Arkansas INBRE 2011 Conference


2011 Presentation Awards

Biological Sciences

1st place oral  Destiny Davis, University of Central Arkansas (B20)
2nd place oral Daniel Meeker, Harding University (B28)

1st place posterMikki Gaines, Ouachita Baptist University (B23)
2nd place poster Brady Spencer, Harding University (B36)
3rd place posterLynn Nguyen, University of Central Arkansas (B46)

Chemistry and Biochemistry

1st place oral Jessica Hartman, University of Arkansas at Little Rock (C4)
2nd place oral Anneli Hoggard, Missouri State University (C28)

1st place poster Marc-Andre LeBlanc, Lyon College (C19)
2nd place poster Kenichiro Saito, Arkansas State University (C18)
3rd place poster (tie) Tanner Simon, Ouachita Baptist University (C24)
3rd place poster (tie) Katherine Dockter, Southern Arkansas University (C14)


1st place oral Thomas Rembert, University of Arkansas (P18)
2nd place oral James Hansen, Missouri State University (P25)

1st place poster Niravkumar Patel and Kristopher Watson, University of Central Arkansas (P22)
2nd place poster William Lewis, University of Arkansas (P11)
3rd place posterJeremy Dunklin, Southern Arkansas University (P10)

Only posters with undergraduate participation and where the presenter is an undergraduate, qualified for the awards. Students who did not receive an award for the oral presentation but presented a poster were considered in the poster competition.

At least two judges selected from various institutions judged each presentation. No judge evaluated an oral presentation or poster from his/her institution.

2011 Speaker Information

Keith A. Baggerly
Department of bioinformatics and computational biology
Division of Quantitative Sciences
MD Anderson Cancer Center
The University of Texas

“The Importance of Reproducibility in High-Throughput Studies: Case Studies in Forensic Bioinformatics”

Abstract: Modern high-throughput biological assays let us ask detailed questions about how diseases operate, and promise to let us personalize therapy. Careful data processing is essential, because our intuition about what the answers “should” look like is very poor when we have to juggle thousands of things at once. Unfortunately, documentation of precisely what was done is often lacking. When such documentation is absent, we must apply “forensic bioinformatics” to infer from the raw data and reported results what the methods must have been. The issues are basic, but the implications are far from trivial.

We examine several related papers purporting to use microarray-based signatures of drug sensitivity derived from cell lines to predict patient response. Patients in clinical trials were allocated to treatment arms on the basis of these results. However, we show in several case studies that the results incorporate several simple errors that may put patients at risk. One theme that emerges is that the most common errors are simple (e.g., row or column offsets); conversely, it is our experience that the most simple errors are common. We briefly discuss steps we are taking to avoid such errors in our own investigations, and discuss reproducible research efforts more broadly.

These issues have recently led to the formation of an Institute of Medicine Review of the use of Omics-Based Signatures to Predict Patient Outcomes. Some of the issues raised and topics of debate will also be addressed.

Baggerly is best known as a practitioner of “forensic bioinformatics,” where raw data and reported results are used to reconstruct what the methods must have been. His research interest involve the analysis of high-throughput biological data, and centers on themes of experimental design and reproducible research.

Faculty Talks

The invited faculty talks in physics, biology and chemistry will take place Friday afternoon at the auditorium at the Continuing Education Building (CTED 204).

The talks are open to the public and do not require registration.

Physics – Salvador Barraza-Lopez
Assistant Professor of Physics
Physics department, University of Arkansas

“Waking up to Your Senses: Ion and Molecular Sensing with Carbon-Based Materials”

Abstract: In this talk I will describe the physics behind sensing devices involving novel carbon materials such as carbon nanotubes and graphene. The underlying idea is that those materials have an extremely large area-to-volume ratio. As a result of this, ions or molecules in close proximity can in principle modify the electronic properties of these materials. The change in these properties can be measured by changes in the resistance of two-terminal junctions.

My research is related to the quantum transport of charges in novel materials. This research involves the development of computational tools for this purpose. I have worked in problems related to the adsorption of carbon nanotubes and graphene in technologically-relevant semiconductors, and more recently into understanding the signatures that metal contacts imprint into the resistance of two-terminal graphene junctions.

Barraza is a new faculty member at the University of Arkansas, begining fall 2011.

Biology – Richard C. Murray
Associate Professor of Biology
Chair, biochemistry and molecular biology program
Hendrix College

Murray Website

“The Role of Neurogenin1 in Neural Fate Determination in the Mouse Dorsal Root Ganglion.”

“The Role of Neurogenin1 in Neural Fate Determination in the Mouse Dorsal Root Ganglion.”Abstract: Sensory neurons of the dorsal root ganglia (DRG) are responsible for transmitting sensory input from the periphery to the central nervous system in vertebrates. These neurons arise from neural crest cells that migrate from the dorsal aspect of the neural tube during embryonic development. Neural crest cells give rise to the different types of sensory neurons as well as the glial cells that make up the DRG. The development of the differentiated cells appears to involve two decisions; first the cells decide to become neurons or glia (neural fate determination), then those that have committed to become neurons decide what type of neuron to become (neural subtype specification). The neurogenin1 (ngn1) gene is known to be involved in these decisions since mouse embryos lacking the ngn1 gene are missing one subtype of neuron (nociceptive neurons) in the DRG (Ma et al., 1999, Genes Dev. 13:1717-1728). While the loss of one specific subtype of neuron in the DRG of ngn1 knockout mice seems to imply a role for this gene in neural subtype specification, it is also possible that ngn1 is involved in neural fate determination of one type of progenitor cell that specifically gives rise to this subtype of neuron. Based on its homology to Mash1, a gene involved in neural fate determination in the olfactory epithelium (Murray et al., 2003, J. Neurosci. 23: 1769-1780), we hypothesize that ngn1 is involved in neural fate determination in the DRG. To test this hypothesis, we are pursuing two experimental approaches. In one set of experiments, have used a conditional lineage tracing approach to label embryonic cells expressing ngn1 so that we can identify the progeny of these cells later in development. If ngn1 is involved in neural fate determination instead of neural subtype specification, we might expect to find glial cells that are derived from ngn1-expressing progenitor cells. In another set of experiments, we are examining the fate of progenitor cells in the DRG in the absence of functional ngn1. If ngn1 is involved in neural fate determination, we would expect to see an increase in the proportion of glial or progenitor cells combined with a decrease in neural cells in ngn1 knockout embryos. The results of these two approaches will be presented and at present, they are consistent with the hypothesis that ngn1 is involved in neural fate determination. Supported by NIH Grant # P20 RR-16460 from the IDeA Networks of Biomedical Research Excellence (INBRE) Program of the National Center for Research Resources.

Murray’s research interests involve understanding how extracellular growth factors and intrinsic patterns of transcription factor expression regulate neuronal progenitor cells in order to generate proper numbers and types of neurons during mammalian nervous system development.

Chemistry – Floyd Beckford
Associate Professor of Chemistry
Lyon College

Beckford Website

“Towards the Development of Metal Complexes Potentially Useful as Therapeutic Agents”

“Towards the Development of Metal Complexes Potentially Useful as Therapeutic Agents”Abstract: The investigation of ruthenium (Ru) complexes as potential pharmaceutical agents is continuing to attract increasing attention. This is due in part to inherent chemical properties of such compounds. As examples, two Ru(III) complexes, namely NAMI-A ([ImH][(Im)RuCl4(dmso)], Im = imidazole) and KP1019 ([IndH][(Ind)2RuCl4], Ind = indazole) have recently completed Phase I clinical trials as anti-metastatic and anticancer drugs, respectively. Another class of Ru complexes that is generating significant interest is the organometallic complexes [(arene)Ru(LL)Cl]+. Though these complexes have yet to be clinically assessed, they show wide ranging medicinal properties.  This is due to their structure which provides an ideal template for modification in order to generate medicinally-active compounds. In particular variation of the arene and/or the LL ancillary ligand provides potentially extensive variations in both geometry and electronic properties. In our research lab we synthesize complexes of this type where LL = a thiosemicarbazone. Thiosemicarbazones are well-known in medicinal chemistry as bioactive compounds. The arenes we use are p-cymene and benzene but we have also been investigating the use of 1,4,7-trithiacyclononane (9aneS3) as an alternative face-cap to the arenes. Our compounds are evaluated for their anticancer and antibacterial properties. In addition their biochemical and biophysical characteristics are investigated through their reactions with nucleic acids and model proteins. In general the bioactivity can be related to the nature of the thiosemicarbazone and current research is aimed at seeing the effect of the face-cap of the complexes.

Beckford’s research interest is in the potential of organometallic and inorganic complexes of ruthenium and copper to act as anticancer and antimicrobial agents.


Conference participants are expected to attend a workshop as part of the conference program.

No registration is required for the workshops.

Workshop 1 (CTED 403) 10 a.m. to 11:20 a.m.
“Calorimetry Techniques to Characterize Stability and Interactions of Biomolecules”
T.K.S. Kumar, associate professor, department of chemistry and biochemistry, University of Arkansas

Abstract: Differential Scanning Calorimetry (DSC) and Isothermal Titration Calorimetry (ITC) are valuable calorimetric techniques to characterize stability and interactions of biological macromolecules. DSC directly measures heat changes that occur in biomolecules during controlled increase or decrease in temperature, making it possible to study the thermal unfolding and phase transitions. On the other hand, ITC is a versatile technique to directly measure the binding affinity (Kd), binding stoichiometry, and the thermodynamics of biomolecular interactions. The workshop will cover the wide range of applications of DSC and ITC in modern biology.

Workshop 2 (CTED 107) 10 a.m. to 11:20 a.m.
“Introduction to Mass Spectrometry: Fundamental Principles and Applications”
Jennifer Gidden, senior scientific research specialist, Arkansas Statewide Mass Spectrometry Facility, University of Arkansas

Abstract: Mass spectrometry is a versatile analytical tool that essentially measures something very simple – the molecular weight of gas phase ions. While mass spectrometry has its roots in early 20th century particle physics, it has evolved over time into becoming a key player in all branches of science, analyzing anything from single elements to huge proteins. Applications in both academia and industry cover a wide range of topics such as identifying components in mixtures, quantifying trace levels of contaminants, and elucidating 2-D and 3-D structures of both small and large ions. This talk will present an introduction to the basic elements of mass spectrometry. It will cover the underlying principles upon which mass spectrometry is based, the central components of mass spectrometry instruments (including different ionization methods and mass analyzers), and approaches to correctly analyzing the resulting mass spectra.

Workshop 3 (CTED 204) 10 a.m. to 11:20 a.m.
“NextGen Sequencing: Introduction to Methods and Applications”
Douglas Rhoads, professor, department of biological sciences and director of the graduate program in Cell and Molecular Biology, University of Arkansas, and Young Min Kwon, assistant professor, poultry science department, University of Arkansas

Abstract: This workshop will start with a short history of manual and automated sequencing, and progress through the competing chemistries now employed in Next Generation Sequencing (NGS). The basic advantages and disadvantages of the three major NGS, and how NGS is evolving will be discussed. It will also cover NGS applications to address various biological questions on transcriptomics, genome/ metagenome sequencing, functional genomics, and bacterial genotyping.

Workshop 4 (CTED 409) 10 a.m. to 11:20 a.m.
“Crazy Materials”
Jak Tchakhalian, associate professor of physics, University of Arkansas

Abstract: Very recently in the world of materials a new remarkable class of compounds called phase change materials has been discovered. This workshop will demonstrate several truly fascinating materials belonging to this group, such as non-Newtonia liquid, super cooled water and high temperature superconductivity when after application of either external pressure or temperature those materials drastically alter their behavior and illustrate their unquestionable importance for the next generation of real world applications and devices.

Workshop 5A (CTED 406) 10 a.m. to 10:40 a.m.
“Multidisciplinary Approaches in the Study of Osmoregulation and Growth in Fishes”
Christian Tipsmark, assistant professor, department of biological sciences, University of Arkansas

Abstract: Today multidisciplinary approaches (e.g. molecular biology, biochemistry, immunology, genomics, and organismal physiology) are used to address questions concerning endocrine and physiological factors that i) allow animals to live in specific environments and ii) control growth. Ion and water homeostasis is the basic requirement for all multicellular life to keep a separate defined chemical internal condition irrespective of external influence. Therefore, the physiological research on transport epithelia is fundamental for the understanding of vertebrate life and also many pathological situations. The workshop will discuss the use of multidisciplinary approaches in my lab where we seek to understand mechanisms of ion and water transport in vertebrates in general by focusing on a series of specialized conditions of transport epithelia using fish as a model. Overall the goal of the research is to increase our understanding of key transport proteins localization, hormonal regulation and physiological function. The studies provide new insights into basic physiological mechanisms which ultimately will enhance our understanding of related pathological conditions. The fish species we study can move between diverse salinities and are therefore ideal research models in the study of proteins involved in transitions in epithelial function. In fish, the gill, gut, and kidney perform the necessary regulation of water and salt transport and a unique functional plasticity is seen in these organs. The endocrine factors controlling ion and water balance is in part the same as growth determining hormones, like growth hormone and insulin-like growth factors. The stress hormone cortisol in addition to being a flight or fight hormone also plays a role in growth, as well as, osmoregulation. Therefore, we also have projects in the lab trying to understand the endocrine control of growth with the ultimate goal to enhance aquaculture and food production.

Workshop 5 B (CTED 406) 10:40 a.m. to 11:20 a.m.

“Methanogens as Model Systems to understand the Archaea and Beyond”
Dan Lessner, assistant professor, department of biological sciences, University of Arkansas

Abstract: Life is divided into three domains, the Bacteria, Archaea, and Eukarya. Despite the global importance of Archaea, the biology of this domain is far less understood compared to our understanding of the Bacteria and Eukarya. It is known that components of the biological machinery found within Archaea resemble that found in both bacteria and eukaryotes. For example, archaea lack a nucleus and arrange genes within their genomes similar to bacteria. However, archaeal RNA polymerase (RNAP), the multi-subunit enzyme that transcribes genes, is more similar to RNAP found in the nucleus of eukaryotes rather than to RNAP found in bacteria. This workshop will discuss the use of the methane-producing archaea (methanogens) as model systems to understand the biology of the Archaea and to confer relationships to the Bacteria and Eukarya. In particular, results will be presented from ongoing research to determine the role of iron-sulfur cluster cofactors found in subunits of archaeal and eukaryotic RNAP, but absent from bacterial RNAP. The equipment needed to work with methanogens, which are strictly anaerobic microorganisms, will also be discussed.

Workshop 6 (CTED 404) 10 a.m. to 11:20 a.m.
“Bioinformatics Systems Development”
Roger Hall, technical director, MidSouth Bioinformatics Center at UALR

Abstract: This high-energy session will illuminate the context of various open source technologies in a complex research system, with examples, handouts, and free code covering Cloud Computing (AWS), scripting (Perl), databases (MySQL), browsers (with JavaScript), statistics programming (R), and visualization (Processing). Research problems illustrated include lab management, genomic sequence searching and analysis, functional annotations, and high-dimensional data visualizations.