Biology

BIOL 5302 Teaching Apprenticeship (3 semester credit hours) Development and practice of teaching skills in the classroom and/or laboratory in the biological sciences. Pass/Fail only. Prerequisites: Graduate standing in biology and department consent required. (3-0) S

BIOL 5303 Introduction to Microbiology for Graduate Students (3 semester credit hours) Microbes contribute to major biogeochemical processes, live in environments inhospitable to other organisms, and may comprise the majority of biomass on Earth. They form beneficial symbioses with multicellular organisms and play critical roles in the development of those organisms. In contrast to these beneficial roles, certain microbes are global public health concerns. This course surveys the form and function of the microbial world. Instructor consent required. (3-0) S

BIOL 5312 Programming in the Biological Sciences for Graduate Students (3 semester credit hours) This course is an introduction to programming practices using C++ designed specifically for graduate students in the biological sciences with no prior programming experience. Special emphasis will be put in particular features of C++ like object oriented programming, data structures as well as applications to process, model, and analyze biological data. One goal of this course is to provide a strong background on programming skills on a basic level while leaving more advanced techniques of software development and algorithms for other advanced courses. Students work on programming assignments as well in a research project that can be addressed with the tools taught in this class. (3-0) S

BIOL 5322 (SCI 5322) Basis of Evolution (3 semester credit hours) From Assembling the Tree of Life to new drug developments, evolution theory is at the core of biology advancements. The concept of evolution is discussed for its relevance as a basic understanding for a scientifically literate society and processes and mechanisms of natural selection are examined. Topics include pertinent history, the fossil record, extinction, emergent species, the human experience, and applied evolution technologies. Students will explore the origins of evolution theory, public misconceptions, teaching, and evolution education research. An intensive scientific argumentation component (rather than debate) through discourse, advanced readings, presentations, panel discussions, and formal writing is required. Viewpoints examined include those of evolutionary biologists and research scientists. (3-0) T

BIOL 5324 (SCI 5324) Ecology (3 semester credit hours) This course will examine interrelationships between organisms and their environments in both theoretical and field-based contexts. Students will examine general ecological principles and their applications. Communities considered will be as small as the roadside and as vast as interconnected global systems. Topics analyzed by students in the context of ecological studies will include the flow of energy and matter through systems, predator/prey relationships, genetic diversity, evolution, population dynamics, interactions between microscopic and macroscopic organisms, and human impacts. Fieldwork examining North Texas ecosystems may be required. Critical thinking, metacognition, and reflections on the relevance of ecology in the teaching and learning of life and environmental sciences will be emphasized throughout the course. (3-0) T

BIOL 5330 (SCI 5330) Emerging Topics in Biology (3 semester credit hours) The media frequently announce biology advancements and research that affect human health, basic living needs, and biology education without critical analysis, often resulting in confusing the public and curtailing scientific literacy. Examination of resources and methods to critically evaluate biological information and scientific articles for sound theory development, research methods, and practical application. Topics include recent discoveries in the life sciences that meet the needs of society, health, and environmental issues. Although the topics build on emerging issues, they may include content areas such as cell and molecular biology, agriculture, epidemiology, and global warming. Students will examine effective ways to bring in new curricula into established course settings. Advanced curriculum writing component focused on science literacy. Viewpoints include those of biological research scientists, health professionals, and science education researchers. Additional prerequisites may be required depending on the specific course topic. (3-0) T

BIOL 5375 Genes to Genomes (3 semester credit hours) is an expansive coverage of molecular genetics with emphasis on genomes rather than genes. Students will gain a new perspective on how genes function together and in concert in living cells, focusing at the genome level. Students also will learn how to study genomes, inspect genome anatomies, analyze how genomes function and determine how genomes replicate and evolve. The course is structured to involve students directly in individual topics by class discussions of research papers and reviews, the latest advances in genome science and new and innovative techniques. Instructor consent required. (3-0) Y

BIOL 5376 (BMEN 6387) Applied Bioinformatics (3 semester credit hours) Genomic information content; data searches and multiple sequence alignment; mutations and distance-based phylogenetic analysis; genomics and gene recognition; polymorphisms and forensic applications; nucleic-acid and protein array analysis; structure prediction of biological macromolecules. Prerequisites: At least one semester of undergraduate statistics and probability, and two semesters of undergraduate calculus or instructor consent required. (3-0) T

BIOL 5381 Genomics (3 semester credit hours) Genome sequence acquisition and analysis; genomic identification; biomedical genome research; DNA microarrays and their use in applied and healthcare research. (3-0) T

BIOL 5382 Applied Genomics (3 semester credit hours) This laboratory course will cover a broad range of concepts, techniques, strategies, and current developments in genomic analysis. With hands-on exercises in analyzing genomic data, students will learn the essential state of the art skills in data filtering, management, statistical analysis and interpretation in the field of genomics. Department consent required. (2-1) R

BIOL 5385 Computational Molecular Evolution (3 semester credit hours) This course describes principles and models of evolutionary theory at the molecular level. It focuses primarily on the evolution of nucleotide sequences including genes, pseudogenes, and genomes as well as amino acid sequences used to study the evolution of proteins, protein complexes, and interactions. Phylogenetics and current leading quantitative models of sequence evolution are discussed in detail. Recent methods on amino acid evolution and its connections to molecular structure and function are also studied. Relevant examples of evolution at the molecular level presented in this course include protein interactions, signaling networks, and viral evolution. (3-0) S

BIOL 5410 Biochemistry (4 semester credit hours) Emphasis is on metabolic biochemistry, especially as it relates to human disease states. Prerequisite: at least one semester of undergraduate biochemistry and instructor consent required. (4-0) Y

BIOL 5420 Molecular Biology (4 semester credit hours) Genetic analysis of gene structure (mutations and their analysis, complementation, and recombination), gene expression (transcription, RNA processing, translation), and the regulation of gene expression in selected model systems (viral, prokaryotic, organellar, eukaryotic); principles of genetic engineering (cloning and recombinant DNA technology). Instructor consent required. (4-0) Y

BIOL 5440 Cell Biology (4 semester credit hours) Molecular architecture and function of cells and subcellular organelles; structure and function of membranes; hormone and neurotransmitter action; growth regulation and oncogenes; immune response; eukaryotic gene expression. Prerequisite: BIOL 5420 or equivalent or instructor consent required. (4-0) Y

BIOL 5460 Quantitative Biology (4 semester credit hours) Fundamental mathematical and statistical concepts; hypothesis testing. Quantitative approaches to studying gene expression and protein-DNA interactions. Prerequisites: at least one semester of undergraduate calculus and one semester of general physics or instructor consent required. (4-0) Y

BIOL 5V00 Topics in Biological Sciences (1-6 semester credit hours) May be repeated for credit as topics vary. Instructor consent required. ([1-6]-0) Y

BIOL 5V01 Topics in Biological Sciences (1-6 semester credit hours) Includes a laboratory component. May be repeated for credit as topics vary (9 semester credit hours maximum). Instructor consent required. Lab fee of $30 required. (1-[0-10]) Y

BIOL 5V95 Advanced Topics in Molecular and Cell Biology: Individual Instruction (1-6 semester credit hours) May be repeated for credit as topics vary. Instructor consent required. ([1-6]-0) Y

BIOL 6100 Biological Sciences Department Seminar (1 semester credit hour) A weekly seminar that features accounts of current research by outstanding investigators in biology and related scientific areas. Pass/Fail Only. May be repeated for credit. Prerequisites: Graduate standing in Biology and department consent required. (1-0) S

BIOL 6193 Colloquium in Molecular and Cell Biology (1 semester credit hour) Required for all degree students except non-thesis MS, to be taken before a Supervising Committee is appointed. Pass/Fail only. (1-0) Y

BIOL 6252 Current Research in Molecular Biology (2 semester credit hours) Recent developments in biosynthesis, structure, function, and expression of nucleic acids in prokaryotes and eukaryotes. Students will participate in a critical analysis of current research publications. Pass/Fail only. May be repeated for credit as topics vary (8 semester credit hours maximum). (2-0) S

BIOL 6315 Epigenetics (3 semester credit hours) Almost all cell types in our body share the same genetic information, but they perform very distinct functions. For example, our nerve cells are morphologically and functionally distinct from our muscle cells. How can the same genome give arise to hundreds of distinct cell types in our body? How can different diseases affect identical twins sharing the same genetic information? Why our parents and grandparents' diet and health may have lasting influences on our own health? The field of epigenetics emerged over the past decades to tackle these fundamental questions that intersect our genome, development, environment, and disease. The course will provide a broad overview of epigenetic phenomena and epigenetic mechanisms with weekly lectures and small group discussions of primary literature. The course will introduce students to seminal works in epigenetics and recent developments with the goal of instilling critical knowledge of the field. (3-0) Y

BIOL 6317 Pathobiology and Animal Models of Human Diseases (3 semester credit hours) This course is designed to provide graduate students with comprehensive and integrated advances of recent biomedical research within a clinically oriented framework. Topics including cancer, metabolic diseases, inflammation, and tissue injuries are presented with the aim that students will become aware of the contributions of various animal models to future developments of diagnosis and treatments. Students are also expected to acquire the necessary skills to interpret and present recent landmark research articles. Sessions include lectures, seminars from invited guest lecturers, and journal article presentation. (3-0) S

BIOL 6327 RNA World (3 semester credit hours) The nature of modern RNA suggests a prebiotic RNA world. This course will begin with a presentation of the arguments that a RNA world existed before the evolution of protein synthesis. Additional topics will include RNA evolution, the origin and evolution of introns, RNA replication, the evolution and involvement of tRNAs and rRNAs in protein synthesis, the structure and mechanism of large catalytic RNAs such as Group I and Group II introns and the RNase P RNA, the structure and mechanism of small nuclear RNAs such as hammerheads and hairpins, RNA editing, and the mechanism of telomerase. (3-0) R

BIOL 6331 Molecular Genetics (3 semester credit hours) A graduate survey of the phenomena and mechanisms of heredity, its cytological and molecular basis, with a focus on bacterial and model eukaryotic systems. Topics will include fundamentals of Mendelian Genetics, genetic recombination and genetic linkage, as well as gene structure and replication, gene expression and the transfer of genetic information, mutation and mutagenesis, and applications of recombinant DNA techniques to genetic analysis. For students who have not had undergraduate genetics. Instructor consent required. (3-0) Y

BIOL 6333 Macromolecules: Structure, Function, and Dynamics (3 semester credit hours) This course includes a discussion of DNA structures, protein structures, the folding and stability of domains, and the binding of proteins to DNA. Methods used to investigate the relation of structure to function are emphasized. Types of protein structures whose structure and function are considered include transcription factors, proteinases, membrane proteins, proteins in signal transduction, proteins on the immune system, and engineered proteins. Instructor consent required. (3-0) Y

BIOL 6337 Regulation of Gene Expression (3 semester credit hours) An in depth look at how the cell makes use of its genetic information, with a primary focus on the mechanisms of transcription regulation. The course emphasizes a critical discussion of techniques and results from the recent scientific literature. Topics are taken from eukaryotic and/or prokaryotic systems and typically cover areas such as promoter organization, RNA polymerase and transcription factor structure and function, the organization and packaging of chromosomes, whole-genome analyses, and the pathways that control gene expression during growth and development. (3-0) Y

BIOL 6339 Regulation of Eukaryotic Protein Synthesis (3 semester credit hours) This course will focus on how mRNAs are decoded by ribosomes to produce proteins in cells. The course will discuss insights from model organisms, cancer, neurodegeneration, learning, and memory. Topics will cover a range of mechanisms spanning editing, programmed frame-shifting, cap-dependent and independent scanning, elongation, the integrated stress response, termination, recycling, rescue, and collision resolution. The course will consist of lectures, presentations of journal articles, guest lectures, and group discussions. As a capstone to the course, students will produce a brief research proposal related to a topic visited in the course. Department consent required. (3-0) R

BIOL 6341 Oncogenes (3 semester credit hours) Properties of cancer cells, in vivo and in vitro. Telomeres and cellular immortality. The role of DNA and RNA viruses in human cancers. Molecular biology of chronic leukemia retroviruses and the acutely transforming retroviruses. Retroviral oncogenes; the role of mutation, amplification, and chromosomal translocation of cellular oncogenes in human cancer. Regulation of the eukaryotic cell cycle, and the role of tumor suppressor genes. The role of oncogenes in growth hormone signal transduction. The role of apoptosis, and developmental signaling pathways in cancer. (3-0) Y

BIOL 6342 Stem Cell Biology in Development, Regeneration, and Cancer (3 semester credit hours) Stem cells are present throughout the tree of life and play integral roles in development, tissue homeostasis, regeneration, and disease. The course will introduce students to key concepts and advances in the stem cell field. It will cover principles of stem cell biology (properties, potency, cell division, stem cell niche, molecular mechanisms), different stem cell types and their roles (embryonic, adult, iPSCs), various tools/technologies for studying stem cells, applications of stem cells in understanding/treating medical conditions (cancer, injury, autoimmune diseases) and ethical considerations. The course will consist of lectures, journal club classes, and interactive discussions. Department consent required. (3-0) Y

BIOL 6343 Molecular Neuropathology (3 semester credit hours) This course is designed to give students a 360 degree view on pathology and the corresponding molecular basis of this pathology in different diseases linked to the brain and spinal cord. Here students acquire an in depth understanding of these diseased states and are able to analyze and critically review published journal articles. Instructor consent required. (3-0) S

BIOL 6344 Molecular Neuropathology II (3 semester credit hours) This course is designed to give students a 360 degree view on pathology and the corresponding molecular basis of this pathology in different diseases linked to the brain and spinal cord. Here students acquire an in depth understanding of these diseased states and are able to analyze and critically review published journal articles. Instructor consent required. (3-0) Y

BIOL 6345 Molecular Basis of Acquired Immune Deficiency Syndrome (3 semester credit hours) Topics include an analysis of the molecular basis of the infection of target cells by HIV, the intracellular replication of retroviruses, with special attention given to the HIV tat and rev genes, and an analysis of the roles of the HIV accessory genes: vif, vpr, vpu and nef. The immunological response of the host to HIV is considered, as is the biological basis for the ultimate failure of the immune system to contain this virus, with attendant immune collapse. The molecular basis of a variety of existing and potential anti-retroviral therapies is considered. (3-0) Y

BIOL 6351 Cellular and Molecular Biology of the Immune System (3 semester credit hours) Innate and adaptive immunity. Structure and function of immunoglobulins and MHC molecules, and their role in the adaptive immune response. Function of the primary and secondary lymphoid tissues, and the role of professional antigen presenting cells. The molecular basis for the generation of diversity during cellular development of B and T lymphocytes. The role of complement in innate immunity, and details of T cell and B cell mediated immunity. (3-0) Y

BIOL 6352 Modern Biochemistry I (3 semester credit hours) Structure and function of proteins, including enzyme kinetics and catalytic mechanisms; structure and metabolism of carbohydrates, including oxidative phosphorylation and electron transport mechanisms. For students who have not had undergraduate biochemistry. Instructor consent required. (3-0) S

BIOL 6353 Modern Biochemistry II (3 semester credit hours) Continuation of BIOL 6352. Structure and metabolism of lipids, including membrane structure and function. Nitrogen metabolism: amino acids and nucleotides. Polynucleotide replication, transcription, and translation. For students who have not had undergraduate biochemistry. Instructor consent required. (3-0) Y

BIOL 6354 Microbial Physiology (3 semester credit hours) Microbial physiology considers the basic processes of microbes, especially those variations that are unique to microbes: energy generation, fermentations, and other pathways specific to bacteria, cellular structure and differentiation, and bacterial responses to the environment. Instructor consent required. (3-0) Y

BIOL 6355 The Nucleus (3 semester credit hours) The nucleus is the defining feature of all eukaryotes. It contains our chromosomes and is the command center of all our cells. In the nucleus, our genetic information is interpreted, protected, duplicated and modified. Central control of gene expression occurs in the nucleus by transcription and post-transcription mechanisms. Moreover, the nucleus is organized into various functional compartments that specialized in transcription, splicing, rRNA processing and repression. The course will provide a broad overview of functional organization of the nucleus using recent primary literature from the field, focused particularly on genomic analyses of nuclear function. The course will introduce students to seminal works in the field and recent developments with the goal of instilling critical understanding of structure and function of the nucleus. Advanced knowledge of molecular biology is essential. Prior course work on genetics, genetic analysis and genomics is strongly recommended. Instructor consent required. (3-0) Y

BIOL 6356 Eukaryotic Molecular and Cell Biology (3 semester credit hours) Regulation of cellular activities in eukaryotic cells; structural and molecular organization of eukaryotic cells; molecular basis of cell specialization; membranes and transport. For students who have not had undergraduate cell biology. Instructor consent required. (3-0) S

BIOL 6360 Medical Cell Biology for Biotechnology (3 semester credit hours) This course will explore cell structure, the structure of DNA, mutations in DNA, gene therapy, stem cells, cell signaling, and the immune system, etc. Emphasis will be placed on understanding the cellular and molecular basis of health and disease. For students who have not had undergraduate cell biology and/or molecular genetics. Instructor consent required. (3-0) S

BIOL 6370 Microbial Genetics (3 semester credit hours) This course uses primary scientific literature to teach students concepts and methods in microbial genetics. Assessments include open-ended experimental design challenges, data analysis, literature research, and problem solving. Class discussion and group assignments are major components of the class. Prerequisites: BIOL 5420 and department consent required. (3-0) R

BIOL 6373 (BMEN 6391) Proteomics (3 semester credit hours) Protein identification, sequencing, and analysis of post-translational modifications by liquid chromatography/tandem mass spectrometry; determination of protein three dimensional structure by x-ray crystallography; its use in drug design; understanding protein interactions and function using protein chip microarrays. Prerequisites: one semester of undergraduate biochemistry and one semester of graduate biochemistry or instructor consent required. (3-0) T

BIOL 6384 Biotechnology Laboratory (3 semester credit hours) Laboratory instruction in LC/MS/MS mass spectral analysis of protein sequence, ICAT (isotope coded affinity tag) reagents, and MS analysis of cellular proteomes, PCR and DNA Sequencing, and DNA microarray analysis; fluorescence and confocal microscopy and fluorescence activated cell sorting. Instructor may require students to demonstrate adequate laboratory skills in order to enroll. Lab fee of $30 required. (1-4) S

BIOL 6385 (BMEN 6389 and MATH 6343) Computational Biology (3 semester credit hours) Machine learning and probabilistic graphical models have become essential tools for analyzing and understanding complex systems biology data in biomedical research. This course introduces fundamental principles and methods behind the most important high throughput data analysis tools. Applications will cover molecular evolutionary models, DNA/protein motif discovery, gene prediction, high-throughput sequencing and microarray data analysis, computational modeling gene expression regulation, and biological pathway and network analysis. Prerequisite: Some background in elementary statistics/probability or introductory bioinformatics, or instructor consent required. (3-0) Y

BIOL 6684 Biotechnology Laboratory (6 semester credit hours) Instruction of laboratory methods that have relevance to investigational approaches to study cell function, such as in differentiation, growth, and division, as well as understanding changes related to diseases and responses to drugs, experimental manipulations and treatments. The course highlights essential aspects of applications involved in analyzing DNA, RNA, proteins, and cells, and aims to build hands-on skills transferrable to biosciences research and biotechnology product development. Activities are organized in modules central to key practices, including laboratory biosafety, proper waste disposal, scientific methodology, experiment design, lab notebook keeping, molecular cloning, plasmid DNA preparation, restriction fragment analysis, cell culture and aseptic laboratory techniques, transfection of mammalian cells, protein extraction, SDS PAGE, immunoblot analysis, RNA isolation, polymerase chain reaction, DNA sequencing, gene and protein expression profiling, fluorescence and confocal microscopy, fluorescence activated cell sorting, and enzyme-linked immunosorbent assay. Instructor may require students to demonstrate adequate prior knowledge in biochemistry, molecular and cell biology, and laboratory skills to enroll. Lab fee of $30 required. (2-[other]) S

BIOL 6V00 Topics in Biological Sciences (1-6 semester credit hours) May be repeated for credit (9 semester credit hours maximum). Department consent required. ([1-6]-0) Y

BIOL 6V01 Topics in Biological Sciences (1-6 semester credit hours) Includes a laboratory component. May be repeated for credit as topics vary (9 semester credit hours maximum). Lab fee of $30 required. (1-[0-10]) Y

BIOL 6V02 The Art of Scientific Presentation (1-2 semester credit hours) Students learn how to give an effective seminar by reading scientific articles on a central theme in biology and then delivering a presentation, first to their classmates, followed by another presentation to the Molecular and Cell Biology faculty and students. While learning the focused theme, students acquire skill sets in critical reading of scientific literature and oral presentation. Required for all PhD students. Pass/Fail only. ([1-2]-0) Y

BIOL 6V03 Research in Molecular and Cell Biology (1-9 semester credit hours) Pass/Fail only. May be repeated for credit as topics vary. Instructor consent required. ([1-9]-0) S

BIOL 6V19 Topics in Biochemistry (2-5 semester credit hours) May be repeated for credit as topics vary (9 semester credit hours maximum). ([2-5]-0) Y

BIOL 6V29 Topics in Molecular Biology (2-5 semester credit hours) May be repeated for credit as topics vary (9 semester credit hours maximum). ([2-5]-0) Y

BIOL 6V39 Topics in Biophysics (2-5 semester credit hours) May be repeated for credit as topics vary (9 semester credit hours maximum). Department consent required. ([2-5]-0) T

BIOL 6V49 Topics in Cell Biology (2-5 semester credit hours) May be repeated for credit as topics vary (9 semester credit hours maximum). Department consent required. ([2-5]-0) Y

BIOL 6V50 Internship in Biotechnology/Biomedicine (1-6 semester credit hours) Provides faculty supervision for a student's internship. Internships must be in an area relevant to the student's coursework for the MS in Biotechnology. Pass/Fail only. May be repeated for credit as topics vary. Instructor consent required. ([1-6]-0) R

BIOL 6V51 Biotechnology Project Design (1-6 semester credit hours) The course engages students to design a theoretical application that addresses a problem or need with a biotechnological solution. It aims to build students' multidisciplinary knowledge and integrative skills with case-based learning. The central theme is the development of a self-guided project in which students propose conception of inventive and visionary products. The projects may involve applications concerning medicine, agriculture, energy, or the environment, such as therapeutic drugs and biologicals to treat diseases and disorders, bioanalytical applications with mechanical and electronic adaptations for measuring biological markers, genetically modified plants with enhanced traits for increasing food and feed production, metabolic engineering approaches to design microbes for the production of biofuels and industrial biochemicals, or ecosystem bioremediation, etc. Projects are expected to combine theoretical concepts and practical approaches within a multistage decision-making process in which ideas are modeled towards application development. Projects are evaluated from procedural, integrative, and organizational perspectives. Emphasis is given to problem definition, scientific valuation, simplicity and specificity of the approach, and real-life application potential. Assessment is done critically at three levels: to monitor students' progress, to check the completion of specific points that describe the approach-goal-motivation-scope, and to evaluate the final report. Report should include work that substantiates comprehension of the background information, knowledge and use of gene/protein sequences and structures, molecular and cellular processes, scientific methodology, application design, and/or process development. The course is appropriate for students interested in applying engineering principles to develop comprehensive and multidimensional hypothetical approaches. Students are encouraged to perform preliminary research and bring potential ideas for project development. Instructor consent required. ([1-6]-0) R

BIOL 6V95 Advanced Topics in Molecular and Cell Biology: Individual Instruction (1-6 semester credit hours) May be repeated for credit as topics vary. Instructor consent required. ([1-6]-0) Y

BIOL 6V98 Thesis (3-9 semester credit hours) Pass/Fail only. May be repeated for credit. Instructor consent required. ([3-9]-0) S

BIOL 8V01 Research in Molecular and Cell Biology (1-9 semester credit hours) Pass/Fail only. May be repeated for credit as topics vary. Instructor consent required. ([1-9]-0) S

BIOL 8V99 Dissertation (1-9 semester credit hours) Pass/Fail only. May be repeated for credit. Prerequisites: Open to PhD students only and instructor consent required. ([1-9]-0) S