell in the C. elegans tail. Here, we show that the asymmetry of T-seam-cell division and morphogenesis of the male sensory rays require NHR-25, an evolutionarily conserved nuclear receptor. NHR-25 ensures the neural fate of the T-seam-cell descendants in cooperation …

Ecological Genomics Of Nematode Community Interactions: Model And Non-Model Approaches, Michael A. Herman, Joseph D. Coolon, Kenneth L. Jones, Timothy Todd

School of Biological Sciences: Faculty Publications

The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to …

Something Old, Something New, Something Borrowed; How The Thermoacidophilic Archaeon Sulfolobus Solfataricus Responds To Oxidative Stress, Walid S. Maaty, Blake Wiedenheft, Pavel Tarlykov, Nathan Schaff, Joshua Heinemann, Jim Robinson-Cox, Jacob Valenzuela, Amanda Dougherty, Paul H. Blum, C. Martin Lawrence, Trevor Douglas, Mark J. Young, Brian Bothner

School of Biological Sciences: Faculty Publications

To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts …

An Introduction To The Biocomplexity Of Sanak Island, Western Gulf Alaska, Hd G. Maschner, M Betts, J Cornell, B Finney, J A. Dunne, Nancy J. Huntly, J W. Jordan, N Misarti, K L. Reedy-Maschner, R Russell

Biology Faculty Publications

The Sanak Biocomplexity Project is a transdisciplinary research effort focused on a small island archipelago 50 km south of the Alaska Peninsula in the western Gulf of Alaska. This team of archaeologists, terrestrial ecologists, social anthropologists, intertidal ecologists, geologists, oceanographers, paleoecologists, and modelers is seeking to understanding the role of the ancient, historic, and modern Aleut in the structure and functioning of local and regional ecosystems. Using techniques ranging from systematic surveys to stable isotope chemistry, long-term shifts in social dynamics and ecosystem structure are present in the context of changing climatic regimes and human impacts. This paper presents a …

Differences In Nitrate Uptakeamong Benthic Algal Assemblages In A Mountain Stream, Michelle A. Baker, G. De Guzman

Biology Faculty Publications

We evaluated how benthic algal assemblages that vary in composition, richness, and other diversity metrics remove NO 3 -N from the water column of a mountain stream. Ecological theory and empirical studies suggest that ecosystem process rates should increase as richness increases because of niche separation or activity of dominant taxa. Accordingly, we predicted that algal assemblages with highest richness would show the highest rates of NO 3 -N uptake. To test this prediction, we transplanted 225 rocks representing 3 patch types (green, yellow, and brown) that differed macroscopically in algal composition from a lake outflow stream to a lake …

The Immature Stages And Natural History Of Veladyris Pardalis (Salvin, 1869) In Eastern Ecuador (Lepidoptera, Nymphalidae, Ithomiinae), H. F. Greeney, Ryan I. Hill, M. R. Hualinga, W. R. Simbana, G. Gentry

College of the Pacific Faculty Articles

We describe the immature stages and oviposition behavior of Veladyris pardalis (Salvin, 1869) from northeastern Ecuador. An unidentified species of Solanum (Solanaceae) is the larval food plant. Eggs are laid singly on leaves, stems or epiphytes growing on the host. Veladyris pardalis has four larval stadia, and takes 64–70 days to mature from oviposition to adult.

Project Medusa In The Context Of Its Historical Time, John H. Costello, Sean Colin, William M. Graham, John O. Dabiri, Adam Benović, Davor Lučić, Vladimir Onofri, Mira Morović, Alenka Malej, Valentina Turk, Vesna Flander-Puterle, Hermes Mianzan, Gustavo Alvarez Colombo, Marcelo E. Acha

Arts & Sciences Faculty Publications

In 2000, the National Science Foundation, in union with Croatian and Slovenian science ministries, provided initial support for the international collaboration that has become Meduza project. The program was started with the goal of international collaboration. Our initial objective was simple - use this international collaboration to develop exiting scientific research involving medusae in Southern Adriatic waters. This international collaborationa has been of great importance personally and professionally to all of the investigators and institutions involved in the project, but we now ask what objective difference has the project made scientifically. We approach this question by comparing what we might …

The Round-Eared Sengi And The Evolution Of Social Monogamy: Factors That Constrain Males To Live With A Single Female, M. Schubert, N. Pillay, David O. Ribble, C. Schradin

Biology Faculty Research

Animal dispersion in space and time results from environmental pressures, and affects the outcome of a species’ social organization. When females are solitary, males may either roam or be pair-living. We studied possible environmental influences affecting the social organization of the round-eared sengi (Macroscelides proboscideus) in a semi-desert in South Africa, using trapping and radio-tracking across 2.5 yr. Adult sex ratios did not deviate from 1:1 and we found no indication of sexual dimorphism in body mass. Females maintained exclusive areas, which had little overlap (

Incidence And Post-Pollination Mechanisms Of Nonrandom Mating In Arabidopsis Thaliana, Ann L. Carlson, Megan Telligman, Rob Swanson

Biology Faculty Publications

Compatible pollinations from many differenttaxa display nonrandom mating. Here we describe a systemfor examining questions of nonrandom mating in Arabidopsisthaliana. Using this system, we demonstrate thatArabidopsis thaliana displays nonrandom mating betweendistinct accessions. Statistical analysis of these data demonstratesaspects of both pollen competition and male–female complementarity in these matings. Cytologicalexperiments implicate pollen germination and pollen tubegrowth rates as possible causal factors in these nonrandommating efficiencies.

Lap3, A Novel Plant Protein Required For Pollen Development, Is Essential For Proper Exine Formation, Anna A. Dobritsa, Shuh-Ichi Nishikawa, Daphne Preuss, Ewa Urbanczyk-Wochniak, Lloyd W. Sumner, Adam Hammond, Ann L. Carlson, Rob Swanson

Biology Faculty Publications

We isolated lap3-1 and lap3-2 mutants in ascreen for pollen that displays abnormal stigma binding.Unlike wild-type pollen, lap3-1 and lap3-2 pollen exine isthinner, weaker, and is missing some connections betweentheir roof-like tectum structures. We describe the mappingand identification of LAP3 as a novel gene that contains arepetitive motif found in b-propeller enzymes. Insertionmutations in LAP3 lead to male sterility. To investigatepossible roles for LAP3 in pollen development, we assayedthe metabolite profile of anther tissues containing developingpollen grains and found that the lap3-2 defect leadsto a broad range of metabolic changes. The largest changeswere seen in levels of a straight-chain hydrocarbon …

Cyp704b1 Is A Long-Chain Fatty Acid V-Hydroxylase Essential For Sporopollenin Synthesis In Pollen Of Arabidopsis, Anna A. Dobritsa, Jay Shrestha, Marc Morant, Franck Pinot, Michiyo Matsuno, Rob Swanson, Birger Lindberg Møller, Daphne Preuss

Biology Faculty Publications

Sporopollenin is the major component of the outer pollen wall (exine). Fatty acid derivatives and phenolics are thought to be itsmonomeric building blocks, but the precise structure, biosynthetic route, and genetics of sporopollenin are poorly understood.Based on a phenotypic mutant screen in Arabidopsis (Arabidopsis thaliana), we identified a cytochrome P450, designatedCYP704B1, as being essential for exine development. CYP704B1 is expressed in the developing anthers. Mutations in CYP704B1result in impaired pollen walls that lack a normal exine layer and exhibit a characteristic striped surface, termed zebraphenotype. Heterologous expression of CYP704B1 in yeast cells demonstrated that it catalyzes v-hydroxylation of long-chainfatty acids, …

Compensatory Evolution Of Gene Regulation In Response To Stress By Escherichia Coli Lacking Rpos, Daniel M. Stoebel, Karsten Hokamp, Michael S. Last, Charles J. Dorman

All HMC Faculty Publications and Research

The RpoS sigma factor protein of Escherichia coli RNA polymerase is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they evolve in an osmotically stressful environment. We found that strains lacking RpoS adapt less variably, in terms of both fitness increase and changes in patterns of transcription, than …

Global Chloroplast Phylogeny And Biogeography Of Bracken (Pteridium: Dennstaedtiaceae), Joshua P. Der, J. A. Thomson, J. K. Stratford, Paul G. Wolf

Biology Faculty Publications

Bracken ferns (genus Pteridium ) represent an ancient species complex with a natural worldwide distribution. Pteridium has historically been treated as comprising a single species, but recent treatments have recognized several related species. Phenotypic plasticity, geographically structured morphological variation, and geographically biased sampling have all contributed to taxonomic confusion in the genus. We sampled bracken specimens worldwide and used variable regions of the chloroplast genome to investigate phylogeography and reticulate evolution within the genus. Our results distinguish two major clades within Pteridium , a primarily northern hemisphere Laurasian/African clade, which includes all taxa currently assigned to P. aquilinum , and …

Ecomorphology Of The Mexican Fence Lizards Of The Sceloporus Formosus Group (Squamata: Phrynosomatidae), Gloria Andrea Acevedo

Biology Theses - Archive

A central belief of ecomorphological studies is the link between morphology and performance, but, surprisingly few analyses demonstrate this relationship. Fence lizards of the genus Sceloporus offer a useful system for addressing correlations between morphology and performance because they possess keratinized and keeled scales, a distinctive morphological character that might influence water balance. A common observation across different taxa of reptiles is that many organisms in dry habitats have few scales on their bodies, compared to organisms inhabiting moist environments. This pattern is also present in fence lizards. I investigated if the number of dorsal and lateral scales varies across …

Analysis Of Novel Regulatory Region And Function Of A Young Drosophila Retrogene: Dntf-2r, Mansi Motiwale Kunte

Biology Dissertations - Archive

Dntf-2r is a young retroposed gene that originated from the nuclear transport gene Dntf-2. Here the function, quality and evolutionary origin of the regulation of this retrogene are explored. In Chapter 1, I introduce the background of what is known of Dntf-2r as well as the function of its parental gene. This includes their evolutionary histories, and known functional and regulatory aspects. Chapter 2 describes my work on the novel regulatory region recruited by the retrogene and I explore the tissue specific expression pattern (i.e. testis expression) driven by this region. In Chapter 3 I set myself up to review …

Thermal Tolerance, Physiologic Condition, And Population Genetics Of Dreissenid Mussels (Dreissena Polymorpha And D. Rostriformis Bugensis) Relative To Their Invasion Of Waters In The Western United States, John T. Morse

Biology Dissertations - Archive

Zebra mussels, Dreissena polymorpha, and quagga mussels, D. rostriformis bugensis, Eurasian freshwater bivalves, invaded the North American (NA) Great Lakes in the mid 1980's. Subsequently, they invaded water bodies east of the Rocky Mountains. Their more recent expansion into warm, isolated, southwestern U.S. water bodies suggests that both species are developing thermally-tolerant physiological races. Chronic upper thermal tolerance limits were determined for D. polymorpha populations from Winfield City Lake (KS) (WCL), Lake Oologah (OK) (OL) and Hedges Lake (NY) (HL), and the D. rostriformis bugensis population from Lake Mead (NV/AZ) (LM). Individuals from WCL had 12-d and 28-d incipient upper …

Sex, War And Disease: The Effects Of Infection On Horn Size And Intra-Sexual Competition In The Broad-Horned Flour Beetle, Gnathocerus Cornutus, Amrita Naidu

Biology Theses - Archive

Sexual selection is widely used to explain the evolution of mating systems where most often it is manifest as the competition among males for access to females. This competition takes the form of direct male-male interactions in broad-horned flour beetle Gnathocerus cornutus and often results in exaggerated male phenotypes. Sexually selected traits are interesting because in many cases their existence appears to contradict natural selection. For example, the "handicap hypothesis" suggests that there may be a trade-off between immune response and horn size because mounting an immune response necessary for survival (natural selection) may divert resources away from growing longer …

Determining The Phylogeographic Dynamics Of The Edge Relationships Between Aphonopelma Hentzi (Girard) And Its Neighbors Along The Colorado River Basin (Araneae, Mygalomorphae, Theraphosidae), Chris A. Hamilton

Biology Theses - Archive

Theraphosids, commonly known as “tarantulas”, are a group of large, hirsute spiders that have drawn relatively little interest in ecological, behavioral, or evolutionary research from biologists. The lack of research on theraphosids is problematic because of conservation concerns for this group and the need to compile good life history data, and determine taxonomic and phylogenetic relationships. I examined the phylogenetic relationships among populations of tarantulas of the genus Aphonopelma along the Colorado River basin in Texas to construct a framework within which to test ecological, evolutionary, and biogeographical hypotheses in an area of species transition and possible Pleistocene refugia. In …

Assessment Of Biology Majors’ Versus Nonmajors’ Views On Evolution, Creationism, And Intelligent Design, Guillermo Paz-Y-Mino C., Avelina Espinosa

Arts & Sciences Faculty Publications

The controversy around evolution, creationism, and intelligent design resides in a historical struggle between scientific knowledge and popular belief. Four hundred seventy-six students (biology majors n=237, nonmajors n=239) at a secular liberal arts private university in Northeastern United States responded to a five-question survey to assess their views about: (1) evolution, creationism, and intelligent design in the science class; (2) students’ attitudes toward evolution; (3) students’ position about the teaching of human evolution; (4) evolution in science exams; and (5) students’ willingness to discuss evolution openly. There were 60.6% of biology majors and 42% of nonmajors supported the exclusive teaching …

The Mckillop Library Waste Stream, Kalyna Macko, Kelsy Patnaude, Other Students

BIO140 Carbon Footprint Project

The McKillop Library's resources come at an environmental cost because more resources are being used than is realized. The focus is on the amount of carbon emissions and waste that is being produced by the library. Carbon emissions are the leading cause of climate change, and through recycling the library can lower the amount of carbon the library is producing. If recycling and re-using materials becames more of a common procedure in library, there is little doubt that it would be more environmentally friendly.

Effects Of Temperature On Reproduction And Survival Of The Calanoid Copepod Pseudodiaptomus Pelagicus, Andrew L. Rhyne, Cortney L. Ohs, Erik Stenn

Arts & Sciences Faculty Publications

Four experiments were conducted on the calanoid copepod, Pseudodiaptomus pelagicus, to determine the effects of temperature (24, 26, 28, 30, 32, and 34 °C) on survival, development time, reproductive output, and population growth in order to define the optimal temperature for culture. The first experiment stocked early stage nauplii into 1 L beakers and cultured them using standard procedures until five days after the first mature adults were observed; from this survival, sex ratio, time to maturation, and fecundity were measured. The second and third experiments evaluated the effects of temperature on nauplii production by stocking individual pairs and …

In Situ Manipulation Of Vertically Migrating Gelatinous Zooplankton Using Nighttime Blue-Water Scuba In The South-Central Adriatic Sea, William M. Graham, John H. Costello, Sean Colin, Alenka Malej, Davor Lučić, Vladimir Onofri, Adam Benović

Arts & Sciences Faculty Publications

Technological advance in undersea exploration (e.g. tethered cameras, remotely operated vehicles [ROVs], Autonomous Underwater Vehicles [AUVsG, and manned submersibles)have opened new windows into diversityand distribution of fragile gelatinous organisms in the vast mesopelagic realm(300 m-1000 m deep). While exstraordinary in expanding our view of its richness, mesopelagic exploration remains largely a "look but don't touch" environment and this limits of our ability to understand these animals through physical manipulation relevant to the finer scales of the individual organism. We have been conducting a series of in situ observations and manipulations using blue-water SCUBA during the night at a 1, 200 …

In Vitro Inhibition By Aerosol-Ot Of Bacillus Anthracis Sterne Endospores, Andrea M. Rendziperis

Senior Honors Theses and Projects

Bacillus anthracis is an endospore-forming, Gram-positive bacterium that is the causative agent of the disease anthrax. The sodium ion surfactant Aerosol-OT (AOT) has been shown to kill some species of Gram-positive bacteria. This study examined the effect of AOT on B. anthracis endospores and vegetative cells, to show any changes in germination and growth that could potentially affect host development of disease. B. anthracis endospores and vegetative cell cultures were exposed to varying levels of AOT and samples were heated to show the proportion of endospores, or washed of the supernatant to show any temporary inhibitory effects on growth. B. …

Species Richness And Host Associations Of Lepidoptera-Attacking Tachinidae In The Northeast Ecuadorian Andes, John O. Stireman Iii, Harold F. Greeney, Lee A. Dyer

Biological Sciences Faculty Publications

Most of the unknown biological diversity of macro-organisms remaining to be discovered and described lies in the tropical regions of the world and consists primarily of insects. Those insects with parasitoid lifestyles constitute a significant portion of insect diversity, yet parasitoids are among the most poorly known of major insect guilds in the humid tropics. Here we describe and analyze the richness of one diverse taxon of parasitoids, flies in the family Tachinidae, reared from Lepidoptera as part of a biological survey of Lepidoptera and their parasitoids in one mid-elevation (2000 m) area in the northeast Ecuadorian Andes. One hundred …

Habitat Variation Among Aquatic Gastropod Assemblages Of Indiana, U.S.A., Mark Pyron, Jayson Beugly, Matthew Spielman, Jennifer Pritchett, Stephen J. Jacquemin

Biological Sciences Faculty Publications

We collected aquatic gastropods at 137 sites in lakes and streams of Indiana and tested for patterns of assemblages with environmental variables. The survey resulted in 32 species with a mean of 2.8 species at each site, and a mean abundance at each site of 144 individuals. Nonmetric multidimensional scaling (NMS) multivariate analyses resulted in watershed drainage area, water conductivity, substrate category frequency, and dissolved oxygen as significant correlates of gastropod assemblage structure. Gastropod assemblages of lakes were not significantly different than assemblages of streams in the ordination. Prosobranch taxa occurred in higher abundances than pulmonate taxa at sites with …