Summer Undergraduate Research Program (SURP)
Summer Undergraduate Research Program (SURP) is a competitive program with applications due in the Fall. SURP students are paid to do research during the summer ($3000/10 weeks). If selected, you must sign up for Readings (BIOL 3185, with your faculty mentor) in the Spring to help prepare you, then work full time during the summer in the lab/field. All Biology summer research students present their research in poster form at a formal science symposium at the end of the summer. The following Fall, you sign up for both UG research (for 3 credits) and UG Research Seminar (BIOL 3189), where you will give an oral presentation of your work. There is no summer tuition charged for this program (the credits are awarded in the Fall).
• 2014 SURP
Cell Cycle Distribution of HepG2 Cells Exposed to Atrazine Metabolites DEA and DIA
Kavita Dhanwada, Ph.D., Department of Biology
Atrazine is one of the most commonly used herbicides in the United States, however, altered health effects have been seen in non-target organisms with decreases in cell growth and development. The herbicide produces two primary metabolites: Deethylatrazine (DEA) and Deisopropylatrazine (DIA). As there is not much information on cellular effects of DEA and DIA, this study used immortalized HepG2 cells to determine if there were any alterations in cell cycle distribution. Flow cytometry results showed cells exposed to 500 parts per billion (ppb) DIA had significantly fewer cells in S phase compared to untreated controls. Additionally, it was found there were fewer cells in the G2/M phase after 72 hours of exposure to 500 and 750 ppb DEA compared to control cells. This study demonstrated that exposure to the atrazine metabolites, DIA and DEA, can affect the distribution of cells in the cell cycle. Funding for this project was supported in part by the National Science Foundation Grant Number EPSC-1101284 and the McNair Scholars Program.
Who's your Crawdaddy? Genetic Identification of Crayfish Species of the Cedar River Basin.
Carl Thurman, Ph.D., Department of Biology
Peter Berendzen, Ph.D., Department of Biology
While there are over 350 species of crayfish in North America, the rusty crayfish, Orconectes rusticus, poses a threat to native species of crayfish, aquatic plant abundance, and fish populations. It continues to invade non-native environments, including much of Iowa, Minnesota, Wisconsin, Michigan, and Illinois. Identification of the rusty crayfish is important in documenting the distribution of this species, along with possible displacement of native species of crayfish such as the golden crayfish, Orconectes luteus, and the virile crayfish, Orconectes virilis. Crayfish are usually identified based on morphological characteristics such as coloration, carapace measurements, dactylus/propodus length ratios, etc. However, many crayfish are morphologically similar, making identification difficult and sometimes erroneous. Therefore, identification based on genetic relationships could aid in accurately identifying crayfish species, especially the rusty crayfish. In our study, we sampled 51 sites along the Cedar River and several of its tributaries using wire mesh traps. The 528 base pair region of the mitochondrial 16s ribosomal RNA gene (16s-mt DNA) was examined using the primers 16s-1472 and 16s-17sub. Genomic DNA was extracted from frozen (-80ºC) claw muscle of each crayfish using cetrimonium bromide (CTAB) buffer extraction protocol. This extract was purified, then amplified using standard PCR procedure, and sequenced. After creating a phylogenetic tree from individual crayfish DNA sequences and comparing them with previously published data, the results indicated that all crayfish species from the Cedar River Basin are monophyletic, including the rusty crayfish. These results suggest that genetic and morphological identification are mutually supportive and that the 16s-mt gene can be used to accurately identify crayfish. This project was funded, in part, by the Iowa Department of Natural Resources.
The Significance of a Significant P-Value: Does Sample Size Change P-Value Interpretation?
Kenneth Elgersma, Ph.D., Department of Biology
The p-value is a popular tool used by many for statistical decision-making. However, the complexity of the p-value is often underestimated causing people to misinterpret p-values as the probability that the null hypothesis is true. The absurdity of this misinterpretation is highlighted by Lindley's Paradox, a phenomenon that occurs when a significant p-value provides more support for the null hypothesis than the alternative. We randomly sampled p-values published in well-known ecological journals from the last 35 years to estimate how often Lindley's Paradox occurred in the published literature. We also aimed to see how sample size affected the occurrence of Lindley's Paradox and variability of p-values. To discover if the collected p-values exhibited the paradox, computer simulations were used to convert published p-values into posterior probabilities assuming that scientists tested true null hypotheses either: 50% of the time, or 5% of the time. The resulting posterior probabilities are the probability that the null is true based on the observed data. The results showed that when scientists test true hypotheses 50% of the time, Lindley's paradox occurred in 2% of the published values. However, when scientists tested hypotheses that were true 5% of the time, no instances of Lindley's paradox occurred. The distribution of effect sizes observed in the literature showed that approximately 5% of null hypotheses that scientists were testing were true. Additionally, results demonstrate that larger sample sizes and/or high significant p-values (near 0.05) were often present where the paradox did occur. Along with this, a significant 2.3 fold increase in sample size occurred over the 35-year timespan sampled, which also resulted in an increased variance of the p-values. These results suggest that scientists are doing experiments where they are fairly certain of the outcome. They also suggest that the sample size is increasing over time, which in the future could lead to an increase in cases of Lindley's Paradox. This research supported by a 2013-2014 Capacity Building grant from the Office of the Vice President and Provost for a Student-Faculty Collaboration and funds from the Office of the President.
The effectiveness of mowing, burning, and herbicide application on managing invasive cattail growth and spread.
Kenneth Elgersma, Ph.D., Department of Biology
Typha x glauca, a cattail formed through hybridization of a North American and a European species, is thought to be a superior competitor for nitrogen. Due to this, it often dominates nutrient-enriched wetlands. We investigated the most effective means to control T. x glauca, either by burning, mowing, or herbicide application. We grew plants in pots in a greenhouse along a nitrogen gradient. Three separate control dates were set up over the course of the summer, and on each date, a cohort of plants was burned, cut, or sprayed with herbicide. Preliminary results show that herbicide application, burning, and cutting killed 100%, 75%, and 13% of the plants, respectively. Additionally, out of the plants that survived, the mean aboveground biomass 4 weeks after treatment from burning or mowing was 0.9g, and 1.9g, respectively, compared to 8.0g for untreated control plants. Ongoing computer simulation modeling studies are being conducted to confirm effectiveness of these treatments over decadal timescales.
Plant Nitrogen Use in Bioenergy Feedstocks.
Mark Sherrard, Ph.D., Department of Biology
Increasing global energy demand and decreasing fossil fuel reserves have created the need for renewable sources of energy. Diverse perennial vegetation could be an ideal biomass crop in Iowa because they contain legumes which reduce the need for costly fertilizer inputs. In this study, we tested whether switchgrass plants grown in low-diversity mixtures show evidence of nitrogen depletion relative to switchgrass plants grown in high-diversity bioenergy feedstocks. We systematically selected 200 switchgrass plants in four diversity treatments: 1 species – a switchgrass monoculture, 5 species – a warm season grass mix, 16 species – a grass, forb, and legume mix, and 32 species – a grass, forb, legume, and sedge mix. We measured 4 traits associated with plant nitrogen content: chlorophyll concentration, leaf florescence (FvFm), photosynthetic rate, and leaf tissue nitrogen and one trait associated with growth rate (specific leaf area). Preliminary results show that plants have higher chlorophyll concentration, FvFm, and photosynthetic rate in high-diversity mixtures than the 5 warm season grass mixes but not the switchgrass monocultures. Our results suggest that nitrogen depletion is greater in the 5 warm season grass mix than the other three treatments. Previous studies have shown that big bluestem, little bluestem, and indiangrass have faster nitrogen uptake than switchgrass which could account for these patterns. This project funded, in part, by EPSCOR. In addition, MS received a pre-tenure fellowship from the Graduate College during this project."
Effect of Cp2Ru2(bipy)2(DMSO)2 on Growth of Human Liver Cells.
Martin Chin, Ph.D., Department of Chemistry & Biochemistry
Kavita R. Dhanwada Ph.D. Department of Biology
Ruthenium compounds have shown potential to be used as a substitute for platinum-based compounds in chemotherapy. Cisplatin, a chemotherapy drug, can have harsh side effects and primary or required resistance. The objective of this study was to determine how a compound we developed, Cp2Ru2(bipy)2(DMSO)2, affected human liver cells (HepG2). The compound was added to HepG2 cells for 24, 48 and 72 hours in concentrations ranging from 5-100 uM. A MTT cell proliferation assay was performed. The results showed that 5 uM Cp2Ru2(bipy)2(DMSO)2 produced a significant decrease in cell growth after 24 and 72 hours while 10 uM was needed for 48 hours. A tumorigenic pancreatic cell line (AsPC-1) was also used and 10 uM of the compound for 72 hours was needed for a significant decrease in cell growth. The findings suggest that Cp2Ru2(bipy)2(DMSO)2 works well at low concentrations, and that it works better at lower concentrations when compared to cisplatin. Funding for this project was supported, in part, by the Dr. Robert and Brenda Good Undergraduate Research Fellowship in Biology.
Analysis of Archaea that Inhabit Soil Particles of Varying Size.
Alex P. Meirick
Marek K. Sliwinski, Ph.D., Department of Biology
Of all life on the planet, Archaea is the least understood yet it is the most ecologically diverse of the three domains. Although they are thought to be important in the global nitrogen and carbon cycles, only a handful of representative species have been cultured in a lab setting. Our goal for this study was to determine whether the Archaea adhering to large soil particles differ from Archaea that are free living or attached to small soil particles. To do this, three samples were taken at two different locations, these were then fractionated resulting in 12 total samples to be further tested. DNA samples were taken from each sample using the MoBio PowerSoil DNA extraction kit, their DNA was then amplified using the polymerase chain reaction (PCR) and visualized using agarose gel electrophoresis. To test which species of Archaea were present in each soil sample, PCR reactions were processed for 1-dimensional terminal restriction fragment length – single stranded conformational polymorphism profiling (1-D TRFLP-SSCP). This test showed that soil sites and soil fractions contain different archaeal phylotypes using 1-D TRFLP-SSCP profiling. One phylotype was reproducibly more abundant at site 2, indicating a difference between the archaeal communities inhabiting the sites, and a different phylotype was more abundant in the pellet fraction indicating at least one archaeal species in Iowa is attached to the larger soil particles in this fraction.
Ground Arthropod Abundance in Switchgrass and Diverse Prairie Agroenergy Crops.
Mark Myers, Ph.D., Department of Biology
Ground arthropods are the most taxonomically and ecologically diverse group of organisms in terrestrial ecosystems and are known to respond rapidly to environmental change. We studied ground arthropod communities in experimental plantings of tallgrass prairie species of varying plant species richness. In 2009, the University of Northern Iowa's Tallgrass Prairie Center converted corn and soybean fields in the Cedar River Natural Resource Area to four mixes of native perennial tallgrass prairie plants. Research plots were randomly seeded with one of four vegetation treatments including a Switchgrass monoculture and a 32-species Prairie Mix. We studied ground arthropod abundance in Switchgrass and the Prairie Mix at various distances from the nearest woody edge using pitfall traps in July 2014. We hypothesized that ground arthropod abundance would be greater in traps set closer to a woody edge and that the Prairie Mix would support greater numbers of ground arthropods than Switchgrass. Arachnid captures were greater nearer to a woody edge, but catch rates of other arthropods studied did not vary with distance from a wooded habitat. Contrary to our expectation, ground arthropod abundance was similar in monoculture and diverse perennial prairie plant communities after 5 years of management. We are currently identifying ground arthropod specimens and plan to test for differences in ground arthropod assemblage composition among habitat types in the future.
Grassland Bird Nest Survival in Perennial Agroenergy Crops.
Mark Myers, Ph.D., Department of Biology
The demand for alternative fuel sources has dramatically increased the planting of monoculture crops such as corn and soybeans for ethanol production. Consequently, native prairie habitats are disappearing, leading to dramatic declines in native grassland bird populations. Current monoculture crops provide minimal nest habitat for grassland birds. The University of Northern Iowa's Tallgrass Prairie Center is growing alternative perennial prairie crops which can be harvested for agroenergy production while also providing nesting habitat for grassland birds. We studied bird nest survival in four perennial agroenergy crops: 1) Switchgrass, 2) Grasses (5 warm-season grass species), 3) Biomass (16 species of grasses and forbs), or 4) Prairie (32 species of graminoids and forbs) replicated on three soil types at an experimental site in Black Hawk County, Iowa. We found and monitored 97 bird nests every 3-4 days until the nest failed or nestlings fledged. We calculated Mayfield nest survival estimates and developed logistic exposure models in R using a stepwise process to assess the effects of nest age, calendar date, year, and soil and crop type on the survival of all nests (N = 97) and Dickcissel (Spiza americana, N = 61) nests. Among the set of candidate models, we determined the best fitting models using an information theoretic approach. We used all models carrying weight to calculate model-averaged parameter estimates for the year, crop, and soil type variables. We hypothesized that nest success would be higher in the more diverse Biomass and Prairie plots than in low-diversity Switchgrass and Grasses. Mayfield and logistic exposure estimates of nest success were 34.8% and 27.6% respectively for all nests, and 37.7% and 26.2% for Dickcissel. Generally, temporal effects (nest age, calendar date, and year) most strongly influenced nest success, and the effects of soil type were greater than those attributed to crop type. For all nests, nests on clay loam were 197% more likely to survive than nests on sandy loam, and nests in Biomass16 were 156% more likely to survive than nests in Grasses. Birds successfully nested in all four agroenergy crops, and site-wide nest success rates were similar to those reported for other grassland habitats in the region. Our findings suggests that implementing perennial prairie crops for use in agroenergy production would provide nesting habitat for grassland birds, and that temporal and soil type effects are likely to more strongly influence nest survival rates than the crop seed mix selected.
Analysis of Protein Expression as Potential Biomarkers in Human Pancreatic Tumor Cell Lines.
Jade A. Simpson,
Nalin Goonesekere, Ph.D., Department of Chemistry & Biochemistry
Kavita R. Dhanwada, Ph.D., Department of Biology
Pancreatic cancer (PC) is an aggressive cancer with many types having extremely low survival rates. It can be quite lethal because of its asymptomatic early stages. Thus, research is focused on finding potential biomarkers in tumor cell lines to help in earlier diagnosis of this disease leading to better treatment options. Based on previous work that suggested four cancer genes as potential biomarkers, we wanted to determine if the protein expression level of these genes was altered in a variety of human pancreatic tumor cell lines. Protein isolation and quantification followed by Western blot analysis was used. In this early stage of this study, no target bands have been visualized and we are still optimizing the protocol to make any conclusions with regard to alteration in protein levels. Our future work will be to find primary antibodies that better recognize target proteins to determine if these proteins can act as potential pancreatic cancer biomarkers. Funding for this project was provided, in part, by the National Science Foundation Grant Number EPSC-1101284.
Do Crayfish from the Same Location have Identical Patterns of Daily Activity?
Peter Berendzen, Ph.D., Department of Biology
Carl Thurman, Ph.D., Department of Biology
Circadian rhythms are essential for survival and existence. All aspects of life are regulated by biological clocks and the rhythms that they produce. In any habitat, resources are partitioned among species in a community based on the available spatial and temporal spectrum. Locomotor rhythms were studied in two sympatric species of crayfish, Orconectes immunis and Orconectes luteus, to compare the properties of their biological clocks. The crayfish were individually isolated under either constant illumination (LL) or 24-hr light-dark cycles (LD) where their movements were recorded over several days. As in nature, both species were nocturnal in the laboratory with peaks of activity during the dark. However, O. luteus expressed greater activity levels than O. immunis during the light phase. Both displayed a free running circadian rhythm under constant illumination. Consequently, patterns of daily locomotor activity in the crayfish are regulated by an underlying biological clock. In conclusion, the two species of Orconectes appear to partition the same habitat, in part, based on their different patterns of daily activity. This project was funded, in part, by the Iowa Department of Natural Resources.
Graded Response of Dorsal Root Ganglion Neurons to Increasing Concentrations of Folic Acid.
Darrell Wiens, Ph.D., Department of Biology
Folic acid (FA, folate, a water-soluble vitamin B9) is essential for DNA synthesis, repair, and methylation. Although well known that it is needed for neural development, recent studies suggest a possible link between excess maternal FA intake and incidence of autism spectrum disorder. This, together with brain imaging studies has led to a hypothesis of brain developmental underconnectivity as a contributing cause of autism. Insufficient FA early in brain development can lead to failure of neural tube closure, leading to spina bifida and anencephaly. However, the consequences of too much FA intake have not been fully investigated. Previously we observed a significant inhibition of the development of neural connectivity in cultured chick embryo dorsal root ganglia (DRGs) using 5 micromolar (μM) FA. Normal plasma FA averages 11 nanomolar, however it can vary greatly with diet. To study the effect of FA on developing neurons, DRGs were excised from the lumbosacral region of eight day old chick embryos, as they are about to extend nerve processes (neurites) led by growth cones to make contact with target tissues. DRGs were then cultured for 36 hours, fixed, and immunostained to reveal synaptic vesicles. We found a dose-response relationship with significant reduction in neurite length with increasing FA concentrations from 0.25 to 20μM. The average total of antibody-positive synaptic areas surrounding each cultured DRG was significantly reduced in FA-treated DRG explants as well. Our results show that FA exceeding 250 nanomolar reduces neurite extension and synapse formation in a dose-dependent manner during neurogenesis. Preliminary data shows that folinic acid, a coenzyme form of folate, bypasses the FA inhibition, rescuing the neurogenic activity of cultured DRGs. Plans are underway to investigate the effect of FA on the NMDA receptor. Such a rescue would demonstrate that FA competes for binding this receptor. This research project was supported by the Myrna & Gary Floyd Undergraduate Research Fellowship for the summer of 2014.
Valproic Acid Enhances Embryonic Neural Development.
Darrell Wiens, Ph.D., Department of Biology
Valproic acid (VPA) is a valuable drug used in the treatment of epilepsy and a number of other disorders, but evidence suggests that in-utero exposure may cause Autism Spectrum Disorder (ASD). It is hypothesized that VPA may cause ASD by increasing production of Brain-Derived Neurotropic Factor (BDNF), resulting in neural overgrowth and hyperconnectivity in certain regions of the brain. To test this hypothesis, buds of developing neural tissue known as Dorsal Root Ganglia (DRGs) from 8-day-old chicken embryos were explanted to medium containing either 0.2 millimolar (mM) VPA, 2 mM VPA, or 0 mM VPA (control). Explants were incubated for approximately 36 hours before attached DRGs were fixed in cold DMSO/methanol and immunostained with monoclonal antibody SV2 (Developmental Studies Hybridoma Bank, Iowa City, Iowa) to highlight synaptic areas. Microscopic photos were taken and images were analyzed for neurite length and number, as well as for the total stained synaptic area per DRG. Results show that the lengths and numbers of neurites increased when DRGs were treated with VPA; however, synaptic area did not increase in response to VPA treatment.