BIOL 491 is an independent research course supervised by various faculty members in the department (1-4 credit hours). Based on the information below, students should select their area of interest, pick up a 491 form from the Undergraduate Advising Office (107 Butler) or click here and then contact the appropriate professor to schedule a meeting to discuss their options. Upon completion of the form by the supervising professor, the student will return the form to an undergraduate advisor in 107 Butler. At this time the advisor will rule on whether or not the course is acceptable and exactly how it will be used in the degree plan. Up to 8 credit hours may be used as a directed elective (BIOL, BOTN, MICR, ZOOL). Additional credit hours may be used as general electives. The following is not a complete listing of all professors that students may do independent research with.

Dr. Karl Aufderheide | kauf@mail.bio.tamu.edu
Developmental biology of Paramecium : morphogenesis of the cytoskeleton (light, SEM, TEM studies); molecular aspects of serotype gene expression; nuclear development and differentiation (laser tweezers). Note: Short projects are available for 1 semester students; courses are also available for students interested in the Fellows Program dealing with more complex level projects. Several topics concerning the developmental biology and developmental genetics of Paramecium tetraurelia are available. All students should have some background or experience in microbiology (sterile techniques) and genetics (Mendelian crosses and meiosis).

Advanced light microscopy and photomicrography.
As part of an ongoing study of patterning and the cytoskeleton in the cell, various advanced light microscopic procedures may be performed using cells in various stages of the cell cycle or of various mutant types. Techniques include: Application of the laser optical force trap (laser tweezers), Nomarski differential interference contrast microscopy, phase contrast, immunofluoresence, and advanced silvering techniques. Photomicrography of cells followed by developing and printing the exposed films are part of the project. Students may benefit from some previous knowledge of microscopy and physical optics and the theory and practice of photography, but this is not essential.

Other topics relating to electron microscopy, and cell physiology are possible. Times and credit may be negotiated.

Dr. Deborah Bell-Pedersen | dpedersen@mail.bio.tamu.edu
Research Opportunities in Molecular-Genetics and Biological Rhythms
Research in my lab focuses on understanding the molecular and biochemical makeup of the biological clock, using the filamentous fungus Neurospora crassa as a model organism. In Neurospora , the clock controls daily rhythms in asexual spore development, providing a convenient means to assay the clock. In addition, the ability to do genetics and sophisticated molecular studies in Neurospora has led to the identification of genes that are required for clock activity and genes which are controlled by the clock. Currently, we are investigating the function and regulation of these genes. In addition, we are using genetic mutant screens to identify novel components of the biological clock.

 Students interested in pursuing research projects in my lab will gain experience in general laboratory techniques and fungal genetics by assaying mutant strains of Neurospora for defects in the clock. After successful performance, students will have the opportunity to characterize the mutant strains using both genetic and molecular approaches or to select an alternate research project. The amount of time required to spend in the lab and credit hours are negotiable.

Dr. Vincent Cassone | vmc@mail.bio.tamu.edu
Research opportunities in Neuroscience and Biological Rhythms. Research in the Cassone lab is directed at the neurobiology of biological rhythmicity. This research is primarily concerned with birds and mammals, but there is a very strong commitment to 1) comparative anatomy and physiology and 2) addressing biological questions using intelligent choices of model species. In other words, we are open to the study of any organism, provided it is a rational choice directed at an interesting biological question.

Biological rhythms in mammals and birds are controlled by an endogenous biological clock or circadian system. This system is known to comprise at least 4 structures: 1) the pineal gland, which produces the hormone melatonin, 2) the hypothalamic suprachiasmatic nucleus (SCN) which receives direct visual input from the retinohypothalamic oscillators, and 4) extraocular photoreceptors in the brain, behavioral research on the effect of surgical removal of the abovementioned structures and brain slice physiology.

Students interested in 491 research projects will begin by assisting in the research projects of graduate students, technicians and/or Dr. Cassone. After satisfactory performance, these students may begin an independent research project under Dr. Cassone's supervision.

Dr. Jim Golden | jgolden@tamu.edu
The general research area of my lab is molecular biology and genetics of cyanobacterial gene regulation. Cyanobacteria are organisms that obtain energy from photosynthesis and that are capable of both carbon and nitrogen fixation. The main topic of the research in my lab is on the regulation of heterocyst development and the expression of nitrogen-fixation genes. Heterocysts are terminally differentiated cells that are specialized for nitrogen fixation. We are particularly interested in studying three developmentally regulated genome rearrangements that occur during heterocyst differentiation.

My laboratory personnel use a variety of molecular and genetic techniques in their research including gene cloning, analysis of gene expression, DNA sequencing, DNA-protein interactions, cyanobacterial genetics, and transposon tagging.

I normally have 1 or 2 students doing 491 research each semester. I only accept talented and dedicated students that are planning on going to graduate or professional school. Students should expect to spend an average of at least 12 to 15 hours per week in the lab, and I prefer students that can take two consecutive semesters of 491 research.

Dr. Susan Golden | sgolden@tamu.edu
My lab group studies two biological questions using a unicellular cyanobacterium as our experimental organism. One question is how environmental cues, in our case light quality and intensity, can regulate gene expression. We study several photosynthesis genes whose expression is controlled by light. The other project is aimed at understanding how a biological clock works. Our organism exhibits circadian rhythms of gene expression, and we use methods of molecular genetics to try and understand the function of the clock.

All projects require mastering techniques of molecular biology, so students should be prepared to commit themselves to two semesters of research to develop these skills, and to spend at least 12 hours per week in the laboratory (for up to 3 hours of 491 credit.)

Dr. Ira Greenbaum | ira@mail.bio.tamu.edu
The research in the Greenbaum laboratory is focused around questions concerning the causes and effects of chromosomal mutations in natural populations of vertebrates (primarily mammals.) Analyses of variable chromosomes within populations and of chromosomal differences between species are evaluated in terms of the mechanisms of karyotypic evolution. Critical components of these evaluations include: assessing the effects of chromosomal heterozygosity on reproductive fitness, determining how the meiotic process responds to the challenge of chromosomal mutation, evaluating population-genetic parameters associated with spatial and temporal partitioning of chromosomal variation, and investigating mutational non-randomness as relates to overall chromosomal structure. Most of the current research is designed to elucidate the genetic basis and biomedical and evolutionary implications of chromosomal fragile sites.

Biology 491 projects usually allow students to work with basic karyotype construction and analysis (typically including both G- and C- banded chromosomes.) Advanced students may also become involved with basic cytogenetic techniques including cell culturing, karyotyping of cells, chromosome banding, and computerbased imaging.

Dr. Larry Griffing | griffing@mail.bio.tamu.edu
The 491 projects in Dr. Griffing's lab currently relate to his interest in plant endocytosis and generating a 3D spatially accurate map of the plant cytoplasm. The techniques you would learn in the lab may include: 3D modeling using modern computer graphics packages, biochemical subcellular fractionation of plant cells, sophisticated, quantitative video microscopy techniques, and assay of transiently-expressed and stably-expressed reporter genes (GUS and GFP) in transgenic plant tissues.

The questions of the lab currently include: What regulates endocytosis of membrane and receptors in plants? How do early plant endosomes differ from late endosomes biochemically? How can 3D reconstructions of cellular dynamics in plant cellsbe combined into a single model? How does the plant hormone, auxin, affect secretion and endocytosis? How do plant roots tolerate high ground temperature extremes? What is the role of a purple acid phosphatase in the uptake of phosphate by Arabidopsis? What is the targeting mechanism of lipid desaturases in plant cells? These questions are rather broad, but 485 students can make a significant contribution to finding the answers.

I also have interests in using image analysis for non-perturbing environmental assessment. A publication about 7 years ago from my lab set the stage for doing video-based analysis of environmental features. I am advising Sarah Bernhardt on a similar project over the next couple semesters and she could use some help.

1) Environmental Imaging Project 1:

Scanning slides for environmental monitoring of Stetson Bank.  Student would interact with supervising graduate student, Sarah Bernhardt and advising faculty, Larry Griffing and Mary Wicksten.  1 credit unit, one afternoon (5 hr) per week.  Contact Sarah (sbernhardt@mail.bio.tamu.edu, 845-3422).

2) Environmental Imaging Project 2:

Image analysis, using previously-defined routines, of scanned images of Stetson Bank. Some familiarity with Photoshop would be desirable.  Student would interact with supervising graduate student, Sarah Bernhardt and advising faculty, Larry Griffing and Mary Wicksten.  2 credit units, two afternoons (10 hr) per week.  Contact Sarah (sbernhardt@mail.bio.tamu.edu, 845-3422).

Dr. Timothy C. Hall | tim@mail.bio.tamu.edu
My lab is interested in regulatory mechanisms of gene expression. Current foci of interest include the involvement of chromatin and DNA topology in both transcriptional activation and silencing of genes. Our target is a gene encoding phaseolin, a seed storage protein that is very highly expressed in embryogenesis but is absolutely silent in vegetative tissues. We have recently shown that a nucleosome is rotationally and translationally-positioned over the TATA box region of this gene and we are now investigating protein and other factors that are involved in displacing or remodeling this nucleosome to achieve transcriptional activation during early embryogenesis. These studies, and allied research to determine the influence of shape or toppology of the promoter structure on expression, involve extensive work with transgenic plants.

Another aspect of our work is transformation of rice. As one of the most important food crops worldwide, rice is a very attractive candidate for improvement as a crop plant through biotechnological approaches. We have transformed rice with several important genes and are especially interested in conferring resistance to the rice water weevil, the major insect pest in Texas rice. Previously, we used direct transformation techniques (electroporation, biolistics), but these approaches lead to gene silencing and other forms of unreliable expression. We have become interested in various mechanisms of gene silencing and are publishing a series of papers in this area. However, we are now able to transform rice reliably and routinely using Agrobacterium vectors and are looking forward to characterizing the expression of a series of genes in this monocot plant.

Another facet of gene silencing has arisen in our plant virus studies. As a means to investigate the replicase of brome mosaic virus, we transformed tobacco with the replicase gene encoded by RNA-2, one of the three BMV genomic RNAs. As anticipated, the p2 protein expressed in these plants was able to assist in supporting replication of RNAs 1 and 3 in trans but, amazingly, silences replication of added RNA-2. Future studies with these transgenic plants and BMV are designed to determine the basis for the observed silencing and to gain further insight to virus replication mechanisms.

Dr. Duncan MacKenzie | duncan@mail.bio.tamu.edu
Comparative endocrinology of reproductive and thyroid function, comparative physiology.
Biology 491 students in the MacKenzie lab participate in ongoing studies of the hormonal regulation of growth, reproduction, and metabolism in nonmammalian vertebrates (primarily fish and reptiles). Training is initially provided to develop expertise in basic endocrine techniques such as animal handling, blood sample collection, hormone administration, gel electrophoresis, RNA and DNA isolation, and assay of blood hormones using radioisotopes and column chromatography. This training takes approximately one semester. Students will then be expected to organize and conduct an independent research project. Students are expected to work at least two, but preferably three, afternoons a week for a minimum of two credit hours a semester. Weekend and night work, as well as participation in routine animal care duties, is usually required.

Priority for 491 positions will be given to:
1) Students who are seriously interested in pursuing zoological research as a career; 2) students who have successfully completed Zoology 388, Principles of Animal Physiology; 3) students who are sophomores or juniors, and are willing to take 491 hours for a minimum of three semesters (allowing successful completion of a project following the one semester training period); 4) students who are zoology majors and especially active members of the TAMU Zoological Society.

Dr. Michael Manson | mike@mail.bio.tamu.edu
1) Our laboratory uses genetic, biochemical, and molecular and cellular biological techniques to investigate bacterial motility and chemotaxis. We focus on the function of "complex" chemoreceptors, transmembrane signaling by chemoreceptors, and the structure and function of the bacterial flagellum, especially the mechanism by which the electrochemical potential across the cell membrane is converted into the mechanical work of flagellar rotation.

2) I also have a strong and life-long interest in natural history. I am a reasonably competent birder, and I have spent a good deal of time observing plants and other wildlife. I am also past President of the Rio Brazos Chapter of the National Audubon Society.

One of our great local natural assets is Lick Creek Park. This 515-acre, relatively undisturbed tract is owned by the City of College Station. The park contains a variety of micro-environments, including: the creek itself; the associated riparian woodland, oxbow ponds and unique sedge meadow; and the upland post oak savannah. The assorted habitats support a large diversity of plant species, including the endangered Navasota Ladies' Tresses and the Houston Meadow Rue, and a range of animal species characteristic of the different plant communities.

I offer a variable credit Zoology 491 for students who are interested in contributing to an ongoing resource survey of different vertebrate groups at Lick Creek Park. Ideally, these studies will encompass both the Fall and Spring Semesters (as well as summer session, if possible), in order to provide seasonal distribution data for birds and for reptiles and amphibians. The bird surveys primarily involve passive observation and listening to calls and songs. The herpetological surveys will require a more active search for the animals being censused, since they tend to hide in and under things, and their visibility is also strongly dependent on weather conditions and time of day.

An essential part of each project will be to prepare a summary of data suitable for presentation to the College Station Parks Department and the Texas Department of Wildlife and Fisheries. Examples of reports from past students are available.

Dr. Rita Moyes | rita@mail.bio.tamu.edu
Students interested in working with bacterial cultures, learning media and culturing techniques, analyzing bacterial populations, and performing epidemiological surveys are welcome. Completion of introductory microbiology is required. Also BIOL 491 involving immunological techniques are available to students who have completed MICR 454/455.

Dr. C.O. Patterson | cop@mail.bio.tamu.edu
Stress responses in micro-organisms are the current focus of research in my lab. We are examining the effects of toxic components of crude oil on marine phytoplankton. Our previous investigations have shown that harmful effects of oil on marine algal cells are at least partly due to disruption of membrane structures. The most toxic components of crude oil are the volatile aromatic hydrocarbons (VAH: benzene, toluene, xylene, etc.). The VAH act as lipid solvents, solubilizing and disrupting the lipid bilayer structure of membranes. If sub-lethal doses of VAH are given, so that cells are damaged but not killed outright, the cells can recover and protect themselves by actively altering the lipid composition of their membranes. We are now trying to deten-nine whether the toxic VAH also affect the protein components of membranes, and how cells detect VAH damage and control their protective responses to these stresses.

Students working in my lab are expected to learn the techniques and procedures for growing and harvesting the cells (preparing and sterilizing media, operating the bioreactors, collecting cell suspensions), for isolating and identifying membranes and membrane fragments (preparing buffer solutions, operating low-speed and ultracentrifuges, carrying out assay procedures with specific reagents, operation of spectrophotometers, etc.), for measuring enzyme activities in purified membrane fractions before and after exposure to VAH, and for separation and identification of classes of membrane proteins.

Hours are flexible, and can usually be arranged to fit the schedule of the student. I expect that a 491 student will spend about 3 hours per week in the lab for each hour of course credit (if student signs up for 3 hours of credit, about 9 hours per week should be spent working in the lab). Students will be expected to keep a notebook, with a daily log of their lab work, and will submit a written report at the end of the semester.

Dr. Hongmin Qin | hqin@mail.bio.tamu.edu
My lab is interested in understanding the process of ciliogenesis and how the cilium perceives and relays sensory signals. These investigations make use of two model organisms: the biflagellate green alga Chlamydomonas and the small roundworm Caenorhabditis elegans.
Cilia and flagella, including primary cilia and sensory cilia, are highly conserved organelles that project from the surface of many cells. Although many cilia and flagella serve as motility structures, some forms are not motile but function as sensory organelles instead. Abnormal or dysfunctional cilia are associated with several human diseases, including polycystic kidney disease (PKD), retinitis pigmentosa and Bardet-Biedl syndrome (BBS). Current research in my lab is aimed toward dissecting a process called intraflagellar transport (IFT). IFT is a microtubule-dependent transport system, which is universally required for assembling and maintaining cilia/flagella from molecular components in the cytosol. We use molecular, cellular and biochemical methods to characterize the components of the IFT system, to understand how IFT is regulated and how it functions in ciliary sensory signal transduction.
Students interested in pursuing research projects in my lab will first get training in general laboratory techniques. After essential skills are developed, students, with appropriate supervision will select and work on their own independent research projects within the lab interests.

Dr. Bruce Riley | briley@mail.bio.tamu.edu
In my lab, we use genetic analysis of the zebrafish to uncover conserved mechanisms of vertebrate embryonic development. Our research focuses on development of the hindbrain and inner ear, both of which have complex structures arising from an intricate array of developmental processes. We systematyically identify and characterize the molecular mechanisms controlling development of the hindbrain and inner ear by analyzing mutants with specific defects in these tissues.

Dr. Timothy P. Scott | tims@mail.bio.tamu.edu
Parasitological research is performed in my laboratory. Participants may be expected to assist in collections and/or research in the field. The host organism I work with is the American alligator ( Alligator mississippiensis ). I am especially concerned with tracing the life cycle of parasites that utilize the alligator as the definitive host. Therefore, other aquatic organisms may also be evaluated that are part of the food chain of alligators. Additionally, the lab is called upon from time to time to characterize or identify parasites reported to us from other agencies (e.g., Texas Parks and Wildlife; Rockefeller Wildlife Refuge Center; Padre Island National Seashore). This lab may also work in conjunction with Dr. Rita Moyes in determining the bacterial flora of host organisms.

Students will employ a number of techniques in my laboratory. Students should be familiar with the current literature surrounding a given Parasitological project. Students will use a minimum of chemical skills in the staining, dehydrating and fixing processes of the parasites. Good, solid microscope techniques are a must. Some studies may lend themselves to field biology techniques. Such field experiences would require some travel and basic knowledge of anatomy and dissection/necropsy skills. The average time required in the lab per week for three hours of credit will be at least nine hours. There is some flexibility in this schedule dependent on the outside work required in the field.

Dr. Thomas Stidham | furcula@mail.bio.tamu.edu
My lab focuses mostly on the fossil record and evolutionary history of life around the world. Unlike many of the research labs, my lab is fundamentally an organismal biology lab and focuses on entire organisms--their morphology, anatomy, ecology, evolution, etc. While my research is mostly on birds (alive and dead), I have materials and independent projects available on a variety of fossil organisms from microfossils, plants, invertebrates, and vertebrates. I also am active in collecting data on living bird ecology and behavior and living insect (mostly grasshoppers) geographic distribution and natural history. The research in the lab is mostly specimen-based, but there are opportunities for field work across the state. These projects are potentially publishable and could form the basis for a senior thesis.

Dr. Max Summers | m-summers@tamu.edu
The Molecular Biology of Baculoviruses
The baculovirus studies emphasize current aspects of virus-host interactions and eukaryotic cell molecular biology. The insect baculoviruses are genetically complex (genome of 134 kilobase pairs) and have a unique life cycle: virions may assemble by budding at the cell surface early after infection, or in the nucleus late in infection by inducing the synthesis and assembly of unit membrane structures to become viral envelopes. We have determined that baculovirus infection results in G2/M phase arrest of the host cells [Braunagel et al. Virol. 243:195-211 (1998)]. This arrest correlates with the induction and abundant amplification of intranuclear unit membranes and microvesicles which serve, in part, to become viral envelopes. We have identified several proteins specific to the intranuclear membranes and the viral envelope which we are using as molecular markers to follow biosynthesis, trafficking and assembly [Beniya et al. Virol. 240:64-75 (1998): Hong et al. PNAS 94:4050-4055 (1997)]. One of these is a unique virus encoded protein with cyclin-like functions [Belyavskyi et al. PNAS 95(19):11205-11210 (1998)]. Our data strongly suggests that most of these proteins are integral membrane proteins and traffic via membrane-mediated pathways. Our results also suggest that the trafficking and targeting of these proteins involve accessory protein interaction(s) of both viral and cellular sources.

Dr. Terry Thomas | terry@mail.bio.tamu.edu
My interests are evolutionarily broad and include animals, plants and fungi. A major focus of the lab is the genomic analysis of gene expression programs during plant gene expression programs, particularly during embryogenesis and seed development, and the underlying regulatory mechanisms required for the initiation and maintenance of these programs. This work has illustrated the combinatorial interactions of cis and trans -acting factors that result in specific gene regulatory events. We are also using genomics tools to study the interaction of the rice blast fungus, Magnaporthe grisea , with plant hosts; the circadian control of gene expression; and the development of the vertebrate retina. An additional focal area is the utilization of molecular and cellular approaches for crop improvement. As part of these research activities, we have developed or adapted high throughput genomics approaches to accelerate the gene discovery process and subsequent analysis of gene expression and function.

Dr. Mary Wicksten | wicksten@mail.bio.tamu.edu
Depending on current interests and projects, undergraduate students can undertake projects in curating and identifying invertebrate specimens, maintaining marine aquaria, rearing marine organisms, or using our computers for numerical or digital analysis of ecological data. Field work along the coast of Texas may be available.

Dr. Ryland Young | ryland@tamu.edu
Bacterial viruses inject their DNA into cells and, at a programmed time, cause a breakdown of the cell membrane and wall, allowing the progeny viruses to escape. This process is called "lysis". My lab works on the genes which mediate host lysis. We want to know how these genes accomplish their lethal tasks, how the protein products cause the cells to burst open and how the timing of lysis is so precisely regulated. In a sense, the timing of phage lysis is the simplest "molecular clock", and we want to know how it keeps time.

In typical projects, 491 students will learn molecular genetics of bacteria and bacteriophage, and basic cloning and DNA sequencing technology. For example, you might isolate mutants which were defective in lysis, then clone out the defective genes, sequence the DNA, and characterize the protein products by gel electrophoresis and Western-blotting. 491 research students are only accepted if they are going to do at least two consecutive semesters (Fall-Spring, Spring-Summer, or Summer-Fall). 491 students are not relegated to menial tasks but instead conduct bench research projects under the direct supervision of a graduate student or a post-doctoral scientist, with Dr. Young in overall supervision.