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STEP Early Undergraduate Research

2004-2005 Projects  2005-2006 Projects  2006-2007 Projects  2007-2008 Projects   2008-2009 Projects   2009-2010 Projects


2004-2005 EUR Projects

Following the call for early undergraduate research (EUR) proposals, 6 such proposals have been awarded for 2004-05 as part of the first year of the recently acquired NSF-STEP (National Science Foundation STEM Talent Expansion Program) grant. Whereas undergraduate research is generally widespread in STEM (science, technology, engineering and mathematics) disciplines at UNO, it normally involves students who are already committed to a major and gives them greater depth in that major. The purpose of funding early undergraduate research is to create interest and motivation for students to consider a STEM major. These sub-grants provide funds for supplies, tuition reimbursement and/or faculty summer support.

These EUR sub-grants are just one part of a multifaceted approach towards achieving the fundamental goal of the STEP grant (a collaborative grant with Metro Community College) to increase the number of science, technology and math majors/graduates at UNO (and MCC). To this end, EUR funding is open to all UNO faculty with support going to the most promising proposals. For more information please contact STEP grant co-PI Dana Richter-Egger 402-554-3643.

  • This Experience introduces freshmen & sophomore UNO students, who are inclined towards mathematics, to advanced topics (namely number theory, an important tool for modern cryptography) and to the larger mathematical community (at MathFest - a national conference aimed at college students and their professors). The experience will give these students a tool set that they can apply to mathematical research at an NSF sponsored research experiences for undergraduate(REU), or with a UNO professor. It will enable them to enter (as sophomores and juniors) into our most advanced theoretical classes, abstract algebra and analysis. With these courses in their undergraduate background, these students will have the necessary tools for success in any graduate program in the country.
    Griff Elder - Mathematics
  • In this project, the students will study a hardware programming language, VHDL (an IEEE standard), and use the language to design software algorithms in hardware. For this, special programmable hardware boards from Xilinx will be used. The designs will be downloaded into the boards using PC peripherals. The designs are hardware implementations at the complexity of a small AC-based computer. These designs will then be tested to verify that they conform to specification.
    Hassan Farhat - Computer Science
  • In northwest Nebraska, near Crawford, is Toadstool Geologic Park. Here, numerous fractures, veins and faults deform the sediments, and can be studied in great detail in the excellent badland exposures. These faults and veins are unusually well exposed, creating an almost unparalleled natural laboratory for the investigation of crack and fault geometries. This geologic 'window', in turn, provides insight into how the earth's crust deforms in the middle of a continent and tectonic plate, far away from plate boundaries such as the San Andreas Fault. Using GPS (global positioning system) units we have started to build a very detailed database on the position, orientation and characteristics of these faults, veins and fractures. The purpose of this summer's project involves undergraduates in expanding the database. This project is particularly well suited to providing an early undergraduate research experience involving both field work, and analysis using software tools.
    Harmon Maher - Geography/Geology
Toadstool Geologic Park Survey
Toadstool 2004 GSA EUR Poster    Toadstool 2004 GSA Poster
   
  • Dr. Claudia Rauter's summer research project on the reproductive biology of burying beetles in prairie habitat will provide six undergraduate students first hand research experience. The students will learn basic field and laboratory techniques used for studying insect biology and receive training in conducting independent research projects. The scientific goals of the research project are 1) to determine temporal and spatial distribution of burying beetles in the Allwine Prairie Preserve in June and July, 2) study the reproductive activity of the burying beetles in the field, and 3) investigate details of their reproductive biology in the laboratory.
    Claudia Rauter - Biology
  • Cuscuta pentagona, commonly called dodder, is a rootless and leafless vine that, unlike most plants, performs very little photosynthesis. To make a living, Cuscuta infests a host plant, from which it derives water, minerals and food resources. Several physiological changes have accompanied Cuscuta's adaptation to the parasitic habit, particularly with respect to growth and metabolism. Students will be introduced to standard molecular and biochemical techniques used in physiological research and will apply these toward understanding how Cuscuta has adapted to life as a parasite.
    Mark Schoenbeck - Biology
  • The efficacy of molecular modeling in both research and teaching has prompted our department to present the subject across the chemistry curriculum starting at the freshman level. We would like to solicit interested freshman/sophomores, who recently completed the CHEM 1184 molecular modeling lab, and who plan to take the CHEM 2250/2260 sequence, to enroll in a one credit hour CHEM 4950 molecular modeling research project to be taken concurrently with CHEM 2250. Students will use molecular modeling to explore the physical and chemical properties of various compounds including those pertinent to current faculty research. The results of this research will be presented in a poster session at the end of the fall 2004 semester.
    Douglas Stack - Chemistry
Molecular Modeling in Chemistry
Molecular Modeling in Chemistry Poster    Molecular Modeling in Chemistry Poster



2005-2006 EUR Projects  

  • Evaluation of interior dust collection sites. Omaha anticipates EPA clean-up of surface soils where these have been found to be contaminated with lead and other toxic metals. The process of clean-up has risk of spreading contaminated dust to the interior of homes. An optimum approach to monitoring the extent to which people might be exposed to such contaminated dust is long-term, passive collection such as setting out Petri dishes for several months. There may be more dust present in high traffic areas and more personal exposure as well, but there is more opportunity for collection containers to be disturbed. Because the quantity of collected dust collected is miniscule in any case, such disturbance has the potential to obscure valid conclusions of dust analysis. The proposal is to have six students design collection sites in their own homes and homes of other STEP participants, to place collection containers as designed, and to monitor these over a period of ten months. Monitoring involves collection of some of the containers, weighing them, describing the nature of the dust collected, digest the longer term dust samples, and use ICP-MS equipment to determine the mass of lead in the dust collected.
    James Carroll, Chemistry
  • Visualization in bioinformatics. The main objective of this proposal is to motivate undergraduate students at an early stage of their careers for interdisciplinary research through a variety of activities related to visualization in bioinformatics. This has several facets including computer science aspects such as image management in biology databases, algorithm visualization, etc., as well as biology aspects such as protein structure visualization. Through hands-on practices, freshman or sophomore level students will learn state of the art visualization for bioinformatics, learn how visualization can aid database/information retrieval and develop basic skills needed for visualization. 
    Zhengxin Chen, Computer Science

Visualization in Bioinformatics

  • Influence of population density on brood size in the burying beetle. Manyanimals show a decline in clutch or brood size when population density increases. As brood size declines, offspring size usually increases. Such an increase in offspring size can be advantageous, when individuals compete for resources required for reproduction like territories in birds or seeds in insects. Burying beetles use small dead animals as food resource for their offspring. Carrion is scarce and its occurrence is unpredictable. A carrion is therefore a very valuable resource and burying beetles compete intensively for their possession. The winner of such contests is usually the larger beetle. The females should therefore produce small broods with large offspring at high population densities. By adjusting brood size to current population densities that their offspring will encounter, females have the potential to produce offspring of the size that will maximize their fitness. The goal of this project is to investigate:
    1. whether females do adjust brood size in relation to population density,
    2. whether females can change brood size in a second breeding attempt when the population density changes after the first breeding attempt,
    3. whether there are genetic differences in the females ability to adjust brood size in relation to population density.
    Claudia Rauter, Biology

Influence of population density

  • Physiology and genetics of a parasitic plant Cuscuta pentagona. Cpentagonais a rootless parasite that cannot live without a host plant, as it acquires a majority of its nutrients and energy by piercing the host tissue and withdrawing water and nutrients from the host vasculature. Furthermore, the parasite is essentially leafless, possessing only vestigial scales. In the closely-related but non-parasitic plant, Ipomoea purpurea (morning glory), several importantbiochemical processes occur in the root and leaf tissues, including the reduction of environmental nitrate to ammonia for amino acid synthesis. Several interesting questions thus arise: What physiological and genetic changes have accompanied the switch to the parasitic habit? Are the genes for processeslargely limited to leaf or root tissues extant in the parasite, or have they been lost? Can the parasite still express these genes, and have they been recruited for novel purposes in C. pentagona? Students involved in this work would beexposed to the following philosophical aspects of biological research: 1) learning to ask good questions about an experimental system, 2)developing strategy foranswering these questions, and 3) learning how different methods (physiological, molecular) may be employed in such a strategy. In addition, the students will be exposed to several technical aspects of laboratory work, including the basics of gel electrophoresis, nucleic acid purification, the polymerase chain reaction, DNA cloning and sequencing, and rudimentary spectrophotometric assay techniques.
    Mark Schoenbeck, Biology
  • Laboratory research in organic chemistry. The correlations found from lastyear’s molecular modeling project on the rate of glycosidic bond cleavage inDNA and the structure of various toxic chemicals, will be used to investigatye the specific properties of estrogen quinines. A student (or pair of students) will use UV/Vis spectrometry to obtain kinetic and thermodynamic data on the glycosidic bond cleavage involving estrogen quinines, known carcinogenic metabolites. A second project will be independent of last years work and will involve the development of new synthetic techniques for the production of photochronic materials. There is an attraction for some students in being able to create a new substance from simpler starting components. This is the esscence of organic synthesis, and it provided the author with the motivation to explore a career in science. This project will also involve one or two students and it is anticipated that the results of this early investigation will be the foundation for future undergraduate research.
    Douglas Stack, Chemistry
  • SimuliX. The goal is to develop a client/server architecture in which a 3-dimensional simulation engine resides on the server and broadcasts simulation dataacross a network to one or more clients. As part of the simulation, clients have theability to provide stimulus (input data) influencing the behavior of the simulation forming a feedback loop with the simulator. When completed, the system will havethe ability to simulate the behavior of any model, subject to the constraints that themodel and its behavior be represented in a suitable notation. In particular we have aspecial interest in simulating the behavior of reactive systems such as robaticsystems. In the case of robotic systems, the system model is abstractly partitionedinto sensors and actuators. The clients control the actuators in response to sensor andtrace information provided by the simulation. Actuator commands can be inputmanually from a standard input device such as keyboard or standard in. The latter option opens the door to automatically driving the simulator by client-side controlprograms.
    Victor Winter, Computer Science

     

2006-2007 EUR Projects

- Integrating software algorithms in hardware design. The projects will be at the same level of difficulty as designing microcontrollers or simple microprocessors. Students are required to have taken only one course in the field, Digital Design, CSCI 2710, and to be currently enrolled in Introduction to Computer Architecture, CSCI 3710. Development of a set of tutorials for using hardware units, UP2 Boards, has started. Additional tutorials on a hardware language, VHDL, are also being developed. A design for a small computer has been developed using these boards. Students will explore additional design topics. In all cases project success should result in a designed unit being attached to a monitor and a keyboard. The device is then used as a substitute to a dedicated central processing unit.
Hassan Farhat, Computer Science

Designing a Simple Computer

 - Time series analysis of biological network dynamics. Boolean networks are discrete models used to study complex biochemical systems. They have been effectively applied in various areas including genetic regulatory systems,evolutionary systems and chaotic systems. The UNO mathematical biology group has developed a 135-node protein-protein signal transduction network, based solely on realistic biological data from the literature. This protein-protein network can be viewed as an input-output system evolving over time. It is important to understand the dynamics of the network under chaotic external stimuli. A natural approach to studying this problem is to apply time series analysis. A time series is a sequence of values of a variable over equally spaced time intervals. One objective of time series analysis is to determine if there is an underlying structure or trend in the data. Here it is proposed to study the dynamics of the protein-protein network under a varietyof external conditions and stimuli. The objectives are two fold: (1) characterize the various dynamical behaviors observed in the simulation data in terms of regularityand chaos, and (2) determine the robustness of the network based on responses to specific stimuli.
John Konvalina and Jim Rogers, Mathematics

- Bioinformatics mini-course. Several new courses have been developed for the new undergraduate bioinformatics degree, one of which is Introduction to Bioinformatics, BIOI 1000.The goal of the course is to provide a broad overview of the field by introducing many of its fundamental concepts.In addition the course attempts to stimulate research interest by highlighting some of the open questions inthe field. Despite the success of BIOI 1000, it would be useful to have a shorter version of this semester long course. It is therefore proposed to develop a short (one to four hour) mini-course to provide a hands-on introduction to the field. The course will assume no prior knowledge of molecular biology or computer science and will be based on a case study of a common genetic disease. Sequences will be identified by a Genbank search, downloaded, aligned, and then used to construct a simple tree to highlight the differences among species. Thus the course will be presented from the perspective of solving a research problem.
Mark Pauley, Computer Science

Bioinformatics Outreach
High School Course
Middle School Course

- Influence of population density on offspring number in a burying beetle. Like many other animals, burying beetles produce large, but few offspring at high population density and many, yet small offspring at low population density. The regulation of the number and size of offspring occurs in most animals during egg laying. Burying beetles, however, are known to adjust number of offspring through infanticide when the larvae are 24 to 48 hours old. The first summer project involving undergraduate students will address the question whether the burying beetle Nicrophorus pustulatus regulates offspring number exclusively during the larval stage or whether some degree of adjustment also occurs during egg laying like in other animals. The second project will investigate whether the timing of the regulation of offspring number is affected by population density. Beetles reared at high population density may regulate offspring number earlier than beetles reared at low population density to reduce sibling competition in favor of fast offspring growth. The third project will repeat one of last year’s projects. Jeff Holdsworth (STEP 2005) investigated when the sensitive time period in adult burying beetles occurs that determines whether the beetles produce many or few offspring. Jeff compared two time periods and their effects on the regulation of offspring number: The first time period corresponded to the time between emergence as adult beetle and reaching sexual maturity which lasts about 3 weeks. The second time period chosen for the experiment was the time between the first and second brood. Corroborating the findings by David Bodnar and Adam Yeh (STEP 2004), burying beetles experiencing 3 weeks of high population density before the first brood, produced large, but few offspring. After rearing the first brood, the beetles were exposed for 1 week to either low or high population density. Independently of the population density they had experienced before and after rearing the first brood, all beetles produced more and smaller offspring than they did in their first brood. This result is rather unexpected. Usually, second broods are smaller because production of the first brood involves considerable costs. Because of the small sample size and the unexpected result, this experiment will be repeated this summer.
Claudia Rauter, Biology

 - Characterization of Type III secretion in the bacterium Pseudomonas. The type III secretion is a virulence factor found in many bacteria that acts to secrete toxins into the cells of animals or plants that the bacteria are infecting. These secreted bacterial toxins are major factors that contribute to the virulence of bacterial pathogens. The toxins promote virulence by altering the activities or killing the cells into which they are translocated. The mechanism by which Type III secretion systems are able to specifically secrete the toxins out of the bacterial cells and translocate them into the cytoplasm of animal and plant cells is not yet totally understood. My lab is currently working to understand the regulation of the ability of these bacteria to secrete toxins. The amino-terminal portion of the toxins has been identified as the region of the toxin proteins that mediates the ability of the toxin to be secreted. However, analyses of the sequences of the amino terminus of toxins suggest that the sequence necessary for secretion is somewhat loose or is more in nature structural. To examine this hypothesis, we are testing the effect of alterations of the amino terminal portion of the toxin ExoU of P. aeruginosa on the ability of the proteins to be secreted and translocated into animal cells. The students would help construct a mutated version of the amino-terminal portion of ExoU using recombinant DNA techniques, introduce the mutated gene into P. aeruginosa cells and then test the effect of the mutations of the ability of the bacteria to secrete the proteins using Western immunoassays and the ability of the protein to be translocated into animal cells.
Donald Rowen, Biology

ExoU Secretion

 - Mathematical models for DNA hybridization. The research that students will be involved with, has the following directions:

  • The development of new metrics for the combinatorial coding theory of DNA, that will model the thermodynamic function of distance between DNA sequences.
  • Calculation of the parameters corresponding to the codes endowed with DNA metrics.
  • Discovering the proper solution of the Encoding Problem based on combinatorial and random constructions of ‘‘good” DNA codes.
  • Using the idea of group testing and superimposed codes to more efficiently access encoded information in DNA databases.
  • Statistical estimation of the average thermodynamic distance between random strings generated by Markov sources.
  • Applications of the theory of superimposed codes to models of multiple access information transmission will be considered.

The students involved will work on the development of probabilistic and combinatorial methods for the coding theory of DNA. They will develop the method of random coding for DNA sequences using a new insertion-deletion stacked pair thermodynamic metric. The series of necessary characteristics of DNA metrics (for example, the average value of distance between random sequences in DNA metrics)will be investigated with the help of Monte-Carlo modeling of random sequences representing stationary Markov chains having large lengths,and the subsequent statistical estimations of these characteristics. Work will be needed to analyze the DNA metrics that model the thermodynamic function of distance between DNA sequences and study the processes of DNA hybridization.
Vyacheslav Rykov, Mathematics

Project Report
Student Research

- Molecular physiology of Cuscuta pentagona carbon and nitrogen metabolism III.Premise: The proposed research would make use of my investigation into the physiology of the parasitic plant Cuscuta pentagona (dodder) as a focus for introducing students to the skills and strategies of laboratory research in biology. C. pentagona is a rootless parasite that cannot live without a host plant, as it acquires a majority of its nutrients and energy by piercing the host tissue and withdrawing water and nutrients from the host vasculature. Furthermore, the parasite is essentially leafless, possessing only vestigial scales. In the closely-related but non-parasitic plant,Ipomoea hederacea (morning glory) several important biochemical processes occur in the root and leaf tissues, including the reduction of environmental nitrate to ammonia for amino acid synthesis. Several interesting questions thus arise: What physiological and genetic changes have accompanied the switch to the parasitic habit? Are the genes for processes largely limited to leaf or root tissues extant in the parasite, or have they been lost? Can the parasite still express these genes, and have they been recruited for novel purposes in C. pentagona.
A first step toward answering many of these questions involves the identification and isolation of genes associated with each of these processes, both from the parasite and from the non-parasitic relative (as a point of comparison). At the outset of the research I propose to assign each of the students to attempt to isolate a particular gene fragment from either dodder or morning glory, using a PCR-based strategy, and drawing on information in the NCBI genome databases. If successful in amplifying a promising gene fragment from the source, the student will clone the fragment into a bacterial vector and prepare it for restriction analysis and sequencing. The use of computational methods for both prediction of gene sequences at the beginning of the project, and subsequent analysis of cloned sequences, makes this project an interdisciplinary pursuit between molecular physiology and bioinformatics.
In contrast to the previous two years, the biology department is now sufficiently equipped to perform all sequencing reactions “in-house”, and hands-on DNA sequencing of cloned fragments by students, as well as an introduction to the operation of the sequencing apparatus, will be a significant addition to this year’s course. Furthermore, during the first weeks of “methods practice” the students will perform RNA isolation as well as DNA isolation.
Mark Schoenbeck, Biology

Molecular Physiology Summer 2006 Students

 

2007-2008 EUR Projects

  • Hands-on Experience in Software Porting and Development. This project introduces undergraduate students to topics beneficial to their computer careers through a project called TEAM-Net. TEAM-Net is envisioned to be a site on the Internet that stores/retrieves research accomplishments and activities by the business community and educational institutions within the state of Nebraska. A small prototype of TEAM-Net has already been designed and can be viewed at http://petri1.ist.unomaha.edu/programs. The prototype has been designed with two modes of execution: user mode and system mode. In the user mode the user is able to perform functions like browsing, login, search, and submit information, etc. In the system mode, the administrator is able to manage the system such as removing or adding users, modify system profile, etc. However the prototype needs to be updated. The students involved in this project will be responsible for porting the package to a new platform, and will gradually update, replace and create new features. To keep the students interested in the project, the main focus, after porting the package, will be on features that students would like to see implemented. There are many such features, e.g. creating an environment for presenting students’ research interests, resumes, research questions, and looking for a research partner. Through hands-on experience, the students will learn about UNIX, porting issues, web design, programming (Perl, Java), SQL database, security, and interaction among all of these components.
    Azad Azadmanesh – Computer Science (aazadmanesh@mail.unomaha.edu)

Nebraska TeamNet

  • Phytogeography of Ancient Plant Lineages in Madagascar. The incredibly diverse and endemic biota of Madagascar has long intrigued biologists attempting to explain and conserve it. Several reasons have been proposed to explain this unique assemblage, including long periods of isolation, heterogeneous topography & climate, optimal location for immigration from several diverse regions, and large island size. Botanists interested in the origins and biogeography of the Malagasy flora have noted comparisons to the flora of Africa, India, and Austral-Indonesia-Malaysia. However recent discoveries and international efforts to describe the vanishing Malagasy flora and surrounding regions have greatly changed the floral lists used in these past comparisons, and new biogeographic analyses are essential. As a focal point for the project, two plant groups in particular are highly diverse in Madagascar, the ferns (pteridophytes) and flowering plants (angiosperms). These major plant groups underwent a substantial evolutionary radiation during the Crustaceous (65-144 million years ago) when tectonic events transformed Madagascar into an island. Research will focus on selecting fern and angiosperm taxa at the root of their respective lineages as supported by molecular phylogenies. Specific hypotheses to be tested include: 1) whether Madagascar’s extant flora contains a higher proportion of families of basal ferns and angiosperms than derived: 2) if the composition of the Malagasy basal taxa is more similar to those from India, which was the last continent to split from Madagascar, compared to other Southern Hemisphere floras; and 3) if Madagascar’s ancient lineages are greater in number compared with the other floras, implying that its relative isolation helped preserve these relict taxa.
    Lisa Boucher – Biology (lboucher@mail.unomaha.edu)

Participating Students and Contributions

  • Research in Bioinformatics Programming. The goal of this proposal is to develop a new sophomore-level bioinformatics course, Bioinformatics Programming. This course would be an elective for bioinformatics majors and would also be appropriate for other STEM majors interested in developing their programming skills for research. As an important step towards this course, we propose to develop over Summer 2007 an online tutorial of bioinformatics programming for the programming language Perl. We would be assisted in the development of this tutorial by undergraduate students who would participate as part of a three credit hour independent-study research course. We expect two outcomes from the proposed project: 1) A new bioinformatics course for the undergraduate bioinformatics degree that would also be appropriate for other STEM majors; and 2) A web tutorial on how to write Perl scripts to solve bioinformatics problems. The new course would fill a gap in the current course offering for sophomores. This would help in the retention of bioinformatics majors—currently, with no bioinformatics courses in their sophomore year, it is easy for students to lose focus on the degree during this time—and could also help to recruit new students into the bioinformatics program, an important goal of the STEP program. In addition, the knowledge and experience gained in this class would allow students to attempt more challenging research projects as upperclassmen (e.g., for BIOI 4970, Senior Project in Bioinformatics, a required course for all majors). Two existing external models are: the Cold Spring Harbor Laboratory course titled Bioinformatics: Writing Software for Genome Research ( http://stein.cshl.org/genome_informatics/) and the Weizmann Institute of Science, which offers a course titled Programming Course for Bioinformatics and Internet ( http://bioportal.weizmann.ac.il/course/prog/general/general_info.html).
    Guoqing Lu and Mark Pauley – Biology and Computer Science (glu3@mail.unomaha.edu and mpauley@mail.unomaha.edu)

    Summer Research in Bioinformatics

  • Research in Chaos and Fractals. The objective of this STEP EUR project is to introduce undergraduate mathematics and science students to the exciting world of chaos and fractals with applications to discrete dynamical systems. Students will study the theoretical aspects of linear and nonlinear discrete dynamical systems and then perform computer experiments on specific systems. The observed outcomes will be characterized in terms of periodicity, chaos, randomness, and fractal dimensions. Some specific topics to be investigated are: one and two dimensional maps, fixed points and periodic orbits, fractals, complex dynamical systems, Julia sets and the Mandelbrot set.

    Projects selected by students:
    Dynamics with cubic polynomials
    Chaos in physics (e.g. circuit, oscillations)
    Chaos and psychology
    Random fractals
    The Cantor Set
    Noise: white, pink, brown, and black
    Cellular automata
    Dynamics in Number Theory
    Conway's Game of Life
    The n-body problem and chaos

    John Konvalina –Mathematics (jkonvalina@mail.unomaha.edu)
  • Investigation of Vein-Crack Patterns in the White River Group of Nebraska and South Dakota. Students will be mapping and analyzing patterns of locally occurring distinctive chalcedony veins within a geologic unit known as the White River Group that outcrops in northwest Nebraska and southwest South Dakota (Big Badlands). It is part of a larger, long term project investigating intraplate strain in the Great Plains. This larger project has had the following undergraduate research products to date: 3 senior theses, 3 presentations by students at professional meetings, 3 capstone mapping exercises in the structural geology course, a STEP undergraduate research experience (described below), a professional presentation on the STEP experience, and development of a GIS database used by students in coursework. The chalcedony veins are easily understood, relatively simple tensile features, and are cognitively accessible in a short time to those untrained in geology. This makes them ideal features for undergraduates to work with. At the same time, these localities provide some very interesting basic questions about how one documents orientation patterns, why different patterns exist, and the phenomenon of pattern scaling. Preliminary work shows that very different patterns exist, from those with a strong preferred direction to those which are statistically random. The specific research is novel and has publication potential.
    Harmon Maher – Geology (hmaher@mail.unomaha.edu)
  • Ecology of Urban Canada Geese: Searching for a Solution to Human- WildlifeConflicts. We are initiating a new project in collaboration with the Nebraska Game and Parks Commission (NGPC) to study the ecology of urban Canada Geese (Branta canadensis) in Douglas and Sarpy Counties. The research goals of this project address one of the key gaps in our understanding of this widespread species and is designed to meet the immediate need of state wildlifemanagers for information that will help prevent a growing conflict between peopleand wildlife. Although many populations of Canada Geese were threatened by human exploitation early in the 20 th century, the recovery of goose populations is one of the great conservation success stories. Canada Geese have proved especially successful at adapting to life in urban and suburban environments. While the sight of few geese with their young goslings is a welcome site in our human dominated environments, urban Canada Goose populations can quicklygrow to be a nuisance and even a threat to human health and the environment. Geese can become aggressive during breeding and their droppings can pollute lakes and ponds and are possible disease vectors to humans and other wild birds. Finding solutions to the conflict between humans and Canada Geese that are compatible with responsible resource management and that are acceptable to the members of the public with widely divergent opinions has become one of the most intractable problems facing wildlife biology. The Omaha metropolitan area is onlystarting to experience conflicts between Canada Geese and people. NGPC is hoping to prevent development of a problem by finding effective, publicly acceptable ways to maintain urban goose populations at a manageable level. With this goal in mind, we are starting a collaborative research project between UNO (JPM and LLW) and NGPC wildlife biologists (M. Vrtiska, Ph.D.) to determinepopulation dynamics of the urban goose population and to explore effective, non-lethal approaches to limiting their population growth.
    John McCarty and LaReesa Wolfenbarger – Biology (jmccarty@mail.unomaha.edu and lwolfenbarger@mail.unomaha.edu)

Canada Geese poster

  • Effect of Population Density and Body Size on Timing of Egg Laying in a Burying Beetle. Burying beetles use small carrion as a food resource for their offspring. Carrion is a resource of high quality, but rare and unpredictable in occurrence. Hence, at high population density competition for carrion is fierce. Large individuals are more likely to win fights over carrion and to defend carrion successfully against competitors. Consequently, burying beetles produce large, but few offspring at high population density and many, yet small offspring at low population density (David Bodnar and Adam Yeh STEP 2004; Andria Bethelmie, Laureen Opere, Amberle Pariseau, LaFonda Tanner, and John Harnish Step 2006). Further at high levels of competition, burying beetles lay eggs faster than at low levels of competition (Renae Rust, Andria Bethelmie and John Harnish Step 2006). This reduces the time span during which carrion is attractive to other burying beetles: the earlier the larvae hatch the faster the carrion is depleted. Small individuals should therefore forgo consumption of large amounts of carrion before laying eggs. Instead they should lay eggs immediately at the cost of losing mass and thus reducing their own chances of survival after the current reproduction bout. To test this hypothesis we will investigate the effect of body size and population density on timing of egg laying and whether this affects the timing when carrion becomes unattractive to competitors. We will manipulate population density by rearing female beetles either individually or in groups of four. Based on their mass, the beetles from the laboratory colony will be classified as small, medium, and large individuals. Only the small and large individuals will be used for this experiment. To test the attractiveness of the carrion for other burying beetles, we will remove the larvae from the carrion at different time points (i.e. when the larvae are 12 hrs, 24 hrs, 36hrs, 48hrs, or 60 hrs old) and offer the carrion to a new female. The degree of attractiveness will be measured as whether and how many offspring this new female produces.
    Claudia Rauter – Biology (crauter@mail.unomaha.edu)

Summer Research in Biology

  • Effect of Adjacent Residential Housing Development on Seep and Spring Water Composition in Restored Tall Grass Prairie of Eastern Nebraska. We plan to study the composition of emerging ground water from seeps and springs in the Allwine Prairie Preserve for the purpose of 1) establishing baseline data of the current composition and 2) monitoring for any changes in the water composition that may arise from a planned residential housing development on the adjacent property over the next few years. Having developed and successfully tested a sample collection device for this type of emerging ground water this past fall, we will begin monitoring water composition this spring as soon as the ground has thawed. Parameters measured include elemental content by ICP-MS, polyatomic ion content by IC, turbidity, pH and dissolved oxygen. The study is particularly relevant and timely due to the aforementioned a residential housing development planned for the adjoining property in the next few years. A significant portion of this property slopes towards the prairie preserve and development plans also include sewer lines through the prairie preserve. This longitudinal study is expected to last for 3-5 years initially and would involve 2-6 undergraduate student research students each semester during that timeframe. Students would be involved in all aspects of the research: placement of sample collection devices, water sample collection, water analysis, data analysis and presentations. Water samples will be collected monthly and following irregular events such as rainfall and construction activity. As such, students will be active both in the field (literally) and in the lab, providing them an excellent opportunity to make connections between laboratory science and the world around them. It is also a great opportunity to showcase connections between chemistry and biology/ecology.
    Dana Richter-Egger and Leanne Martin – Chemistry and Allwine Prairie ( drichter-egger@mail.unomaha.edu)
  • Role of the Chaperone SpcU in Type III Secretion by Bacterium Pseudomonas.I would like to provide an opportunity for four early undergraduate students to participate in my ongoing research on the role of chaperones in Type III secretion in the bacterium Pseudomonas aeruginosa. The type III secretion is a virulence factor found in many bacteria that acts to secrete toxins into the cells of animals or plants that the bacteria are infecting. These secreted bacterial toxins are major factors that contribute to the virulence of bacterial pathogens. The toxins promote virulence by altering the activities or killing the cells into which they are translocated. Many of the toxins secreted by Type III secretion systems require a specific chaperone protein for efficient secretion to occur. The role of the chaperones proteins in Type III secretion is not fully understood. One recent theory we are trying to test is whether chaperones cover membrane localization domains commonly found in toxins while the toxins are in the bacterial cells. The membrane localization domains act to target the toxin once it is secreted into the eukaryotic host cell. The presence of uncovered membrane localization domains is hypothesized to cause the protein to form aggregates inside the bacterial cell and to be degraded. We are testing this theory with the toxin ExoU and its specific chaperone SpcU. ExoU is unusual in that is has a membrane localization domain on its carboxy terminus, while most toxins have a membrane localization domain near it amino terminus. To test the theory, we wish to test whether ExoU forms aggregrates and is degraded if the protein contains a membrane localization domain without the chaperone being present. The STEP students will help construct mutant versions of ExoU by using PCR and recombinant DNA techniques. The mutant versions of ExoU will be expressed in P. aeruginosa cells so that the levels and localization of the ExoU proteins can be examined by fractionation experiments, SDS-PAGE and immunoblots.
    Donald Rowen – Biology (drowen@mail.unomaha.edu)

Students Involved
Results of Students Efforts

  • Mathematical Models for DNA Hybridization. In summer 2007 we will continue our research started in 2006 and will start a new project focusing on developing an advantageous screening method for improved environmental and biological testing methodology using group testing theory. This opportunity for novel research in mathematical biology will give early undergraduate UNO students beneficial insights into the process of interdisciplinary research in today’s world and the current problems in applied mathematics. More importantly, as a result of their involvement in the research process, they be will challenged and motivated to expand their knowledge of mathematics by participating in and understanding the advanced-level mathematics courses offered at UNO. Having received such knowledge in their undergraduate career, the students will then have the opportunity of succeeding in any graduate program in the country. The experience will also enable the students to participate in NSF sponsored research programs held nationwide. We will continue to work on practical problems in which the fundamental property of hybridization of DNA molecules according to Watson-Crick complimentary pairs is used. One of the substantial difficulties in the mathematical modeling of the process lies in the absence of adequate, and at the same time simple, mathematical models for the calculation of the energy of hybridization. The technical goal of this work is the development and implementation of a classical information theoretic approach to read, translate, and unlock the massive information potential of DNA computing operations. There is a need to efficiently access the information that is locked inside DNA output of biomolecular computing. In the new project group testing theory will be applied to screening multitudes of samples order to find potential hazardous particles in environmental and biological samples. If the probability of a contaminated sample is very low, while the number of samples analyzed is very high, then a laboratory will expend valuable financial resources in time, reagents and labor to determine if a sample is likely contaminated. In order to decrease the number of samples tested while also reducing the cost to analyze an individual sample we propose to develop and adapt special algorithms based on group testing mathematical theory.
    Vyacheslav Rykov – Mathematics (vrykov@mail.unomaha.edu)

Group Testing
Partition Code
Superimposed Code

  • Molecular Physiology of Cuscuta Pentagona Seedling Ascorbate Metabolism. The proposed research will make use of my investigation into the physiology of the parasitic plant Cuscuta pentagona (dodder) as a focus for introducing students to the skills and strategies of laboratory research in biology. C. pentagona is a rootless parasite that cannot live without a host plant, as it acquires a majority of its nutrients and energy by piercing the host tissue and withdrawing water and nutrients from the host vasculature. Furthermore, the parasite is essentially leafless, possessing only vestigial scales. Because of its simple shoot anatomy, I have developed an in vitro experimental system for observing C. pentagona as a model of shoot development. The most striking result to date is the observation that a pharmacological agent, the b-glucuronidase ( b-GUS) inhibitor saccharic acid 1,4-lactone (SAL), can arrest development of the seedling at early growth stages but appears ineffective at later stages, implying a developmentally-regulated role for b-GUS. Preliminary results suggest that growth inhibition by SAL can be reversed by application of the anti-oxidant ascorbate. These observations, taken together with prior works from other researchers, suggest that the role of plant b-GUS is related to the regulation of plant cell or cell wall redox status regulation or perhaps the control of active oxygen species. A first step toward answering many of these questions involves the identification and isolation of genes associated with glucuronate and ascorbate metabolism, and other functions controlling the cellular redox state. At the outset of the research I propose to assign each of the students to attempt to isolate a particular gene fragment from either dodder or morning glory, a close relative of dodder, using a PCR-based strategy, and drawing on information in the NCBI genome databases. If successful in amplifying a promising gene fragment from the source, the student will clone the fragment into a bacterial vector and prepare it for restriction analysis and sequencing. The use of computational methods for both prediction of gene sequences at the beginning of the project, and subsequent analysis of cloned sequences, makes this project an interdisciplinary pursuit between molecular physiology and bioinformatics. In addition to the molecular work, this year’s program will include physiological studies using the in vitro seedling growth system. Students well set conduct growth experiments to examine the physiological phenomena that form the basis of the molecular portion of the investigation.
    Mark Schoenbeck – Biology (mschoenbeck@mail.unomaha.edu)

2007 Gene Discovery

  • Cosmic Ray Observatory Project. With the guidance of the members of CROP (the Cosmic Ray Observatory Project) from the University of Nebraska at Lincoln, I will supervise a small group of early undergraduate physics students to build a set of cosmic ray detectors, learn how to operate and read out the detector signals, and have each student perform a summer research project using the equipment.From the CROP website (http://crop.unl.edu/): “Project Description – CROP is a statewide outreach project whose goal is to involve Nebraska high school students, teachers and college undergraduates in a multi-faceted, hands-on research effort to study extensive cosmic-ray air showers. High energy cosmic rays continuously strike the Earth’s atmosphere from outer space and create avalanches of daughter particles which cover areas up to 50 square miles on the Earth’s surface. Using simple particle detectors placed in numerous locations, measurements of the original cosmic ray energy and incident direction can be made.” Examples of possible student experiments are to measure: 1) rate of cosmic rays versus daytime/nighttime, 2) rate of cosmic rays versus barometric pressure, 3) rate of cosmic rays versus zenith angle of the sky, 4) rate of cosmic rays versus humidity, 5) rate of cosmic rays versus amount of cloud cover, 6) rate of cosmic rays versus number of sunspots, and 7) rate of cosmic rays versus solar flare activities. At the end of the research, students would plot the results, write a paper summarizing their results to be available on the UNO Early Undergraduate Research website and/or present a poster presentation at a college-level meeting such as for the Society of Physics Students or Sigma Xi (research organization).
    Kendra Sibbernsen – MCC Physics and Astronomy (ksibbernsen@mccneb.edu)

CROP report (power point)


  • Inhibition of Staphylococcus Aureus by Osmorhiza Longistylis Root Extracts. Melvin R. Gilmore, in his Uses of Plants by the Indians of the Missouri River Region, described how members of the Winnebago and Omaha tribes used a poultice made from the roots of Osmorhiza longistylis to treat boils and wounds. We have tested alcoholic extracts made from the roots, stems, and leaves of this plant for effectiveness in inhibiting the growth of Staphylococcus aureus. Cultures of S.aureus were incubated with the extracts for two hours and 24 hours. The leaf and stem extracts had no effect on S.aureus growth, but the root extract inhibited growth by 12.2% and 25% after 2 hours and 24 hours, respectively. Future plans include the fractionation of the root extract by HPLC, and the assay of the fractions obtained for anti-S.aureus activity.
    Del Stallwood – MCC Biology (dstallwood@mccneb.edu)

2008-2009 EUR Projects

  • Phytogeography of Ancient Plant Lineages in Madagascar: Part II.The incredibly diverse and endemic biota of Madagascar has long intrigued biologists attempting to explain and conserve it. Several reasons have been proposed to explain this unique assemblage, including long period of isolation, heterogeneous topography & climate, optimal location for immigration from several diverse regions, and large island size among others. Botanists interested in the origins and biogeography of the Malagasy flora have noted comparisons to the flora of Africa, India, and Austral-Indonesia-Malaysia. However, recent discoveries and international efforts to describe the vanishing Malagasy flora and surrounding regions have greatly changed the floral lists used in these past comparisons, and new biogeographic analyses are essential. Funding is requested to mentor at least six early undergraduate students to construct and analyze phytogeographic data of ancient plant lineages in Madagascar and surrounding regions. Aspects of this project that may attract students include its interdisciplinary nature and exploration of the biodiversity in this exceptional region.
    As a focal point for the project, two plant groups in particular are highly diverse in Madagascar, the ferns (pteridophytes) and flowering plants (angiosperms). These major plant groups underwent a substantial evolutionary radiation during the Cretaceous (65-144 million years ago) when tectonic events transformed Madagascar into an island. The timing of this radiation makes this an ideal place to examine the extent of fern and angiosperm distribution and the influence of isolation on the origin of Madagascar's flora. This study is part of a larger project intending to bridge the gap between our knowledge of the plant fossil record and the development of Madagascar's current floral diversity.
    Research will focus on selecting fern and angiosperm taxa at the root of their respective lineages as supported by molecular phylogenies. The current distribution of these taxa in Madagascar, Africa, India, Australia, Indonesia, and Malaysia will be used in phytogeographic analyses. Specific hypotheses to be tested include: 1) whether Madagascar’s extant flora contains a higher proportion of families of basal ferns and angiosperms than derived; 2) if the composition of the Malagasy basal taxa is more similar to those from India, which was the last continent to split from Madagascar, compared to other Southern Hemisphere floras; and 3) if Madagascar's ancient lineages are greater in number compared with the other floras, implying that its relative isolation helped preserve these relict taxa. Some aspects of these hypotheses were addressed in Part I of the project last year (notably 2); however, hypotheses 1 & 3 were not fully addressed, and will be the focus of this summer.
    Students involved in this project will construct a plant geographic database from existing resources (public databases, etc.) and test biogeographic hypotheses. No previous background is necessary. The project is interdisciplinary involving statistical analysis of biological data, geography, and bioinformatics. Students will develop skills and knowledge in: 1) constructing complex biological databases, 2) mapping, 3) phylogenetics and evolutionary theory, and 4) spatial and statistical analysis. Based on my personal experience, undergraduate research is one of the best ways to recruit and retain STEM majors. I have successfully recruited and supervised over 30 students in both field and laboratory research in the past 10 years, and serve as a female role model. I have also worked in the past with high school students interested in science (NSF-supported Banneker program), and underrepresented students who have continued in STEM areas. I teach in our introductory non-major and major courses, where I can interact and recruit students effectively, and have met with several dual enrollment students this year.
    This is a long-term project in its full scope. There are individual parts that can be completed in one semester. I expect to recruit at least six students during the summer; this number is suitable to the different regions in the study.
    Lisa Boucher - Biology (lboucher@mail.unomaha.edu)

Boucher Recruitment Flier
Final Report

  • Importance of Biparental Care for Larval Growth and Development in a Burying Beetle with Obligate Parental Care. Biparental care is thought to have evolved because one parent alone cannot successfully raise offspring. There is ample empirical support for this hypothesis. However, biparental care does not always enhance quantity or quality of offspring. In some cases it accelerates instead offspring growth and development. This may be advantageous when offspring mortality is high. In burying beetles (Nicrophorus spp.) biparental care does not result in more or larger offspring, even though offspring reared by two parents are fed more often than offspring reared by only one parent. The former offspring beg less often than the latter indicating a lower hunger level. This suggests that offspring reared by one parent may grow and develop slower than offspring reared by two parents. Accelerated growth and development may reduce mortality. Burying beetles bury and prepare carrion as food resource for their offspring. Buried carrion can still be discovered by other burying beetles. If these intruders are successful in taking over the carrion, they kill all eggs and larvae present. Fast larval development resulting in accelerated consumption of the carrion results in an earlier time point when the carrion becomes unattractive for intruders. To test the hypothesis that biparental care will result in accelerated larval growth and development as well as faster consumption of carrion, we will compare body mass and developmental stage of larvae, and mass of carrion between larvae reared by two parents and larvae reared by the female only, when the larvae are 12 hrs, 24 hrs, 36hrs, 48hrs, 60, and 72 hrs old.
    This experiment offers the opportunity to involve up to 10 undergraduate students in data collection. The last four summers have shown that the students quickly learn the skills required for data collection and can run part of the experiments independently. The projects of the previous three summers were very successful. Three manuscripts are currently in preparation reporting the results of these three projects. The students, who participated in last summer project, will present their results at the Annual Meeting of Nebraska Academy of Sciences in April 2008.
    During the summers 2004 through 2007, a total of 21 undergraduate students participated in the research projects supported by STEP Early Undergraduate Research in my lab. The percentage of minorities among these students was high: 11 students were women, one student was of Hispanic, and three students were of black ethnicity.
    Of these 21 students, two students were not Biology majors or Environmental Studies (Life science option) majors: one planned to change her major to Biology after the research experience, whereas the other student is pursuing a double major. Eight of the 21 students pursued afterwards further research opportunities mainly in the Biology Department and at UNMC. Two students were awarded an NE-INBRE scholarship. But only one student accepted the scholarship. One student was awarded an undergraduate research fellowship at NIH in the summers 2005 and 2006. Most students plan to go on to a graduate level school after graduating from UNO. Three students stayed for at least the subsequent fall semester in my lab and conducted an independent research project .
    Each student taking part in this research project is expected to enroll in ‘Supervised Research in Biology’ (BIOL 4050) covering 3 credit hours in first day session in summer 2008. The project requires that data are collected in the morning and in the afternoon. Hence, the students will be split into two groups. One group will collect data in the morning and the other group in the afternoon. Each student will collect data on 5 half-days per week, Saturdays and Sundays included. The data collection of the proposed project will be finished by the end of the first day session in summer 2008. As the data analysis of the experiments will require more than basic statistical knowledge, I will conduct the data analyses. Based on the outcome, a poster or a manuscript will be prepared during the fall semester. Participation in poster and manuscript preparation will be voluntary.
    All of my projects supported by STEP Early Undergraduate Research, including the proposed project for summer 2008, tie in my research program on the evolution of life history traits. Each project provided either preliminary data important for later projects or addressed a specific question contributing to the overall goal of my research program on the evolution of life history traits. Treating undergraduate research as integrated part of my research program, allows me to sustain a strong undergraduate research component in my research. Consequently, I have in addition to the summer semester, also during the fall and spring semester one to two undergraduate students conducting research in my lab. My long-term goal is to continue to offer undergraduate research opportunities in my lab. This will require additional funding. I plan to acquire funding by 1) helping students to apply for undergraduate research funds and scholarships and 2) by requesting undergraduate research support as part of research proposals submitted to funding agencies such as NSF or NIH.
    Claudia Rauter - Biology (crauter@mail.unomaha.edu)

2008 Parental posters

  • Gene discovery in the parasitic plant Cuscuta pentagona: Gene cloning and characterization of expressed sequence tags. The proposed research would make use of my investigation into the physiology of the parasitic plant Cuscuta pentagona (dodder) as a focus for introducing students to the skills and strategies of laboratory research in biology. C. pentagona is a rootless parasite that cannot live without a host plant, as it acquires a majority of its nutrients and energy by piercing the host tissue and withdrawing water and nutrients from the host vasculature. Furthermore, the parasite is essentially leafless, possessing only vestigial scales. In the closely-related but non-parasitic plant, Ipomoea hederacea (morning glory) several important biochemical processes occur in the root and leaf tissues, including the reduction of environmental nitrate to ammonia for amino acid synthesis. Several interesting questions thus arise: What physiological and genetic changes have accompanied the switch to the parasitic habit? Are the genes for processes largely limited to leaf or root tissues extant in the parasite, or have they been lost? Can the parasite still express these genes, and have they been recruited for novel purposes in C. pentagona?
    A first step toward answering many of these questions involves the identification and isolation of genes associated with each of these processes, both from the parasite and from the non-parasitic relative (as a point of comparison). At the outset of the research I propose to assign each of the students to attempt to isolate a particular gene fragment from either dodder or morning glory, using a PCR-based strategy, and drawing on information in the NCBI genome databases. If successful in amplifying a promising gene fragment from the source, the student will clone the fragment into a bacterial vector and prepare it for restriction analysis and sequencing. The use of computational methods for both prediction of gene sequences at the beginning of the project, and subsequent analysis of cloned sequences, makes this project an interdisciplinary pursuit between molecular physiology and bioinformatics
    In previous years, the projects have pursued specific target genes, and the research has culminated in the final week with the students sequencing cloned candidate fragments. In addition to this approach, students in the summer 2008 program will assist in the characterization of “expressed sequence tags”, which are gene fragment clones generated by randomly sampling populations of expressed genes. Since initiating this strategy in the fall of 2007 (with the assistance of past years’ STEP researchers) we have identified more than a dozen genes of interest.
    Students involved in this work would be exposed to the following philosophical aspects of biological research: 1) Learning to ask good questions about an experimental system, 2) developing a strategy for answering these questions, and 3) learning how different methods (physiological, molecular) may be employed in such a strategy. In addition, the students will be exposed to several technical aspects of laboratory work, including the basics of gel electrophoresis, nucleic acid purification, the polymerase chain reaction (PCR), DNA cloning and sequencing, and rudimentary spectrophotometric assay techniques. Finally, we will discuss how research is conducted, and the processes of writing, peer review, and publishing experimental results.
    Outcomes of the 2004-2007 programs - Research : Ten students participated and each of the summer research programs in 2004 and 2005, seventeen in 2006, and ten in 2007. Each year the students have had success in cloning the glyceraldehyde-3-phosphate dehydrogenase, starch synthase, aspartate aminotransferase or sucrose phosphate syntase genes from one or both of the target species.
    Student impact : During the summer 2005 session, Cameron Duncan, a research student during the summer of 2004, served in the position of lab assistant, and helped to lead the labs. He has since been admitted to the veterinary medicine program as Kansas State University, where he is continuing to seek research experience in addition to his veterinary training. Runa Acharya (2005 program) was awarded a summer internship in 2007 and has recently been admitted to the University of Nebraska Medical Center for medical school. Other notable outcomes include the acceptance of several participants from each of these years to advanced degree programs: Eric Ablott, Aaron Schumacher, Emily Hunter, and Todd Mitchell have all been accepted to graduate or professional programs since the summer of 2004.
    Mark Schoenbeck - Biology (mschoenbeck@mail.unomaha.edu)

2008 Gene Discovery

  • Cosmic Ray Observatory Project (CROP). Metropolitan Community College is looking for students interested in doing research in cosmic rays this summer. This is a field which combines the fields of astronomy and high energy particle physics. Students in the program would be signed up for a 4.5 quarter credit hour special topics course at MCC and their tuition for this class would be paid for by the grant. Meeting times would be determined according to students' and instructors' individual schedules. If we schedule a workshop in Lincoln, all expenses would be paid.
    Activities would include:
    Learn how to use MCC's equipment to measure cosmic rays.
    Read about, and watch videos and discuss the background of cosmic ray research.
    Possible travel to Lincoln for a workshop or listen to lectures by distinguished professors in the field of high energy physics.
    With the quidance of the instructor, design a research project.
    Take data and interpret the results.
    Summarize the results in a paper and/or presentation.
    If is sounds interesting to you, but you are concerned about your mathematical abilities or are afraid that since you have not has a physics class, you would not be able to do it, put those fears to rest. You do not need to use advanced mathematics and I will work with you to understand the physical nature of what is happening.
    Background - Last year, this project was funded through the Early Undergraduate Research postion of the STEP grant between UNO and MCC. Students participated in a hands-on workshop at UNL, attending lectures presented by Dr. Greg Snow and Dr. Dan Claes, leaders of the CROP. Students learned how to assemble cosmic ray detectors, how to trouble shoot problems with the detectors, how to view signals with an oscilloscope, and how to collect data with data acquisition electronics. Through the NSF grant that supposts CROP, we were allowed to take this functioning equipment back to MCC to study cosmic rays.
    Five students signed up for Physics 2900 - Special Topics in Physics for the summer session. Each student attended the workshop, helped to design the frame to hold the detectors and help build it, developed their project and started taking data.
    One student took measurements of daily changes of the rate of cosmic rays over several 24 hour periods.
    One student measured the rate of cosmic rays from different directions to see if he could distinquish a preferred direction between east and west as predicted by theory. He presented in September at the Nebraska American Association of Physics Teachers meeting and his talk was well received.
    One student designed an experiment to test the photomultiplier tubes of the cosmic ray detectors in a changing magnetic field.
    A team of two students took data on the telescoping effect of changing the distance between the detectors and the three-fold cosmic ray rates.


2009-2010 Projects

  • Reconstructing Paleoclimates and Ancient Floras Using Fossil Wood Analysis. Fossil wood analysis has been demonstrated to be a powerful approach for studying past climates and biota. Anatomical characters can be used for identification to modern orders and families, as well as providing clues to the physiology and climate existing during the tree’s growth. During the Mesozoic, secondary growth resulting in tree form was established in both gymnosperm and angiosperm lineages and was advantageous in certain environments. In this proposal, well-preserved permineralized wood from southwestern North America and Madagascar will be analyzed for taxonomic, paleoecological and paleoclimatic data. These recently acquired specimens represent a unique opportunity to fill the gap in our knowledge of the flora and terrestrial climate during a critical time interval and geographic location. Funding is requested to mentor at least six early undergraduate students and pre-freshmen to prepare and analyze Mesozoic permineralized wood from New Mexico or Madagascar. Aspects of this project that may attract students include its interdisciplinary nature and exploration of past floral history and paleoclimates.
    Several permineralized logs and in situ stumps were recently collected from the Menefee Formation in New Mexico. The majority of the in situ stumps and larger logs were conifers, however, other trunk remains include eudicot/magnoliids. To date, Late Cretaceous wood from the San Juan Basin has not been fully characterized, and has not been studied from this early Campanian age. Initial examination of the fossil wood indicates that it is well preserved, contains growth rings and insect coprolites, and that several orders are represented. The age and extent of preservation allows for unprecedented study of the flora of this time. Furthermore, access to specimens collected from Madagascar currently in the collection of the Muséum National d’Histoire Naturelle (Paris, France), was recently acquired and specimens are on loan for study. The fossil wood is well preserved and includes eudicot and/or magnoliid taxa. There are only a few limited studies of fossil wood from Madagascar, and none from these ages or locations. This study is part of a larger goal intending to bridge the gap between our knowledge of the plant fossil record and the development of Madagascar's current floral diversity.
    Research will focus on examining characters that are useful in identification (i.e. cross-field pitting, ray structure, etc.) and others that are used in paleoclimate analyses (i.e. mean sensitivity, etc.). Specific questions to be addressed from the New Mexico and Madagascar specimens include: 1) if the fossil wood from the Menefee Formation is less diverse than the younger specimens from the Fruitland/Kirtland Formation (~10 Ma age difference); 2) if the Menefee flora indicates more conspicuous environmental disturbances or seasonality than the Fruitland/Kirtland flora (independent data supports changes in precipitation); 3) if the wood specimens from the Menefee Formation provide evidence of a unique tree community, as compared to other fossil wood assemblages temporally and spatially, and 4) if the fossil wood from Madagascar supports the hypothesis of long-standing endemicity for the island.
    Lisa Boucher - Biology (lboucher@mail.unomaha.edu)

Menefee Formations - New Mexico
Menefee Formations - San Juan
Cretaceous Angiosperms
  • Importance of Biparental Care for Larval Growth and Development in a Burying Beetle with Obligate Parental Care. Biparental care is thought to have evolved because one parent alone cannot successfully raise offspring. There is ample empirical support for this hypothesis. However, biparental care does not always enhance quantity or quality of offspring. In some cases it accelerates instead offspring growth and development. This may be advantageous when offspring mortality is high. In burying beetles (Nicrophorus spp.) biparental care does not result in more or larger offspring, even though offspring reared by two parents are fed more often than offspring reared by only one parent. The former offspring beg less often than the latter indicating a lower hunger level. This suggests that offspring reared by one parent may grow and develop slower than offspring reared by two parents. Accelerated growth and development may reduce mortality. Burying beetles bury and prepare carrion as food resource for their offspring. Buried carrion can still be discovered by other burying beetles. If these intruders are successful in taking over the carrion, they kill all eggs and larvae present. Fast larval development resulting in accelerated consumption of the carrion results in an earlier time point when the carrion becomes unattractive for intruders. To test the hypothesis that biparental care will result in accelerated larval growth and development as well as faster consumption of carrion, we will compare body mass and developmental stage of larvae, and mass of carrion between larvae reared by two parents and larvae reared by the female only, when the larvae are 12 hrs, 24 hrs, 36hrs, 48hrs, 60hrs, and 72 hrs old.
    This experiment offers the opportunity to involve up to 6 dual enrollment students and undergraduate students in data collection. The last five summers have shown that the students quickly learn the skills required for data collection and can run part of the experiments independently. The projects of the previous summers were successful, especially the project in summer 2007. A manuscript reporting the results of this project will be submitted within the next 10 days. The students, who participated in this project, presented their results at the Annual Meeting of Nebraska Academy of Sciences in April 2008.
    Claudia Rauter - Biology (crauter@mail.unomaha.edu)

2009 Poster

  • Gene discovery in the parasitic plant Cuscuta pentagona: Gene cloning and characterization of expressed sequence tags. The proposed research would make use of my investigation into the physiology of the parasitic plant Cuscuta pentagona (dodder) as a focus for introducing students to the skills and strategies of laboratory research in biology. C. pentagona is a rootless parasite that cannot live without a host plant, as it acquires a majority of its nutrients and energy by piercing the host tissue and withdrawing water and nutrients from the host vasculature. Furthermore, the parasite is essentially leafless, possessing only vestigial scales. In the closely-related but non-parasitic plant, Ipomoea hederacea (morning glory) several important biochemical processes occur in the root and leaf tissues, including the reduction of environmental nitrate to ammonia for amino acid synthesis. Several interesting questions thus arise: What physiological and genetic changes have accompanied the switch to the parasitic habit? Are the genes for processes largely limited to leaf or root tissues extant in the parasite, or have they been lost? Can the parasite still express these genes, and have they been recruited for novel purposes in C. pentagona?
    A first step toward answering many of these questions involves the identification and isolation of genes associated with each of these processes, both from the parasite and from the non-parasitic relative (as a point of comparison). At the outset of the research I propose to assign each of the students to attempt to isolate a particular gene fragment from either dodder or morning glory, using a PCR-based strategy, and drawing on information in the NCBI genome databases. If successful in amplifying a promising gene fragment from the source, the student will clone the fragment into a bacterial vector and prepare it for restriction analysis and sequencing. The use of computational methods for both prediction of gene sequences at the beginning of the project, and subsequent analysis of cloned sequences, makes this project an interdisciplinary pursuit between molecular physiology and bioinformatics.
    In previous years, the projects have pursued specific target genes, and the research has culminated in the final week with the students sequencing cloned candidate fragments. In addition to this approach, students in the summer 2009 program will assist in the characterization of “expressed sequence tags”, which are gene fragment clones generated by randomly sampling populations of expressed genes. Since initiating this strategy in the fall of 2007, and employing it with students in the summer 2008 program (with the assistance of past years’ STEP researchers) we have identified more than a dozen genes of interest.
    Students involved in this work would be exposed to the following philosophical aspects of biological research: 1) Learning to ask good questions about an experimental system, 2) developing a strategy for answering these questions, and 3) learning how different methods (physiological, molecular) may be employed in such a strategy. In addition, the students will be exposed to several technical aspects of laboratory work, including the basics of gel electrophoresis, nucleic acid purification, the polymerase chain reaction (PCR), DNA cloning and sequencing, and rudimentary spectrophotometric assay techniques. Finally, we will discuss how research is conducted, and the processes of writing, peer review, and publishing experimental results.
    Mark Schoenbeck - Biology (mschoenbeck@mail.unomaha.edu)

Final Report