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Student Research Symposium 2013
Oral Presentations - Tuesday, March 26 [1:00-6:00p.m.]
Bioinformatic analysis of 39 coordinately expressed genes associated with the transition from vegetative growth to asexual development in Fusarium graminearum

Students: Sara Atkinson, Hazel Oseungo-Buyu, Kelley Godbout, Elizabeth Morris
Faculty Mentor: Dr. Joseph Flaherty

Time: 1:00

Many important filamentous fungi propagate and spread via the production of asexual spores (conidia). Conidiation is a defined program of morphological development, which presumably requires the coordinated efforts of many individual genes and signal transduction pathways. In the fungal plant pathogen, Fusarium graminearum, the morphological transition from filamentous growth to conidiation is critical for dissemination and infection. In spite of this, very little is known about the genetic regulation of this important developmental process. From genetic screens designed to identify genes regulating specific aspects of morphogenesis in F. graminearum, we identified several insertional mutants impaired in asexual development, which variously display a range of loss- and gain-of-function phenotypes. We conducted genome-wide analyses of gene expression using microarrays [Fusarias520715 Affymetrix GeneChip] on the wild type and a loss-of-function mutant strain cultured under conditions either favorable or unfavorable for asexual development. A shared subset of 39 genes exhibited altered expression (>4 f.c.) in both strains under both culture conditions. Analysis of these coordinately expressed candidate genes revealed the presence of several signaling homologs, six orphan genes, as well as three putative gene clusters. We have applied bioinformatics tools to search for shared promoter elements and to further examine the genomic signatures of these genes, providing further insight into their relationships and putative functions.

Microwave spectrum and ab initio calculations of 3-vinylbenzaldehyde (3-VBA)

Student: Miranda Smith
Faculty Mentor: Dr. Gordon Brown

Time: 1:15

The main purpose of our study was to use microwave spectroscopy to study the spectrum of 3-VBA, and to determine its precise geometry. In order to accomplish this, we used the Gaussian 03W software package to conduct ab initio calculations of 3-VBA, and then used Coker’s microwave spectrometer to measure the rotational spectrum. We optimized the molecular signal by varying the conditions of the experiment, and then scanned the spectrometer from 7.5 to 18.5 GHz to obtain the 3-VBA spectrum. We analyzed the spectrum using the JB95 software program to obtain the rotational constants for 3-VBA.

From this study, we found that 3-VBA has four conformations, which are as follows: cis,cis-3-VBA; cis,trans-3-VBA; trans,trans-3-VBA; and trans,cis-3-VBA. We were able to perform ab initio calculations on all four conformations and to use the JB95 software to analyze the spectrum of each conformation. Upon comparison to the experimental data, we were able to determine that the calculated rotational constants from the Gaussian 03W software program were very close to the experimental rotational constants, showing that this program is accurate.

A systems-biology approach to build gene-regulatory network models connecting osmotic stress responses and asexual development in Fusarium graminearum

Students: Ashley Thompkins, Megan Sexton, Atticus Lum, and Brendan McCarron
Faculty Mentor: Dr. Joseph Flaherty

Time: 1:30

Fusarium graminearum is a notorious fungal plant pathogen and causes head blight disease in small grain cereals and ear rot disease in maize. Infection with F. graminearum leads to yield losses and mycotoxin contamination. Mycotoxin formation and asexual development are thought to share common modes of genetic regulation. However, the regulatory networks connecting salt/osmotic stress to either is limited or undefined. Salt tolerance is a complex trait that remains poorly understood. Very few genes have been identified that are required for salt tolerance in plants, animals, or fungi. To address this, we screened >5,000 insertional mutants of F. graminearum (PH-1) for gain-of-function or loss-of-function phenotypic classes specific to both asexual development and osmotic stress responses. These screens yielded strains representing all classes and one outlier from each were chosen for additional analyses. Mutant 9E1 exhibits an “osmotic hyper-tolerant” phenotype when cultured on growth media containing either salt or glycerol. In contrast, mutant 11B1 displays an “osmotic-overly sensitive” phenotype, where growth is severely limited on concentrations of solute that have a negligible effect on growth by control strains. Both 9E1 and 11B1 grow normally on non-osmotically adjusted media and were subsequently chosen for transcriptional profiling experiments. Additionally, mining gene expression data of developmental mutants 8B5 (aconidial) and 8E8 (hyperconidial) has revealed putative candidate regulatory genes. Results of various experiments designed to examine each mutant’s response to various stresses (e.g., oxidative stress, high temperature) will be presented. This study provides evidence supporting the likely regulatory connections between stress response and asexual development as we progress towards a clearer understanding of the genes involved in asexual development and osmotic stress responses in F. graminearum.

Microwave spectrum and analysis of meta-Chlorobenzaldehyde

Students: Jessica Garrett and Sean Arnold
Faculty Mentor: Dr. Gordon Brown

Time: 1:45

Our laboratory is interested in the shape of molecules. In chemistry and biology, it is said that “shape determines function,” which means that a chemical’s function is often directly controlled by its geometry. The main purpose of this study was to use microwave spectroscopy to study the spectrum of meta-Chlorobenzaldehyde, which will allow us to determine its precise geometry. The study was completed using Coker’s student-built microwave spectrometer.

In this project, the pure rotational spectrum of meta-Chlorobenzaldehyde (m-ClBA) has been measured from 8 18.5 GHz by chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The spectrum has been analyzed to discover the rotational constants of two conformations of m-ClBA. For each conformation we have found the rotational constants corresponding to both the 35Cl and the 37Cl species. The rotational transitions measured exhibit hyperfine splitting, from which we have uncovered the nuclear quadrupole coupling constant of chlorine for each isotopologue. The rotational constants and the nuclear quadrupole coupling constants have been compared to ab initio calculations performed using the Gaussian 03W software package.

BREAK - 2:00
Breadgivers

Students: Joana Fuller and Christina Vital
Faculty Mentor: Dr. Rhonda Knight

Time: 2:15

This presentation gives an overview of Jewish immigration into America at the turn of the century, beginning with living conditions in Poland, showing images from the Lower East Side tenements, and discussing the pressures to assimilate that Jewish immigrants faced in the US. It is accompanied by a discussion of Anzia Yezierska's novel Breadgivers (1925).

Frida Kahlo and Diego Rivera

Student: Ellen Skipper
Faculty Mentor: Dr. Julia Klimek

Time: 2:30

This presentation introduces the political and personal paintings created by Mexican artists Frida Kahlo and Diego Rivera - this presentation was originally shown in the Modern Poetry course to add to their readings of Latin American poetry of the 20th century.

Mrs. Dalloway

Student: Devan Williams
Faculty Mentor: Dr. Julia Klimek

Time: 2:45

This presentation gives an overview of Sigmund Freud's theories in relation to the British novel Mrs Dalloway by Virginia Woolf (1925), written in the style of stream-of-consciousness, which was discussed in the Women in Literature course.

Continued discussion on research in literature
BREAK - 3:15
Optical answer sheet data extraction via pattern recognition

Student: William Trent Edwards
Faculty Mentor: Dr. Paul Dostert

Time: 3:30

This data extraction project will create a new method of evaluating scores from optical answer sheets. To do this the project will utilize a generic flatbed scanner in conjunction with a MATLAB script for pattern recognition and comparison. An optical sheet will be prepared, scanned, and then algorithmically evaluated based on the comparison between a matrix created by a reference answer sheet and the one being evaluated. The matrices of both the reference and new answer sheets will be compared using various image decomposition algorithms. Using image decomposition, a scanned answer sheet should be able to produce results that will summarize the overall score, as well as produce the answers to individual questions upon request. These comparison methods will allow for an alternative to industry standard optical answer scoring systems in terms of data quality and individualized data extracted.

BREAK - 3:45
Facial recognition using computer vision techniques

Student: James Shumpert
Faculty Mentor: Dr. Paul Dostert

Time: 4:00

Our goal is to analyze various mathematical methods that are used with facial recognition. We will then compare the various methods and explore their uses by creating MATLAB programs.

BREAK - 4:15
Using Data Mining to Place Incoming Freshmen into the Appropriate Math Course

Students: Dylan Bates, James Shumpert, and Jon Moree
Faculty Mentor: Dr. Rachel Manspeaker

Time: 4:30

The purpose of our research was to build off of research conducted by James Shumpert in the spring semester of 2012, which showed that high school GPA and SAT scores do not work effectively as a placement tool in predicting success or failure in college math courses. Over the following summer, Data Mining techniques were used to analyze data from math placement tests. We wanted to discover which pretest questions contributed most to the variation of student data and find interesting and useful patterns to analyze.

Overall, the clustering scheme we employed did a good job of clustering students and even predicting success in the next placement test. When Item Response Theory is used in combination with previous analysis, it becomes clearer as to which questions helped differentiate between students of different levels and which did not. This could be used to create a better placement test in the future, possibly emulating those of other universities, creating random questions that differentiate between students of high and low ability, and will ultimately place incoming freshmen into the appropriate math class.

 

Coming out: A fight against history.

Student: Lauren Brailsford
Faculty Mentor: Dr. Tracey Welborn

Time: 5:00

The research tells the steps of the coming out process, and how history has always held a negative attitude toward such orientation.

Sparrow Scholars Presentation - 5:15
 
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