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The study of biological sciences at St. Mary's University includes a broad-based curriculum and extensive scientific training designed to prepare well-rounded health care professionals. Students develop written and oral communication skills, critical thinking and analytical skills, and an understanding and respect for ethical and moral concerns. Because our students display competence, dedication and compassion, they are readily accepted into graduate programs, the health professions, biomedical research and teaching fields.
The program in biological sciences is built upon a rigorous study of biology and includes courses in chemistry, physics and mathematics that satisfy professional school entrance requirements.
Advanced biology electives include anatomy, general physiology, microbiology, genetics, embryology, endocrinology, cell biology, neurophysiology, comparative physiology, recombinant DNA technology, advanced nutrition and metabolism, immunology, medical microbiology and molecular biology. The final year includes a two-semester biochemistry course. Many biology majors also choose to minor in chemistry.
210-431-4321
traabe@stmarytx.edu
The program in biological sciences is built upon a rigorous study of biology and includes courses in chemistry, physics and mathematics that satisfy professional school entrance requirements.
Advanced biology electives include anatomy, general physiology, microbiology, genetics, embryology, endocrinology, cell biology, neurophysiology, comparative physiology, recombinant DNA technology, advanced nutrition and metabolism, immunology, medical microbiology and molecular biology. The final year includes a two-semester biochemistry course. Many biology majors also choose to minor in chemistry.
Contact Us
Timothy Raabe, Ph.D.210-431-4321
traabe@stmarytx.edu
Program Highlights
Students in the biological sciences program have been accepted into numerous internship and summer programs at universities around the country, including Columbia University, Cornell University, Harvard University, Loyola University, Massachusetts Institute of Technology, Southwest Research Institute, Texas A&M University and the University of Michigan.Students can apply for admission to cooperative partnership programs with The University of Texas Health Science Center at San Antonio in the following fields of study: clinical laboratory sciences, respiratory care, physical therapy, occupational therapy, nursing, medicine, dentistry and physician assistant.
Research Laboratories
The Department of Biological Sciences is housed in the Moody Life Sciences Building, which includes faculty offices, lecture and seminar facilities, research labs, a recently renovated animal facility, a stock room, a large laboratory for introductory classes, four laboratories for advanced courses and a computer laboratory.The department is well supplied with modern equipment essential for studies in cell and molecular biology, microbiology, immunology and biochemistry.
Two of the advanced labs and the computer lab were constructed in 1996 as part of a suite of labs and support facilities using funding from the Howard Hughes Medical Institute. Much of the department's instrumentation and equipment has been purchased in the last few years, using University resources as well as funding from the National Science Foundation and the Howard Hughes Medical Institute.
Available instrumentation and equipment includes: U.V. trans-illuminators and digital- and photo-documentation systems; DNA amplification and sequencing apparatus; Micro-centrifuges; Heated water baths; A DNA hybridization oven; A Class II bio-safety hood; A variety of vertical and horizontal gel electrophoresis systems; An autoclave; A computer operated micro-titer plate reader; Bioresearch grade water purification systems; Two high speed refrigerated centrifuges and assorted rotors; Walk-in refrigerated and heated environmental chambers; Shaking water baths; A refrigerated water bath; -70 and -20 freezers; Tissue culture and bacteriological incubators; Liquid scintillation and gamma counters; Several U.V. scanning spectrophotometers, Digital analytical balances; Electrophoresis equipment and power supplies; epi-fluorescence and visible light microscopes; A video microscopy workstation.
Students in our advanced courses use recently purchased Nikon Alphaphot2 microscopes. In addition, the computer lab used by faculty and students houses 13 Macintosh PowerPC computers. These computers are used for research and course work, and they all have Internet access.
Student Organizations
There are currently four registered student organizations within the department of Biological Sciences. These organizations serve multiple purposes within and outside of the department: they allow students to associate with others who are pursuing similar career goals; they help keep students informed of programs, opportunities, and events within their major and career path; they allow students to meet and network with professionals in career fields which they are interested; and they provide service to the St. Mary s and San Antonio community in the Marianist tradition.MARC U*STAR
The Minority Access to Research Careers (MARC) Undergraduate Student Training in Academic Research (U*STAR) is sponsored by the National Institute of General Medical Sciences (NIGMS). MARC U*STAR provides underrepresented students majoring in biology, biochemistry, chemistry, physics or engineering science opportunities to complete research training and work alongside faculty mentors in the biomedical sciences. Undergraduate students participating in the MARC U*STAR program are provided with academic and research support to prepare them for Ph.D. programs in the biomedical sciences.Facilitated Admissions for South Texas Scholars (FASTS) Program
FASTS is a joint program between the University of Texas School of Medicine at San Antonio and St. Mary's University.Click for more info
Objectives
- Allow students with academic excellence and a demonstrated interest in medicine to receive early acceptance to the University of Texas School of Medicine at San Antonio (UTSOMSA).
- Provide students with a rigorous academic preparation for medical school.
- Provide students with academic enrichment and clinical experiences provided through the Summer Premedical Academy at the School of Medicine, as well as MCAT preparation.
Eligibility and Program Details
- Academically outstanding first year students who plan to study medicine and currently attend St. Mary's University will be eligible for this program.
- In the spring of their freshman year, students will be encouraged to apply for acceptance into the FASTS program.
- Following completion of the application, a committee of St. Mary's faculty, the St. Mary's Premedical Advisor, and the St. Mary's FASTS Coordinator, as well as UTSOMSA faculty/staff will select students for an interview.
- Interviews will be conducted at UTSOMSA during the spring to determine if the applicant possesses the academic abilities and personal qualities that predict success as a medical student and physician.
- The decision to accept a student into FASTS will be made solely by the Admissions Committee of the School of Medicine.
- The student must be a United States Citizen or a permanent resident and a Texas resident.
- Application deadline will be February 1 every year.
- In addition to academic enrichment and clinical experiences at UTSOMSA, students will be offered tutoring and academic counseling at St. Mary's during the school year.
Acceptance Requirements
- Successful completion of the program requires the participant to complete a Bachelor s Degree at St. Mary s University with an overall GPA and a science GPA of at least 3.25. AP coursework will NOT be considered fulfillment of science requirements.
- In the spring of their junior year, qualified participants who meet the premedical coursework requirements will take the MCAT and those who obtain a ratio of science GPA/MCAT scores of 3.25/28, 3.5/26 or 3.75/24 or better will be eligible for acceptance to medical school following an interview by the admissions committee. In addition, participants cannot have a score less than a 7 on any sub-section of the MCAT.
- Participants must satisfy all requirements of the Texas Medical and Dental Schools Application Service (TMDSAS) application process including a letter of recommendation from the Pre-Professional Health Advisory Committee at St. Mary s, have record of ethical behavior while a pre-medical student, and demonstrate a continuing commitment to study medicine.
- While the coursework typically is completed within a four-year period, an exceptional student may request to apply after three years to the Associate Dean for Admission at the School of Medicine.
FASTS Forms
Joint Admission Medical Program (JAMP)
The Joint Admission Medical Program (JAMP) is a special program created by the Texas Legislature to support and encourage highly qualified, economically disadvantaged students pursuing a medical education. Dr. Tim Raabe is the JAMP Faculty Director at St. Mary's University.JAMP "Pathways Into Medicine" Pre-Medical Summer Camp
In 2010, the St. Mary's University Department of Biological Sciences received funding to hold its first pre-medical summer camp. The "Pathways Into Medicine" summer camp is funded by JAMP and has two goals: (1) Recruit and educate potential JAMP students about the JAMP program and the opportunities it provides, and (2) Present students with a unique, hands-on experience with healthcare professionals in a medical school environment.
Learn more
Camp Summary
For five nights, campers stay in residence hall facilities at St. Mary s University and spend their days at the University of Texas Health Science Center at San Antonio (UTHSCSA) School of Medicine.Each day, camp begins with breakfast after which students are transported from St. Mary s to UTHSCSA where they participate in a myriad of activities alongside medical and healthcare professionals.
Some of the activities include:
- Presentations on topics such as the JAMP program, medical school admission, plastic surgery, ethics in medicine, psychiatry, emergency medicine, pediatrics and more
- Hands-on laboratory activities including exploring the human brain, learning the art of suturing and practicing dissections
- Guided tours of University Hospital, UTHSCSA Medical School , and the Gamma Knife Center
- Panel discussion with current JAMP medical students
- Handling and examining plastinated human body parts provided through the Willed Body Program at UTHSCSA
- Special access to the Johnson Center for Surgical Innovation where students participate in hands-on training sessions for various surgical procedures
- Personal discussion with LifeFlight medics along with a tour of the LifeFlight helicopter and landing pad
Camp closes with a special ceremony which parents are invited to attend. Students are presented with a certificate of completion at the closing ceremony, and parents enjoy a slideshow giving them a peek into the week's activities .
Current Faculty Research
Professors never stop learning. In addition to teaching, advising, grading papers and serving on committees, the Biological Sciences faculty are looking for answers to tough questions in their field. Here's a sampling of what they're currently learning.Veronica Contreras-Shannon, Ph.D.
"The Molecular Mechanisms of Antipsychotic-Induced Metabolic Syndrome"Read about it
My teaching and research interests focus on the molecular mechanisms of disease. For the past several years, I have been involved in research investigating the role of specific genes and their protein products, as well as inflammation, in cardiovascular disease, muscle regeneration and cancer. My current work in understanding the mechanism of metabolic side effects associated with atypical antipsychotics with undergraduate students is an appropriate confluence of my doctoral training in metabolic enzymes and mitochondrial function, and my postdoctoral training in the pathobiology of disease.
The underlying biological cause of the associated side-effects of atypical antipsychotics is unknown. It is interesting to note that there is a growing consensus in the obesity field that understanding the mechanisms responsible for the adverse metabolic effects of atypical antipsychotics may shed an important light on the origin of metabolic disease and obesity in the general population. In my research, we use cultured mammalian cells and a yeast model system to test three interrelated hypotheses for why these drugs cause metabolic side effects: 1) these drugs negatively affect the proper functioning of mitochondria and/or the endoplasmic reticulum (ER), 2) these drugs cause increased oxidative stress in cells and tissues, and 3) these drugs promote inflammation.
In addition to clarifying the mechanism of antipsychotic-induced side effects, my goal is to actively involve undergraduates in cutting-edge biomedical research as a means to improve biology training and increase the number of underrepresented students in the sciences.
Current research students:
Herenia Armenta-Espitia, sophomore chemistry major (pre-MARC)
Dina Attia, junior biology major (Biaggini)
Janet Chen, senior biology major (Honor's Thesis)
Andrew Gonzales, junior biology major (Biaggini)
Uche Ozoemena, junior biochemistry major (Biaggini)
Recent publications: (St. Mary's student names are underlined)
Contreras-Shannon V, Heart D, Navaira E, Paredes M, Catano G, Maffi S and Walss-Bass C. Clozapine-induced mitochondria alterations and inflammation in brain and insulin-responsive cells. Submitted to the journal PLOS ONE.
Shireman PK, Contreras-Shannon V, Ochoa O, Karia BP, Michalek JE, McManus LM. MCP-1 deficiency causes altered inflammation with impaired skeletal muscle regeneration. J Leukoc Biol 2007 Mar;81(3):775-785.
Contreras-Shannon V, Ochoa O, Reyes-Reyna SM, Sun D, Michalek JE, Kuziel WA, McManus LM, Shireman PK. Fat accumulation with altered inflammation and regeneration in skeletal muscle of CCR2-/- mice following ischemic injury. Am J Physiol Cell Physiol 2007 Feb;292(2):c953-c967.
Shireman PK, Contreras-Shannon V, Reyes-Reyna SM, Robinson SC, McManus LM. MCP-1 parallels inflammatory and regenerative responses in ischemic muscle. J Surg Res 2006 Jul;134(1):145-157.
Contreras-Shannon V, Lin AP, McCammon MT, McAlister-Henn L.. Kinetic properties and metabolic contributions of yeast mitochondrial and cytosolic NADP+-specific isocitrate dehydrogenases. J Biol Chem 2005 Feb;280(6):4469-4475.
The underlying biological cause of the associated side-effects of atypical antipsychotics is unknown. It is interesting to note that there is a growing consensus in the obesity field that understanding the mechanisms responsible for the adverse metabolic effects of atypical antipsychotics may shed an important light on the origin of metabolic disease and obesity in the general population. In my research, we use cultured mammalian cells and a yeast model system to test three interrelated hypotheses for why these drugs cause metabolic side effects: 1) these drugs negatively affect the proper functioning of mitochondria and/or the endoplasmic reticulum (ER), 2) these drugs cause increased oxidative stress in cells and tissues, and 3) these drugs promote inflammation.
In addition to clarifying the mechanism of antipsychotic-induced side effects, my goal is to actively involve undergraduates in cutting-edge biomedical research as a means to improve biology training and increase the number of underrepresented students in the sciences.
Current research students:
Herenia Armenta-Espitia, sophomore chemistry major (pre-MARC)
Dina Attia, junior biology major (Biaggini)
Janet Chen, senior biology major (Honor's Thesis)
Andrew Gonzales, junior biology major (Biaggini)
Uche Ozoemena, junior biochemistry major (Biaggini)
Recent publications: (St. Mary's student names are underlined)
Contreras-Shannon V, Heart D, Navaira E, Paredes M, Catano G, Maffi S and Walss-Bass C. Clozapine-induced mitochondria alterations and inflammation in brain and insulin-responsive cells. Submitted to the journal PLOS ONE.
Shireman PK, Contreras-Shannon V, Ochoa O, Karia BP, Michalek JE, McManus LM. MCP-1 deficiency causes altered inflammation with impaired skeletal muscle regeneration. J Leukoc Biol 2007 Mar;81(3):775-785.
Contreras-Shannon V, Ochoa O, Reyes-Reyna SM, Sun D, Michalek JE, Kuziel WA, McManus LM, Shireman PK. Fat accumulation with altered inflammation and regeneration in skeletal muscle of CCR2-/- mice following ischemic injury. Am J Physiol Cell Physiol 2007 Feb;292(2):c953-c967.
Shireman PK, Contreras-Shannon V, Reyes-Reyna SM, Robinson SC, McManus LM. MCP-1 parallels inflammatory and regenerative responses in ischemic muscle. J Surg Res 2006 Jul;134(1):145-157.
Contreras-Shannon V, Lin AP, McCammon MT, McAlister-Henn L.. Kinetic properties and metabolic contributions of yeast mitochondrial and cytosolic NADP+-specific isocitrate dehydrogenases. J Biol Chem 2005 Feb;280(6):4469-4475.
S. Colette Daubner, Ph.D.
"Structural basis for regulation of enzymes of neurotransmitter synthesis"Read about it
My group studies the aromatic amino acid hydroxylases. Phenylalanine hydroxylase (PheH) and tyrosine hydroxylase (TyrH). are structurally and functionally related, and genetic analysis reveals that TyrH evolved from PheH about 750 million years ago. They do similar chemistry, using iron and reduced biopterin to incorporate an atom of oxygen into the aromatic ring of an amino acid. PheH is a liver enzyme, and regulates levels of phenylalanine degradation, and hereditary deficiencies of PheH cause phenylketonuria, a disease resulting in mental retardation; TyrH is a nervous system enzyme and regulates levels of the catecholamine neurotransmitters dopamine, epinephrine, and norepinephrine.
We study the chemical and structural differences between the two enzymes that give them their unique substrate specificities. We have identified several amino acids that were critical to the evolution of TyrH; as TyrH regulates neurotransmitter synthesis, this evolutionary step was key for the formation of nervous systems in organisms with catecholaminergic neural tracts. We also study the regulation of PheH and TyrH. They are both regulated by phosphorylation at the end of cellular signal tranduction pathways. We study the conformational changes that result upon phosphorylation. PheH is also regulated by allosteric activation with phenylalanine, and TyrH is regulated by feedback inhibition by the catecholamines; we study the biochemical and biophysical bases for these processes. We use a number of techniques in our lab, including stopped-flow spectrophotometry, fluorimetry, enzyme kinetics, and protein chemistry; we perform site-directed mutagenesis of our enzymes using DNA techniques.
Fig. 1. Similarities and differences between phenylalanine hydroxylase (left) and tyrosine hydroxylase (right). The peptide backbones of the two enzymes, known from x-ray crystallography, are represented as ribbon structures. Their similarity is obvious. Their active sites are portrayed with several amino acids, drawn as stick figures, bound to the active site iron. The large spheres at upper left of each protein accentuate a flexible loop that is very different between the two enzymes. These loops affect catalysis and substrate specificity.
Fig. 2. Both tyrosine and phenyalanine hydroxylase are activated by phosphorylation. This figure presents a model for the conformational change that causes the activation. Each enzyme consists of two domains, one regulatory (R), and one catalytic (C). When a serine residue in the R domain becomes phosphorylated through the action of a protein kinase, the R domain moves with respect to the C domain and allows substrates freer access to the active sites.
Current research students:
Audrey Avila, senior biology major (UTHSCSA R25 neuroscience program student)
Andrew Hansen, senior biochemistry major (MARC)
Jessica Villacorta, junior biochemistry major (MARC)
Ewa Nowara, sophomore biophysics major
Recent publications: (students' names are underlined)
Tormos, Jose R., Taylor, Alex, Daubner, S. Colette, Hart, P. John, and Fitzpatrick, Paul F. (2010), Identification of a Hypothetical Protein from Podospora anserina as a Nitroalkane Oxidase Biochemistry 49, 5035-41.
Daubner, S. Colette, Le, Tiffany, and Wang, Shanzhi (2010), The R Domain of Tyrosine Hydroxylase and Regulation of Dopamine Synthesis. Arch. Biochem. Biophys. 508, 1-12.
Li J, Ilangovan U., Daubner, S. Colette, Hinck Andrew P., Fitzpatrick Paul F. (2011), Direct evidence for a phenylalanine site in the regulatory domain of phenylalanine hydroxylase. Arch. Biochem. Biophys. 505, 250-5.
Wang, Shanzhi, Lasagna, Mauricio, Daubner, S. Colette, Reinhart, Gregory, and Fitzpatrick, Paul F. (2011), Effect of Phosphorylation of Tyrosine Hydroxylase on the Dynamics of the Regulatory Domain, Biochemistry 50, 2364-70.
Avila, Audrey M., Bailey, Johnathan, Barrera, Dimitrios, Bermudez, Jacklyn Y., Fitzpatrick, Paul F., Giles, David, Khan, Crystal A., Oxley, Susan, Shaheen, Noel, Vasquez, Jessica, Thompson, Janie, and Daubner, S Colette. Evolution of Tyrosine Hydroxylase: Substitutions at Position 425 Delineate Active Site Requirements for Tyrosine versus Phenylalanine Hydroxylation, manuscript in preparation.
We study the chemical and structural differences between the two enzymes that give them their unique substrate specificities. We have identified several amino acids that were critical to the evolution of TyrH; as TyrH regulates neurotransmitter synthesis, this evolutionary step was key for the formation of nervous systems in organisms with catecholaminergic neural tracts. We also study the regulation of PheH and TyrH. They are both regulated by phosphorylation at the end of cellular signal tranduction pathways. We study the conformational changes that result upon phosphorylation. PheH is also regulated by allosteric activation with phenylalanine, and TyrH is regulated by feedback inhibition by the catecholamines; we study the biochemical and biophysical bases for these processes. We use a number of techniques in our lab, including stopped-flow spectrophotometry, fluorimetry, enzyme kinetics, and protein chemistry; we perform site-directed mutagenesis of our enzymes using DNA techniques.
Fig. 1. Similarities and differences between phenylalanine hydroxylase (left) and tyrosine hydroxylase (right). The peptide backbones of the two enzymes, known from x-ray crystallography, are represented as ribbon structures. Their similarity is obvious. Their active sites are portrayed with several amino acids, drawn as stick figures, bound to the active site iron. The large spheres at upper left of each protein accentuate a flexible loop that is very different between the two enzymes. These loops affect catalysis and substrate specificity.
Fig. 2. Both tyrosine and phenyalanine hydroxylase are activated by phosphorylation. This figure presents a model for the conformational change that causes the activation. Each enzyme consists of two domains, one regulatory (R), and one catalytic (C). When a serine residue in the R domain becomes phosphorylated through the action of a protein kinase, the R domain moves with respect to the C domain and allows substrates freer access to the active sites.
Current research students:
Audrey Avila, senior biology major (UTHSCSA R25 neuroscience program student)
Andrew Hansen, senior biochemistry major (MARC)
Jessica Villacorta, junior biochemistry major (MARC)
Ewa Nowara, sophomore biophysics major
Recent publications: (students' names are underlined)
Tormos, Jose R., Taylor, Alex, Daubner, S. Colette, Hart, P. John, and Fitzpatrick, Paul F. (2010), Identification of a Hypothetical Protein from Podospora anserina as a Nitroalkane Oxidase Biochemistry 49, 5035-41.
Daubner, S. Colette, Le, Tiffany, and Wang, Shanzhi (2010), The R Domain of Tyrosine Hydroxylase and Regulation of Dopamine Synthesis. Arch. Biochem. Biophys. 508, 1-12.
Li J, Ilangovan U., Daubner, S. Colette, Hinck Andrew P., Fitzpatrick Paul F. (2011), Direct evidence for a phenylalanine site in the regulatory domain of phenylalanine hydroxylase. Arch. Biochem. Biophys. 505, 250-5.
Wang, Shanzhi, Lasagna, Mauricio, Daubner, S. Colette, Reinhart, Gregory, and Fitzpatrick, Paul F. (2011), Effect of Phosphorylation of Tyrosine Hydroxylase on the Dynamics of the Regulatory Domain, Biochemistry 50, 2364-70.
Avila, Audrey M., Bailey, Johnathan, Barrera, Dimitrios, Bermudez, Jacklyn Y., Fitzpatrick, Paul F., Giles, David, Khan, Crystal A., Oxley, Susan, Shaheen, Noel, Vasquez, Jessica, Thompson, Janie, and Daubner, S Colette. Evolution of Tyrosine Hydroxylase: Substitutions at Position 425 Delineate Active Site Requirements for Tyrosine versus Phenylalanine Hydroxylation, manuscript in preparation.
Ahmad Galaleldeen, Ph.D.
"Understanding Pathogenesis through Structural Biology"Read about it
Project 1:
Chlamydia is a genus of gram negative intracellular pathogens that cause various health problems in humans. C. trachomatis infection of the urinogenital tract is the most common sexually transmitted bacterial disease in the world, while ocular infections cause trachoma, potentially leading to blindness. C. pneumoniae is a common cause of pneumonia and often associated with atherosclerosis and coronary artery disease. The nature of Chlamydia as an intracellular pathogen and its presence in cellular inclusions presents a challenge for researchers. The lack of tools for genetic manipulation of Chlamydia has hindered this research and little is known about the molecular mechanism(s) through which Chlamydia interacts with the host cell and manipulates its cell signaling and immune response. Structural biology is an emerging tool that can be used to overcome the difficulties of genetic manipulation and allow us to determine the functions of chlamydial proteins. We are interested in identifying, characterizing and determining the 3D structure of various effector proteins secreted by Chlamydia in the host cell.
Project 2:
Superoxide dismutases (SODs) are a family of metallo-enzymes that protect cells from oxidative damage caused by reactive oxygen species (ROS). ROS are produced as a direct result of aerobic respiration and photosynthesis and if not detoxified, can exert damaging effects via oxidation of DNA, proteins and lipids. Four distinct classes of SOD have been identified based on the identity of the redox-active metal ions bound as cofactors at the active site, which include nickel, iron, manganese, and copper/zinc. We are interested in characterizing SODs from different species and understanding the activation, i.e. metallation and disulfide bond formation, process of these enzymes.
Figure 1: Wild type hSOD1 structure (pdb code 1HL5) showing the Greek key Beta-barrel in grey, the zinc loop (loop IV, residues 50-83) in pink, and the electrostatic loop (loop VII, residues 121-142) in yellow. The zinc and copper ions are shown as orange and blue spheres respectively. Sulfur atoms forming the intrasubunit disulfide bond between residues 57 and 146 are shown as green spheres.
Figure 2: The zinc and copper binding sites in hSOD1 superimposed on a σA-weighted electron density with coefficients 2mFo-DFc contoured at 1.2 σ.
Current research students:
Adrian Mehrtash, sophomore biology major (funded by NIH grant)
Dimitrios Barrera, senior biophysics major (MARC)
Recent publications:
Lin, A. P., Demeler, B., Minard, K. I., Anderson S. L., Schirf, V., Galaleldeen, A., and McAlister-Henn, L. (2011) Biochemistry. 50, 230-239. "Construction and Analyses of Tetrameric Forms of Yeast NAD(+) Specific Isocitrate Dehydrogenase."
Chen, D., Lei, L., Lu, C., Galaleldeen, A., Hart, P. J., and Zhong, G. (2010) J. Bacteriol. 192, 6017-24. "Characterization of Pgp3, a Chlamydia trachomatis Plasmid-encoded Immunodominant Antigen."
Galaleldeen, A., Strange, R., Whitson, L. J., Antonyuk, S., Taylor, A. B., Hasnain, S. S., and Hart, P. J. (2009) Arch. Biochem. Biophys. 492, 40-47. "Structural and Biophysical Properties of Metal-Free Pathogenic SOD1 Mutants A4V and G93A."
Galaleldeen, A., and Hart, P. J. "Human Copper-Zinc Superoxide Dismutase and Familial Amyotrophic Lateral Sclerosis" in: Protein Reviews, Protein Misfolding, Aggregation and Conformational Diseases. (Zouhair Atassi Ed.) (2007) pp. 327-344, Springer, New York.
Chlamydia is a genus of gram negative intracellular pathogens that cause various health problems in humans. C. trachomatis infection of the urinogenital tract is the most common sexually transmitted bacterial disease in the world, while ocular infections cause trachoma, potentially leading to blindness. C. pneumoniae is a common cause of pneumonia and often associated with atherosclerosis and coronary artery disease. The nature of Chlamydia as an intracellular pathogen and its presence in cellular inclusions presents a challenge for researchers. The lack of tools for genetic manipulation of Chlamydia has hindered this research and little is known about the molecular mechanism(s) through which Chlamydia interacts with the host cell and manipulates its cell signaling and immune response. Structural biology is an emerging tool that can be used to overcome the difficulties of genetic manipulation and allow us to determine the functions of chlamydial proteins. We are interested in identifying, characterizing and determining the 3D structure of various effector proteins secreted by Chlamydia in the host cell.
Project 2:
Superoxide dismutases (SODs) are a family of metallo-enzymes that protect cells from oxidative damage caused by reactive oxygen species (ROS). ROS are produced as a direct result of aerobic respiration and photosynthesis and if not detoxified, can exert damaging effects via oxidation of DNA, proteins and lipids. Four distinct classes of SOD have been identified based on the identity of the redox-active metal ions bound as cofactors at the active site, which include nickel, iron, manganese, and copper/zinc. We are interested in characterizing SODs from different species and understanding the activation, i.e. metallation and disulfide bond formation, process of these enzymes.
Figure 1: Wild type hSOD1 structure (pdb code 1HL5) showing the Greek key Beta-barrel in grey, the zinc loop (loop IV, residues 50-83) in pink, and the electrostatic loop (loop VII, residues 121-142) in yellow. The zinc and copper ions are shown as orange and blue spheres respectively. Sulfur atoms forming the intrasubunit disulfide bond between residues 57 and 146 are shown as green spheres.
Figure 2: The zinc and copper binding sites in hSOD1 superimposed on a σA-weighted electron density with coefficients 2mFo-DFc contoured at 1.2 σ.
Current research students:
Adrian Mehrtash, sophomore biology major (funded by NIH grant)
Dimitrios Barrera, senior biophysics major (MARC)
Recent publications:
Lin, A. P., Demeler, B., Minard, K. I., Anderson S. L., Schirf, V., Galaleldeen, A., and McAlister-Henn, L. (2011) Biochemistry. 50, 230-239. "Construction and Analyses of Tetrameric Forms of Yeast NAD(+) Specific Isocitrate Dehydrogenase."
Chen, D., Lei, L., Lu, C., Galaleldeen, A., Hart, P. J., and Zhong, G. (2010) J. Bacteriol. 192, 6017-24. "Characterization of Pgp3, a Chlamydia trachomatis Plasmid-encoded Immunodominant Antigen."
Galaleldeen, A., Strange, R., Whitson, L. J., Antonyuk, S., Taylor, A. B., Hasnain, S. S., and Hart, P. J. (2009) Arch. Biochem. Biophys. 492, 40-47. "Structural and Biophysical Properties of Metal-Free Pathogenic SOD1 Mutants A4V and G93A."
Galaleldeen, A., and Hart, P. J. "Human Copper-Zinc Superoxide Dismutase and Familial Amyotrophic Lateral Sclerosis" in: Protein Reviews, Protein Misfolding, Aggregation and Conformational Diseases. (Zouhair Atassi Ed.) (2007) pp. 327-344, Springer, New York.
Christine E. Gray, Ph.D.
"Cytoplasmic incompatibility in Drosophila and CTCF-dependent insulators in insects"Read about it
I am a geneticist with an interest in gene expression and how it varies with genomic environment. I currently am engaged in two projects. The first of these projects is investigating a potential mechanism to explain a phenomenon known as cytoplasmic incompatibility (CI). CI results in arrested cell division immediately after fertilization and occurs as a direct consequence of infection with a bacterium (Wolbachia). The end result is infertility. The phenomenon is directional. It only occurs when Wolbachia-infected males mate with uninfected females. Understanding just how Wolbachia causes CI in insects may allow other researchers to utilize Wolbachia in efforts to control populations of important insect disease vectors. This project is being done in the fruit fly, Drosophila melanogaster.
The second project involves assessing several CTCF-binding sites from the malaria mosquito vector, Anopheles gambiae, for insulator activity in cell culture. CTCF is a well-characterized DNA binding protein that has been shown to be a potent insulator for gene expression in vertebrate systems. Insulators act as a type of "bookend" for genes and keep regulatory sequences that promote or repress gene expression from interacting with neighboring genes and affecting their expression simply because they are close by. A CTCF-like protein has been identified in fruit flies and in two species of mosquitoes that vector human pathogens. Identification of specific DNA sequences with CTCF-dependent insulator activity would be advantageous in protecting the expression of transgenes which reduce mosquito fertility and/or block expression of key genes required for pathogen replication or transmission.
Current research students:
Tiffany Brown, senior biology major (Biaggini)
Audiel Espitia, senior biology major (SURF)
John Fedorick, senior biology major
Sierra Tamez, senior biology major (Biaggini)
Melissa Valdes, junior biochemistry major (MARC)
Recent publication:
Gray, C.E. and Coates, C.J. (2005) Cloning and characterization of cDNAs encoding putative CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae. BMC Molecular Biology 6:16.
Figure 1. Assessing Wolbachia infection status in experimental and control Drosophila lines. The 16S rDNA gene from Wolbachia (936 bp) and the 12S rDNA gene from Drosophila mitochondria (400 bp) were amplified by PCR with gene-specific primers. Samples in lanes 2-4 and lane 6 are infected, while the sample in lane 5 is uninfected. Lane 7 is a control with no input DNA. Lane 8 is a control with no Taq DNA polymerase.
Current research students:
Tiffany Brown, senior biology major (Biaggini)
Audiel Espitia, senior biology major (SURF)
John Fedorick, senior biology major
Sierra Tamez, senior biology major (Biaggini)
Melissa Valdes, junior biochemistry major (MARC)
Recent publication:
Gray, C.E. and Coates, C.J. (2005) Cloning and characterization of cDNAs encoding putative CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae. BMC Molecular Biology 6:16.
Thomas E. (Ted) Macrini, Ph.D.
"Comparative Anatomy of Mammalian Skulls" and"Knee Osteoarthritis in a Baboon Model"
Read about it
My research in comparative anatomy focuses on internal structures of mammalian skulls, particularly the nasal cavity, braincase, and inner ear. I use X-ray computed tomography (CT) to non-destructively visual these structures in fossil and extant mammal skulls with the purpose of describing skeletal anatomy related to sensory structures, and to utilize these data to reconstruct phylogenetic relationships among mammals. I've worked on a variety of mammalian groups including monotremes, marsupials, bats, primates, sirenians, and a number of completely extinct taxa such as notoungulates, an enigmatic group from South America. I work with colleagues from The University of Texas at Austin and the American Museum of Natural History (New York), among other institutions, and I have ongoing projects involving St. Mary's University (StMU) students.
My other research program examines knee osteoarthritis (OA), a debilitating joint disease in humans, using baboons (Papio hamadryas ssp.) from the Texas Biomedical Research Institute (TBRI) colony in San Antonio. These baboons, like humans, naturally develop OA. This research is conducted in collaboration with Dr. Lorena M. Havill (TBRI, Department of Genetics) among others, and is aimed at uncovering the etiology of early stage OA and understanding the genetic and other factors contributing to disease risk. Ongoing projects involving StMU students include gross anatomical studies of OA in the articular cartilage of the knee joint, and analyses of histological and radiographic evidence of OA in baboons.
Current research students:
Gerardo Astorga, sophomore biology major
Christina Karmann, senior biology major
Celeste Passement, sophomore biology major
Evelia Salinas, sophomore biophysics major (pre-MARC)
Tony Vega, senior biophysics major (MARC)
Recent publications:
Macrini, T. E., J. J. Flynn, D. A. Croft, and A. R. Wyss. 2010. Inner ear of a notoungulate placental mammal: anatomical description and examination of potentially phylogenetically informative characters. Journal of Anatomy 216:600-610.
Rowe, T., T. E. Macrini, and Z.-X. Luo. 2011. Fossil evidence on origin of the mammalian brain. Science 332:955-957.
Macrini, T. E. 2012. Comparative morphology of the internal nasal skeleton of adult marsupials based on X-ray computed tomography. Bulletin of the American Museum of Natural History 365:1-91.
Beatty, B. L., T. Vitkovski, O. Lambert, and T. E. Macrini. 2012. Osteological associations with unique tooth development in manatees (Trichechidae, Sirenia): a detailed look at modern Trichechus and a review of the fossil record. Anatomical Record 295:1504-1512.
Giannini, N. P., T. E. Macrini, J. R. Wible, T. Rowe, and N. B. Simmons. 2012. The internal nasal skeleton of the bat Pteropus lylei K. Andersen, 1908 (Chiroptera: Pteropodidae). Annals of Carnegie Museum (in press).
The above image shows a digital 3-D reconstruction of the semitransparent skull of Hadrocodium wui, a tiny early Jurassic age mammal that weighed just two grams. The cranial endocast, indicating the braincase cavity, is shown in red. The imagery was generated from CT images of the skull and formed the basis of Rowe et al. (2011). Scale: the skull is 13 mm long.
Current research students:
Gerardo Astorga, sophomore biology major
Christina Karmann, senior biology major
Celeste Passement, sophomore biology major
Evelia Salinas, sophomore biophysics major (pre-MARC)
Tony Vega, senior biophysics major (MARC)
Recent publications:
Macrini, T. E., J. J. Flynn, D. A. Croft, and A. R. Wyss. 2010. Inner ear of a notoungulate placental mammal: anatomical description and examination of potentially phylogenetically informative characters. Journal of Anatomy 216:600-610.
Rowe, T., T. E. Macrini, and Z.-X. Luo. 2011. Fossil evidence on origin of the mammalian brain. Science 332:955-957.
Macrini, T. E. 2012. Comparative morphology of the internal nasal skeleton of adult marsupials based on X-ray computed tomography. Bulletin of the American Museum of Natural History 365:1-91.
Beatty, B. L., T. Vitkovski, O. Lambert, and T. E. Macrini. 2012. Osteological associations with unique tooth development in manatees (Trichechidae, Sirenia): a detailed look at modern Trichechus and a review of the fossil record. Anatomical Record 295:1504-1512.
Giannini, N. P., T. E. Macrini, J. R. Wible, T. Rowe, and N. B. Simmons. 2012. The internal nasal skeleton of the bat Pteropus lylei K. Andersen, 1908 (Chiroptera: Pteropodidae). Annals of Carnegie Museum (in press).
Marshall D. McCue, Ph.D.
"Comparative Physiology and Physiological Ecology"Read about it
Animals naturally face many environmental challenges including dehydration, malnutrition or food limitation, extreme temperatures, low oxygen availability, and parasitism. I am generally interested in exploring the physiological and biochemical mechanisms that allow animals to survive - and sometimes thrive - amidst these challenges. I employ a variety of model organisms including fish, reptiles, mammals, birds, and insects in my quest to better understand 'how animals work.'
My most recent research involves using stable isotope labeled metabolic tracers to investigate the physiological 'decisions' that dictate how, when, and where in the body animals allocate the different types of nutrients in the foods they eat and how, when, and were in the body they breakdown and burn different types of nutrients when food resources are scarce.
Current research students:
James Amaya, junior biology major (Biaggini)
Alice Yang, junior biology major (Biaggini)
Agnelio Cardentey, senior biophysics major (funded by Faculty Development Grant)
Roberto de los Santos, junior biology major (SURF)
Recent publications:
McCue, M. D. (2012). "Horizons in starvation research." Chapter 24 in: Comparative Physiology of Fasting, Starvation, and Food Limitation. M. D. McCue, Editor. New York, Springer-Verlag: 409-420.
Munoz-Garcia, A., S. Aamidor, M. D. McCue, S. R. McWilliams and B. Pinshow (2012). "Allocation of endogenous and dietary protein in the reconstitution of the gastrointestinal tract in migratory blackcaps at stopover sites." Journal of Experimental Biology 215: 1069-1075.
Khalilieh, A., M. D. McCue and B. Pinshow (2012). "Physiological responses to food deprivation in the house sparrow, a species not adapted to prolonged fasting." American Journal of Physiology. in press.
McCue, M. D., A. Smith, R. McKinney, B. Rewald, B. Pinshow and S. R. McWilliams (2011). "A mass balance approach to identify and compare differential routing of 13C-labeled carbohydrates, lipids, and proteins in vivo." Physiological and Biochemical Zoology 84(5): 506-513.
McCue, M. D. (2011). "Tracking the oxidative and non-oxidative fates of isotopically labeled nutrients in animals." BioScience 61(3): 217-230.
My most recent research involves using stable isotope labeled metabolic tracers to investigate the physiological 'decisions' that dictate how, when, and where in the body animals allocate the different types of nutrients in the foods they eat and how, when, and were in the body they breakdown and burn different types of nutrients when food resources are scarce.
Current research students:
James Amaya, junior biology major (Biaggini)
Alice Yang, junior biology major (Biaggini)
Agnelio Cardentey, senior biophysics major (funded by Faculty Development Grant)
Roberto de los Santos, junior biology major (SURF)
Recent publications:
McCue, M. D. (2012). "Horizons in starvation research." Chapter 24 in: Comparative Physiology of Fasting, Starvation, and Food Limitation. M. D. McCue, Editor. New York, Springer-Verlag: 409-420.
Munoz-Garcia, A., S. Aamidor, M. D. McCue, S. R. McWilliams and B. Pinshow (2012). "Allocation of endogenous and dietary protein in the reconstitution of the gastrointestinal tract in migratory blackcaps at stopover sites." Journal of Experimental Biology 215: 1069-1075.
Khalilieh, A., M. D. McCue and B. Pinshow (2012). "Physiological responses to food deprivation in the house sparrow, a species not adapted to prolonged fasting." American Journal of Physiology. in press.
McCue, M. D., A. Smith, R. McKinney, B. Rewald, B. Pinshow and S. R. McWilliams (2011). "A mass balance approach to identify and compare differential routing of 13C-labeled carbohydrates, lipids, and proteins in vivo." Physiological and Biochemical Zoology 84(5): 506-513.
McCue, M. D. (2011). "Tracking the oxidative and non-oxidative fates of isotopically labeled nutrients in animals." BioScience 61(3): 217-230.
Current Student Research
Professors never stop learning. In addition to teaching, advising, grading papers and serving on committees, the Biological Sciences faculty are looking for answers to tough questions in their field. Here's a sampling of what they're currently learning.
Anthony Vega
MARC Program traineeMajor: Biophysics
Faculty Research Mentor: Ted Macrini, Ph.D.
Hometown: San Antonio, TX
Career Aspirations: Professor and principal investigator of a lab
What I'm researching
I am examining how well the brain fills the braincase in an extant (living) model mammal, Monodelphis domestica, the gray short-tailed opossum. Analyses of fossil vertebrates rely on estimation of brain volume using endocranial (braincase) volume because soft-tissue structures such as the brain often are not preserved. Even brain volume studies of extant mammals can be plagued by measurement errors when the brain is manually dissected and measured. My study involves digital segmentation (individualization) of brain tissue from in vivo and postmortem MRI scans of heads of M. domestica to measure brain volumes, and segmentation of CT imagery from the same individuals to measure endocranial volumes. This study will provide some ground-truth to brain evolution studies that are based on fossil mammals, by establishing how well the brain fills the braincase in a single species of extant mammal.
Departmental Research and Scholarship Opportunities
Research and scholarship opportunities for biology majors are available for deserving students who demonstrate academic achievement and financial need. Listed below are some of scholar programs available, each with their respective eligibility criteria.Biaggini Research Program
Biaggini Research Program
The Biaggini Research Program in the Department of Biological Sciences was established through an endowment created in honor of Benjamin F. Biaggini - Distinguished Alumnus of St. Mary s University and former CEO of Southern Pacific. Funds are utilized to provide scholarships to junior or senior level biology majors who are named Biaggini Research Scholars. As part of the requirements for receiving these scholarships, Biaggini Scholars are required to actively participate in an ongoing research project with Biaggini Research Fellows or another faculty member in the department. Travel funds are also provided for these students to attend a national meeting or conference to present their research findings.The overall goal of the program is to enhance the ability of faculty members in our department to engage in research projects as a means for professional development in the form of publication(s) and/or additional external funding to continue their research endeavors.
Additionally, funds from this endowment were utilized to establish the Biaggini Endowed Chair in Biological Sciences and to create a research program that provides funding for two faculty members (Biaggini Research Fellows) in the department that are actively involved a research project associated with some aspect of human health and/or disease. The Research Fellow budget includes released time to engage in the research, funds for purchasing supplies, and funds for travel to present findings from their research projects.
Eligibility and Rules
To be considered for the Biaggini Research program, a student:
- must be nominated by a biology professor.
- must be a junior or senior biology major.
- must have a GPA of at least 3.0 overall and major.
- must complete the application by the deadline.
Biaggini Fellows
2012-2013 Biaggini Fellows:
Marshall D. McCue, Ph.D.Assistant Professor of Biological Sciences
Developing a method to directly quantify substrate oxidation and physiological shifts during acute nutritional stress
This project will allow us to test a recently-developed approach to investigate the progression of biological changes in health during fasting and malnutrition. The experimental approach uses special chemical tracers to understand what happens within the tissues of the body. Weight loss is an obvious outcome of fasting, but little is known about how the body burns different types of nutrients when food is not available. We will conduct nutritional experiments using laboratory animals, but the ultimate aim is to develop a technique that can be used to study human nutrition.
Veronica Contreras-Shannon, Ph.D.
Associate Professor of Biological Sciences
The Role of Endoplasmic Reticulum Dysfunction and the MCP-1/CCR2 Pathway in Clozapine-Induced Metabolic Side Effects
While being very effective for the treatment of schizophrenia, atypical antipsychotics have been found to cause severe side effects capable of affecting an individual's metabolism and the body's ability to fight infection. With regard to the former, this includes changes to a person's weight, glucose levels and fat composition which may ultimately lead to diabetes, obesity, and high cholesterol all of which are associated with increased risk for cardiovascular disease. The underlying biological cause of the associated side-effects of atypical antipsychotics is unknown. It is interesting to note that there is a growing consensus in the obesity field that understanding the mechanisms responsible for the adverse metabolic effects of atypical antipsychotics may shed an important light on the origin of metabolic disease itself. There are three interrelated hypotheses for why these drugs cause metabolic side effects: 1) these drugs negatively affect the proper functioning of mitochondria and/or the endoplasmic reticulum (ER), 2) these drugs cause increased oxidative stress in cells and tissues, and 3) these drugs promote inflammation. Because mitochondria are the "powerhouses" of the cell responsible for producing energy, when mitochondrial function is altered, so is the way energy is used and produced by the cell. The ER is responsible for the proper folding and secretion of proteins required for normal cellular functions. Under circumstances of stress, the ER may initiate the unfolded protein response (UPR) which can lead to changes in gene expression or in extreme cases, cell death. Oxidative stress refers to a state in which cells are susceptible to damage caused by reactive chemicals capable of damaging cell components (proteins, DNA, cell membranes and organelles such as mitochondria or ER) or initiating cell death. Under normal circumstances, mitochondria produce these reactive species but the cell has protective mechanisms to keep these reactive chemicals from "stressing" the cell. Inflammation is an innate mechanism that protects the body's tissues and cells from insults caused by trauma and a variety of pathogens, such as chemicals and microorganisms. An inflammatory response causes a number of cells and molecules to elicit a protective response, a response that both utilizes and produces a number of reactive chemical species also capable of causing oxidative stress. ER dysfunction and UPR can elicit or result from inflammation, oxidative stress, and/or mitochondria dysfunction. In addition, inflammation, oxidative stress, and mitochondrial dysfunction can each give rise to the other. In the proposed project, several different cell lines representing the "whole body" will be treated with clozapine, a representative atypical antipsychotic, and examined for alterations in ER function and the UPR. Much of the current work on atypical antipsychotics focuses on the target cells for treatment, neurons and the brain. The proposed work will study cell types known to be responsible for metabolic changes, namely fat, muscle and liver cells. Completion of these studies will produce data that will form the basis for student projects, manuscripts and abstracts for presentation.
S.A.L.E. Scholar Program
San Antonio Livestock Exposition (S.A.L.E.) Scholar Program
Biology majors are selected for the S.A.L.E. Scholar Program based on their high school grades and test scores. The S.A.L.E. Scholar Program is made possible through the generosity of the San Antonio Livestock Exposition (S.A.L.E.) and thousands of volunteers. Each academic year, a cohort of 10 freshman students is selected for this program. Each student will receive $10,000 toward the cost of tuition over four years of studies.Eligibility and Rules
Eligibility and Rules:
- Selected students must formally accept the scholarship by filling out the required forms. Once those forms are completed, $1,250 will be applied to the student s account each semester.
- Students must achieve a minimum GPA of 3.0 each semester and overall to receive the scholarship.
- Students must attend a scholarship reception each year with representatives from S.A.L.E. and are strongly encouraged to volunteer at S.A.L.E.-related events.
Faculty & Staff
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