CCBR Research

Current Research:

Characterization of PRNP in Carnivora

Population Structure of Western Tanager

Invasive plant genetics

Population genetics of the Finescale Dace

Sequencing of Calcareous Mats in Spearfish Creek

Hybridization of Grosbeaks in South Dakota

Bison Purity testing

Phylogeography of the Bushtit

Population Genetics of the Smooth Green Snake

Genetic structure of the American Dipper

Avian malarial parasites

Undergraduate Research

K. Jasper, and J. Miller (mentor: Anderson, C.M.)
A Baseline Survey of the Eukaryotic Microbial Diversity of the Sanford Underground Science and Engineering Laboratory (SUSEL) at Homestake

Project Summary: A metagenomic approach was used to obtain a preliminary assessment of the eukaryotic diversity (Fungi and Protista) of the upper levels of the SUSEL. DNA sequence data were compared to sequences in GenBank in order to identify the organisms within the samples. Some of the samples appear to be unique, classifying to either protist or fungi. A number of the sequences classify to fungi or protista that are commonly found in terrestrial ecosystems and waters. This is likely the result of introduction of microbes to the subsurface both during mining operations, and during the re-entry process itself. Further analysis of deeper, pristine regions of the SUSEL will provide new knowledge of the diversity of the eukaryotic microorganisms capable of surviving in the deep subsurface. Likewise, research into the eukaryotic diversity of the SUSEL will lead to an understanding of how introduced surface dwelling microbes evolve to adapt to life in the subsurface, and how their introduction affects endemic subsurface microbial populations.

Polly Hall, Sheridan, Wyo. (mentor: Anderson, C.M.)
Assessment of effects of Silver-containing compounds on the growth of dermatophylic fungi

Polly Hall

Project Summary: The effectiveness of silver compounds and colloidal silver in the control of fungi that can infect wounds, or cause atopic dermatitis or yeast infections is not entirely clear, yet the homeopathic community touts it as effective.  Polly is studying the sensitivity of dermatophytic fungi and yeast to silver compounds to assess their level of susceptibility.  Once the level of resistance is determined, Polly and the research team led by Dr. Cynthia Anderson will use genomic techniques to elucidate silver's mode of action, or the mechanism of resistance to silver in fungi.

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Laura Kramer
The evolution of avian reproductive proteins: A Comparative Phylogenetic Study

Project Summary: Recent studies in avian speciation have focused on the ZP family of genes, which code for the proteins that make up the membrane of the egg envelope. These proteins show a great deal of homology with mammalian (even human) reproductive proteins and are important in sperm/egg recognition. Thus, many studies of reproductive incompatibility across a broad spectrum of vertebrates have focused on studying variation in these genes. In this study, I will study one of the eight ZP genes identified from the chicken (Gallus gallus) genome. The ZP3 protein is important in egg/sperm binding and recognition. I will sequence the ZP3 gene in several avian species representing many bird families and study these sequences in a comparative phylogenetic framework which will aid in the understanding of how the genes and proteins of avian egg envelope have evolved, and assist in answering questions regarding the evolution of some of the largest cells on Earth and the evolution of reproductive incompatibility (speciation). The techniques used in this study can be applied to understanding how homologous genes evolve in humans at a genomic level.

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Jess Moser, Andrew Elk Shoulder, and Ronald Scott
Comparative Phylogeography of Pine-oak Birds

Project Summary: Since the Modern Synthesis, evolutionary biologists have postulated that the climatic oscillations of the Quaternary promoted speciation in temperate zone organisms. Models of climate-driven allopatric speciation were developed for many groups of temperate organisms, but in no group was an explicit speciation model developed with more detail than in North American birds. During this period, the prevailing paradigm for speciation in North American birds led researchers to suggest that the advancing glaciers of the Quaternary fragmented widespread ancestral species, forming sister species pairs represented today by eastern and western forms. Over the last decade, this paradigm has become the topic of a focused debate. A majority of contemporary studies have used mitochondrial DNA sequences and molecular dating techniques to discern whether divergence times for putative sister taxa are correlated with the timing of Pleistocene glacial advances. Although, these studies contributed considerably to our understanding of North American avian diversity and they continue to incite debate, a comprehensive overview of how temperate zone birds were impacted by Pleistocene events remains elusive. It is now well understood that the single locus (mtDNA) approach used in these earlier works is not sufficient to accurately determine species divergence times, or to describe in detail the demographic events accompanying speciation. A synthesis of both the temporal and spatial aspects of diversification is required in order to fully understand the effect of environmental changes on the birds of North America. We are examining both the temporal and spatial aspects of North American avian diversification in relation to Quaternary environmental change through a multilocus comparative phylogeographic study of co-distributed pine and oak woodland birds.

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Mark Mazza (mentor: Shane K. Sarver)
Geographic variation in genetic resistance to chronic wasting disease in deer in South Dakota

mark mazza research at CCBR

Chronic Wasting Disease (CWD) is a transmissible neurological disease of deer and elk. It is characterized by loss of body condition, behavioral abnormalities and death. CWD is a transmissible spongiform encephalopathy (TSE), and is the same disease as mad cow disease in cattle and scrapie in sheep. The disease has been linked to the prion protein (PrP) encoded by a single (PRNP) gene. In deer and elk the disease can be genetic as well as transmissible. Specific genetic polymorphisms in the PRNP gene have been linked to susceptibility or resistance to chronic wasting disease. In this study we using DNA sequencing to analyze deer samples collected from various locations in South Dakota to determine if geographic patterns of susceptibility or resistance might exist in South Dakota.

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Jay Jacobs, Deadwood, SD
Screening traditional Native American medicinal plants for compounds with biological activity
jay jacobs research at CCBR
Introduction: Plant natural products have long served as a rich source for medicines, e.g. aspirin, paclitaxel and digoxin, just to mention a few. Natural products have also provided leads for new drugs, ultimately requiring structural modification by synthetic chemists to address pharmacodynamic and pharmacokinetic properties before being developed. Many examples of plants serving as leads also exist: physostigmine the lead for rivastigmine which is used treat Alzheimer’s Disease and ∆9-tetrahydrocannabinol the lead for nabilone used to treat nausea from chemotherapy. Discovering a molecule with biological activity is an extremely difficult endeavor, however often a biologically active molecule is identified it may be found to bind to more than one target (i.e. receptor or enzyme) and elicit more than one response. For example, aspirin has a number of biological effects; anti-inflammatory, inhibits platelet aggregation, analgesic and antipyretic. Aspirin has been shown to inhibit the enzyme cyclooxygenase-2 which is the key enzyme in the production of prostaglandins, e.g. PGE2 and thromboxane A2 which accounts for the anti-inflammatory and the thrombus prevention properties but not the analgesic effect and antipyretic effects. Research on the analgesic properties is pointing to the inhibition of the vanilloid receptor, VR1. The antipyretic effect continues to be investigated but appears to be related to the ability of aspirin to prevent oxygen radical formation which is involved in the induction of fever. Thus, aspirin has multiple effects as a result of interactions with multiple target sites. Since often times molecules with biological activity will have more than one biological target, we are investigating whether diseases we face today could in fact be treated by natural products used by Native Americans. Our aim is to test the plants that Native Americans use as medicines as our leads and initially investigate the antimicrobial activity through an interdisciplinary collaboration at BHSU involving Biology, Native American Studies, and Chemistry. This phase involves the selection and collection of plant samples as well as refining an extraction and screening process to effectively identify plants with anti-bacterial properties. Once identified, the specific plant or extract may be purified by chromatography and undergo more extensive screening and analysis in a separate phase of this project.

Recent Publications

  • Miller, J., Anderson, C.M., and S.K. Sarver. 2009. Micro-satellite development and characterization in finescale dace (Phoxinus meogaeus) and inter-specific amplification in northern redbelly dace (Phoxinus eos). (in press, Molecular Ecology Resources).
  • Andrzej Maj, Garth M. Spellman and Shane K. Sarver. 2008. The Complete CDS of the Prion Protein (PRNP) Gene of African Lion (Panthera leo) (Virus Genes 36(2):433-434).
  • Sarver, S.K., Anderson, C.M., Cain, F.H., and B. Smith. Development of polymorphic micro-satellite markers for the smooth green snake (Opheodrys vernalis). (submitted, Molecular Ecology Notes)
  • Anderson, C.M., Spellman, G., Ferrell, C.S., and S.K. Sarver. 2008. Conservation genetics of American Dipper (Cinclus mexicanus): the genetic status of a population in severe decline. (Conservation Genetics 9:939-944)
  • Anderson, C.M. and S.K. Sarver. 2008. Development of polymorphic microsatellite loci for the endangered Topeka shiner, Notropis topeka. (Molecular Ecology Notes 8(2):311-313)
  • Anderson, C.M., Berger, T., Cain, F and S.K. Sarver. 2006. Detection of bison/cattle hybridization in Custer State Park breeding bulls using microsatellite and mitochondrial DNA markers: tools for conservation and management. (Proceedings of the South Dakota Academy of Science 85:119-127)
  • J. Klicka, K. Burns, and G.M. Spellman.  In Press.  Defining a monophyletic Cardinalini: A molecular perspective. (Molecular Phylogenetics and Evolution).
  • G.M. Spellman and J. Klicka.  2007. Phylogeography of the White-breasted Nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands. (Molecular Ecology 16:1729-1740).
  • G.M. Spellman, B. Riddle, and J. Klicka.  2007. Phylogeography of the Mountain Chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change.  (Molecular Ecology 16:1055-1068).
  • J.M. DaCosta, G.M. Spellman, and J Klicka. 2007. Bilateral Gynandromorphy in a White-ruffed Manakin (Corapipo altera). (The Wilson Journal of Ornithology 119:290-292).
  • J. Klicka and G. M. Spellman.  2007.  A molecular phylogenetic evaluation of the North American "grassland" sparrow clade.  (The AUK 124:537-551).