Masters Degree in Integrative Genomics


Alysha Weiler
Medicinal Native American plants within the Black Hills that are effective against microbial agents

I grew up in Sioux Falls, SD, and graduated from the University of Sioux Falls with a Bachelor's in Biology. I never would have imagined myself being a science major growing up. I was interested in writing and the arts. After my first semester in college, I decided to go overseas for a missionary school. I was planning on staying overseas and not going back to college. But after coming back to the States, I realized it would be good to go back to school. I thought a major in biology would help me in the health field if I did go back overseas, and this field was also interesting to me. So I went back to get my degree in biology. It was challenging for me, but it was interesting and I learned a lot.

I applied for the Master of Science degree in Integrative Genomics program because the research project I am working with interested me. My current research involves identifying compounds in medicinal Native American plants within the Black Hills that are effective against microbial agents. The specific microbial agent we are currently working with is Staphylococcus aureus, a common bacteria found in hospitals and the community. The bacterium becomes a problem when it develops resistance to antibiotics used to treat it. One of the well-known resistant types is known as MRSA (methicillin-resistant Staphylococcus aureus). Our research goals are to extract compounds from the medicinal plants that are active against S. aureus, identify them and understand genetic expression within the bacteria that responds to the chemical compound. I know that this research project will expand my understanding and be beneficial in my future.

Jacob D. Alsdurf
Ecological and Genomic Effects of Drought on Black Hills Native Perennial Plants

Overview of Research
The David Siemens Plant Ecological Genetics lab group at Black Hills State University is currently researching a variety of questions concerning range limit development in wild upland perennial plants.  This research may also increase our understanding of the effects of climate change on range distributions. 
We work with a small native mustard species, commonly called “Rock Cress,” whose genome has just been sequenced. The sequenced genome provides a huge advantage when searching for genes that matter.  Much of my work has included conducting growth chamber experiments, where I plant, water, and care for 448 plants simultaneously.  My research for the master’s thesis is on a functional genomic level, where I am asking questions about effects of the parent’s environment on offspring development.  I am using DNA methylation detection techniques to help identify drought response genes and/or gene regions.
In previous lab experiments, we observed that plants whose parents were raised in a drought environment were more drought tolerant.  We believe that this observation could be an epigenetic effect.  Epigenetics includes the inheritance of environmental effects that cause changes in gene expression without changes to the DNA sequence.  
DNA methylation is one of many epigenetic mechanisms that can regulate gene expression trans-generationally.  The assay we used to detect differences in DNA methylation is called a methylation sensitive amplified polymorphism (MSAP or MS-AFLP).  This method generates thousands of DNA fragments.  Consequently, I am also learning about the statistical analysis of huge data sets.  I received funding to attend a statistical genetics workshop this summer at the Fred Hutchinson Cancer Research Center, Seattle, WA.
DNA is composed of varied sequences of only four different molecules called bases.  One of the bases is called cytosine.  The MSAP protocol uses enzymes that are sensitive to methylated cytosine.  The enzymes cut the DNA and produce fragments.  The fragments can be separated electrophoretically, which means that the fragments travel different distances on a gel with an electric current running through it.  The separated DNA fragments can then be excised from gels, amplified, sequenced, and compared to annotated reference sequences.  The Rock Cress is a close wild relative of the model organism for plant molecular biology.  Because their DNA sequences are similar, I will be able to understand the function of genes in the fragments that I sequence.
Thus far, I have extracted DNA from plants in a drought growth chamber experiment, completed the MSAP, and analyzed fragments on a genetic analyzer in BHSU’s DNA core facility.  The data analysis of date has consisted of analyzing the methylation patterns using various statistical methods, including discriminant functional analysis, principal component analysis, and analysis of molecular variance, all of which we do within our lab group.  This fall will involve lab intensive work, involving gel extraction and sequencing of fragments that are differentially methylated, which I believe to be functional drought responsive genes or gene regions. 

My own story is not as exciting as the research I am involved with.  I was raised in Rapid City, SD and have life experiences ranging from cooking in France to being a United States Marine running around the jungles of Okinawa.  My educational background is a B.S. History/English from Minot State University, ND and then after more science training at BHSU, admittance into BHSU’s  Masters of Science in Integrative Genomics program in the fall of 2012.  After graduation I plan to work on a Ph.D. in a related genomics field.  

Brett Montieth

Hello, my name is Brett Montieth. I have attended Black Hills State since the fall of 2007. In the spring of 2012 I graduated with a bachelor’s in Biology and a minor in Chemistry. In the fall of 2012 I was fortunate enough to further my education in the MSIG program. My research includes working with the parasite Plasmodium falciparum or commonly known as malaria. Our team is currently running drug assays on several native South Dakota sages. Our preliminary work shows promising results for anti-malarial activity with several of the crude extracts from these plants. In the near future we would like to do structural determination work to isolate the compound for possible drug trials. 

Jodi L. Massie
Genetic and phenotypic variation of the common garter snake (Thamnophis sirtalis) across South Dakota.

I am interested in studying genetic and phenotypic variation of the common garter snake (Thamnophis sirtalis) across formerly glaciated regions of South Dakota (the Prairie Coteau) and glacial refugia found within the state (the Black Hills).  In addition to this, I am examining phenotypic variation amongst snakes collected within the Prairie Coteau and Black Hills. As part of this project, in late May 2008 we collected 50 gravid T. sirtalis from one den site located at Lake Traverse, South Dakota, within the Prairie Coteau.  These snakes were kept in the Black Hills State University animal care facility until they gave birth to their offspring in late August.  This gave me the opportunity to not only collect genetic and phenotypic data for my thesis, but also to conduct a side project on reproductive effort in this species.

I collected life history data on these snakes and their offspring (n = 1242).  Snout-vent length, weight and sex were recorded for each offspring, and mothers were measured once and weighed several times during their pregnancies and immediately following live birth of the young.  These data will be used in a side project on reproductive effort in South Dakotan common garter snakes wherein I will compare these data with data from previous studies of reproductive effort conducted by others across the range of the species (Gregory 2001).
On each mother and 10 random offspring from each litter, I collected phenotypic data.  I used a technique developed by Westphal (2007) to score two traits, pattern and pigment, of the dorsolateral blotches.  Westphal (2007) has found that color pattern and pigment, as well as population genetics, vary across the range of the species in a pattern that correlates with expansion of the species out of glacial refugia.  Because I have data from females and their offspring, I will also be able to examine heritability of these traits.
Tail tips were also collected from all mothers and 10 random offspring from each litter (the same neonates that were color scored).  They will be used to examine variation in mitochondrial DNA within the Lake Traverse population.  These data will be used as one of my samples from the Prairie Coteau region.
I will be collecting T. sirtalis from the Black Hills next spring and summer.   These snakes will also be phenotypically scored and tail tips taken to examine variation in mitochondrial DNA within Black Hills snakes.  Genetic samples will be compared with samples taken from snakes of the Prairie Coteau.
It is likely that the populations from the Prairie Coteau will more closely resemble populations from post-glacial regions of Manitoba (Westphal 2007) whereas the Black Hills snakes will be more representative of populations found to the west.  

Read an article in the BHSU Campus Currents regarding the garter snakes:  

Pankaj Mehrotra

I am pursuing the biotechnology internship track in the Master’s in Integrative Genomics at BHSU. Molecular Biology and Biotechnology are the two areas of biology that have captured my interest since I began pursuing my undergraduate degree in Applied Zoology with a specialization in Biotechnology. The internship track program includes a modular approach to learning genomic techniques.  My first module included research in the lab of Dr. Garth Spellman, where I learned DNA extraction, quantification of DNA, PCR, PCR purification, Sanger sequencing, and phylogenetic analysis of DNA sequences. Currently, I am conducting research under the supervision of Dr. Cynthia Anderson in the Center for the Conservation of Biological Resources (CCBR). The goal of the project is to assess the efficacy of various silver containing compounds, such as colloidal silver, silver-nitrate and silver-sulfate, against common dermatophytic filamentous fungi and yeasts that can be associated with wound biofilms.  Once the level of susceptibility or resistance is assessed, a genomic approach will be used to study the mode of action of the silver compounds, and/or the mechanism of resistance to silver compounds.

Woody Walstrom
Phylogeography of the white-breasted nuthatch (Sitta carolinensis) in North American pine and oak woodlands:  a multilocus approach.

Pine and oak woodlands are common North American floral communities with distinct regional species composition.  The origination of these distinct communities was the once continentally distributed Tertiary forest.  The orogeny of the late Miocene and Pliocene fragmented the Tertiary forest into separate regional communities. Also, Quaternary glacial cycles further reinforced the isolation and independent evolution of these communities. The fauna that currently live there should reflect the separation of the pine-oak forest and their particular biogeographic histories, if they evolved in situ.  The White-breasted Nuthatch (Sitta carolinensis) is a common resident of these highly disjunct woodlands.  Eight sub-species of White-breasted Nuthatch are described by the AOU, and phenotypic variation of the sub-species is concordant with the boundaries of their respective regional pine-oak communities.  However, only one phylogenetic study has been done showing exactly how the historical fragmentation of these habitats influenced the evolutionary history of the White-breasted nuthatch (Spellman and Klicka 2007). 

According to Spellman and Klicka (2007) the evolution of White-breasted Nuthatch and it’s diversification into disjunct habitats could be explained by three different historical hypotheses: (i) The species evolved in situ. (ii) High rates of migration prevented regional divergence. (iii) A recent expansion occurred and not enough time has allowed for complete lineage sorting.  Spellman and Klicka (2007) presented evidence for four distinct and well-supported clades adhering to their first hypothesis.  However, this data was represented only by one gene, the mitochondrial NADH dehydrogenase subunit 2 (ND2), and this is not sufficient enough to determine accurate species divergence times that are imperative when constructing gene trees (Edwards and Beerli 2000).  Mitochondrial DNA may also be misleading if it was passed recently following a hybridization event, and can be further confounded by its maternal mode of inheritance if males and females have different patterns of dispersal (Freeland 2007).  Lastly, due to its maternal haploid mode of inheritance, mitochondrial DNA has only a quarter the effective population size when compared to nuclear DNA.

Because of this I am studying the North American phylogeography of the white-breasted nuthatch in response to Quaternary climate change using a multilocus approach.  Multilocus data is pertinent when determining the accuracy of gene coalescence and divergence times of populations.  The stochastic variances related to the creation of gene trees can only be reduced by increasing the number of loci sampled as opposed to the number of samples of the same gene.  Previous studies have revealed that the coefficient of variance could be significantly reduced when using ~20 loci (Carling and Brumfield 2007).  I plan to use sequence data from 41 independent loci that includes 1 mitochondrial gene, 20 known single copy nuclear loci, and 20 anonymous loci. The multilocus approach will re-examine the hypotheses put forth by Spellman and Klicka (2007), thus gaining a better interpretation of the evolution of the white-breasted nuthatch in concert with the historical Quaternary dynamics of the North American pine-oak woodlands.