491 Undergraduate Research students

Current Student Researchers

Christopher Bernal

Bernal, Christopher

Supervisor: Adriana Hernandez-Morales

Chamblee, JacobJacob Chamblee

Supervisor: Yi Chen (Irina)

Phage Mu is a lysogenic phage which replicates via replicative transposition. The typical proteins necessary for lysis in phage (SAR endolysin or endolysin, holin, and spanin-complex) have all previously been identified in Mu. However, when a gene of unknown function was knocked out, g25, lysis was not observed after induction, only a plateau due to cell death from the triggering of the holin. This indicates a likely undiscovered regulatory protein is involved in the regulation of Mu lysis. G22, the Mu SAR-endolysin, and g25, were cloned into two different plasmids and transformed into E. coli. Numerous complementation assays were then performed (with the phenotypes being observed via lysis curve). As complementation assay results indicate that the presence of g25 greatly speeds up cell lysis by g22, future work will involve proving a direct interaction of g22 and g25. Proof of a direct interaction between g22 and g25, in combination with already obtained complementation assay data, would be strong evidence of a novel lysis regulatory mechanism in Mu.

Crosby, StephenStephen Crosby

Supervisor: Eric Rasche

Advancements in molecular biology in the past two decades have led to the acquisition of unprecedented amounts of DNA sequence data, but the visualization of this data and its interpretation remain important challenges to the scientific community. Several approaches to create informative plots of sequence data have been devised in response to these challenges, including Circos: graphics software which allows users to design circular plots highlighting interesting genomic features and comparing different organismal genomes. In order to facilitate sequence analyses and Circos plot development, I am developing an online Galaxy tool which will enable scientists to incorporate bioinformatics techniques into their work while bypassing the learning curve associated with command-line tool usage. This new interface to the existing Circos software will enable life scientists to easily and efficiently create informative views of a variety of sequence data formats.

 Gibson, ShelleyShelley Gibson copy

Supervisor: Ramchander Rohit Kongari

We are researching the spanin gp11 by amplifying its expression in gram-negative competent cells and extracting it from the cell membranes. We will then purify it and possibly denature it to learn more about the structure and function.


LeSage, KaylaKayla LeSage

Supervisor: Karthik Chamakura

Composition and Assembly of Bacteriophage P1 Tails

Double stranded DNA phages are divided into three morphological classifications based on their tail structure. These three classifications are: siphophages, known for their long flexible tails, myophages, identified by their rigid contractile tails, and podophages noted for their short tails. Myophage tails are functional in host recognition, penetration, and DNA delivery. The mechanism of action for myophage tails is analogous to other contractile structures such as bacterial type VI secretion systems. Many well studied phages are myophages such as bacteriophage P1. Bacteriophage P1 is a commonly used transducing phage due to its capacity to package approximately 100 kb of DNA into its capsid and its wide host range. Despite the wide usage of P1, very little is known about the proteins that make up the tail or how they assemble. Only a handful of proposed tail genes can be identified using BLAST. It is our aim to identify the proteins composing the tail and study how they assemble. The first step in this process was to utilize a mutant of P1 that produces only tails. Interestingly, these tails were functional despite lacking an assembled capsid. The puncturing action of this tail only mutant has a bactericidal effect. With the intention to isolate phage tails from lysates the tail tip protein of the mutant was tagged and ectopically expressed in Escherichia coli. Utilizing affinity chromatography and the tagged tail protein, P1 phage tails were isolated and their protein components separated by molecular weight. From here the bands will be analyzed using Mass Spectroscopy to identify the proteins.

Marrufo, ArmandoArmando Marrufo copy

Supervisor: Jesse Cahill

Spanins are required for outer membrane disruption of Gram-negative hosts by phages. Therefore, the release of phage progeny is dependent on spanins. Rz and Rz1 of phage lambda are the best-studied spanins and recent evidence suggests spanins achieve the final step of lysis by fusion—fusing the inner and outer membrane of the host. A genetic screen identified single missense mutants of the spanin complex that block lysis. These mutations cluster in three regions of the complex, suggesting these regions are important for spanin function. However there were no single missense mutants identified in certain regions of the spanin complex, such as between two predicted alpha helices of Rz. Our hypothesis was that this region functions as a flexible linker, and has no other function (such as interaction or fusion). To test this hypothesis, we replaced a 15 aa stretch in this predicted linker region with Gly-Ser repeats. If specific residues were required in this region for spanin function, we would expect function to be lost. Surprisingly, the spanin complex functioned with an artificial linker replacing ~10% of the residues of this protein. My project will focus on extending and contracting this linker to probe the functional limits of the spanin complex. Additionally, I will be probing other regions of the spanin complex for regions that can tolerate linker substitution.


 Maughmer, Cory2015-09-10

Supervisor: Eric Rasche

PRUNE (Picking Readable Useful NamEs) is a project to automate name selection for gene products based on database results from BLAST, InterPro, and other sources. It will make selections using fuzzy inference methods based on several input factors for a name such as similarity to other hits, length of the name, and presence of numeric characters. The decision making method will be tuned using a genetic algorithm that tests the program’s results against a selection of test cases curated from past genome annotation work.

 Mijalis, EleniEleni Mijalis

Supervisor: Eric Rasche


 Min, LornaLorna Min

Supervisor: Karthik Chamakura

The single-stranded RNA phage M encodes a single 37 amino acid lysis protein, Mlys, with a predicted transmembrane domain and N-out, C-in topology. We propose to use both a genetic and a biochemical approach to determine its sub-cellular localization, mode of action for lysis, affected host factors, and key Mlys amino acid residues. Mlys is currently proposed to inhibit MraY, an enzyme that catalyzes the formation of the first lipid intermediate in cell wall biosynthesis, based on predicted similarities with the phiX174 phage lysis protein E; E is a transmembrane protein and exhibits an N-out, C-in topology as well. Many current antibiotics cause cell death by inhibiting penicillin-binding proteins (PBP), proteins that catalyze the polymerization and crosslinking of the glycan strands comprising peptidoglycan. However, long-term usage of such antibiotics has led to increased antibiotic resistance. Compounds causing cell death through other methods, then, have potential therapeutic value.

 O’Leary, ChandlerChandler

Supervisor: Jesse Cahill

The final component of phage lambda lysis of E. coli involves the spanins. The lambda spanins Rz and Rz1 disrupt the outer membrane (OM) creating a portal for release of phage progeny.  Recent evidence suggests the spanins collapse the OM  by fusing the two membranes of the cell envelope.  It has been shown that Rz and Rz1 interact in the periplasm before lysis, however the exact sites of spanin interaction remain unknown.  We aim to identify the interaction interfaces of Rz and Rz1 using biochemical and genetic approaches.

Tran, JenniferJenniufer Tran

Supervisor: Karthik Chamakura

MS2 is a male-specific single-stranded RNA bacteriophage, which infects E. coli through the conjugative F pilus. The expression of the lysis protein, L, of this virus has been shown to induce random blebbing and eventual cell lysis although the exact mechanism is still unknown. Previous studies have documented this process after bacteria have grown in aerobic conditions, often in a water shaker bath. However, in nature, E. coli grow anaerobically and in a non-shaking environment – the intestinal tract. In order to more fully understand how L-induced lysis occurs in nature, we mimic these conditions by inducing L in E. coli growing anaerobically in a flow chamber under an optical microscope. Preliminary results show that blebs do not follow the formation and stabilization which is observed in aerobic conditions. The next step will be to repeat the procedure with other known proteins of single gene lysis systems and compare them to peptidoglycan-inhibiting antibiotics.

 Wilder, Josephjoseph Wilder

Supervisor: Adriana Hernandez-Morales

My 491 project this fall involves working with a protein that is produced by phage Petty. Gp38, which encodes an exopolysaccharide depolymerase, is a protein of interest due to its ability to degrade the biofilm surrounding the host bacteria, Acinetobacter baumanii. This protein is composed of three separate domains, one of which is believed to cause it to agglomerate in a fashion that keeps a detailed 3-D structure from being obtained. By making different forms of the functional protein that are devoid of that specific domain, it is hoped a more detailed 3-D structure can be obtained.

Former Student Researchers

Johnson, Bryan graduate school
Shrestha, Ritu PhD program in Biology, Texas A&M University
Kaspar, Justin PhD program in Interdisciplinary Biomedical Sciences at University of Florida
Lessor, Lauren Research Assistant, CPT program, Texas A&M University
Mohan, Sheba Physician Assistant, DFW
Tsau, Joshua MD program, UT Houston Medical School
Dachowski, Michael MD program, University of Texas Medical School, Houston
Herrera, Oscar Clinical Pathology Laboratories, San Marcos
Lawler, Jessica PhD, Dept. of Biological Chemistry & Molecular Pharmacology, Harvard Medical School
Migl, David PhD program in Biophysics, Harvard University
Brahmbhatt, Kirtan MD program, Texas A&M University Health Science Center
Kulkarni, Aneesha PhD program in Molecular Biology focusing in immunology, San Jose State University
Park, Katherine MD program, Baylor College of Medicine
Rasche, Eric Programmer II , CPT  program, Texas A&M University
Simpson, Jacob MS Health Administration TAMU HSC
Edwards, Garrett PhD program in Biochemistry, University of Colorado, Boulder
Khatemi, Brontee the director of education at Sylvian Learning Center, Dallas, TX
Ladzekpo, Tsonyake Medical Scribe at PhysAssist Scribes, Inc., Houston, TX
Luna, Adrian PhD program in Biomedical Sciences, University of New Mexico
Snowden, Jeffrey PhD program in Micro-logy & Cell Biology, University of Texas Medical Branch, Galveston
Church, Kaira certification in Clinic Lab, UT Health Science Center in San Antonio, TX
Lancaster, Jacob Research, Texas A&M University