Biology Undergraduate Programs

First half of an introductory two-semester survey of contemporary biology that covers the chemical basis of life, structure and biology of the cell, molecular biology and genetics. Course includes laboratory that reinforces and provides supplemental information related to the lecture topics.

Prerequisites, be able to:
1. Solve algebraic problems
2. Convert common units of length, mass, volume, and concentration
3. Organize numerical data in a spreadsheet
4. Distinguish between living and non-living entities
5. Recognize that the cell is the basic unit of life
6. Recognize the roles of chemical processes and homeostasis in living organisms
7. Describe the principle of diffusion/osmosis
8. Recognize the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits

Learning outcomes, be able to:
1. Apply scientific reasoning to explain natural phenomena and to distinguish science from pseudoscience
2. Describe the chemical composition and formation of the major biological macromolecules
3. Perform calculations to determine chemical concentrations including pH
4. Compare and contrast prokaryotic and eukaryotic cells in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
5. Describe the composition, structure, and function of cellular membranes and their roles in simple diffusion, transport, cell signaling, and homeostasis
6. Describe the processes of respiration and photosynthesis, and the interdependence of autotrophic and heterotrophic organisms
7. Describe roles of the cell cycle in growth and reproduction of organisms
8. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
9. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated

The second half of an introductory two-semester survey of contemporary biology that covers evolution, history of life, diversity and form and function of organisms. Course includes laboratory that reinforces and provides supplemental information related to the lecture topics. Prerequisite: BIOL 111

Prerequisites, be able to:
1. Solve algebraic problems
2. Convert common units of length, mass, volume, and concentration
3. Organize numerical data in a spreadsheet
4. Apply scientific reasoning to explain natural phenomena and to distinguish science from pseudoscience
5. Compare and contrast prokaryotic and eukaryotic cells in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
6. Describe the roles of membrane transport in cellular function and homeostasis
7. Describe the processes of respiration and photosynthesis, and the interdependence of autotrophic and heterotrophic organisms
8. Describe roles of the cell cycle in growth and reproduction of organisms
9. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
10. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated

Learning outcomes, be able to:
1. Explain the relationship between genes/alleles and variation among organisms
2. Explain how genetic variation contributes to evolution
3. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of species diversity
4. Construct evidence-based phylogenies to describe diversity within an evolutionary framework
5. Define and give examples of natural selection, stabilizing selection, genetic drift, random mating, genetic bottleneck, homology, phylogeny
6. Calculate allele frequencies in a population
7. Describe examples of evolutionary adaptations in plants and animals in which structure fits function at the cellular and organismal levels
8. Describe plant and animal organs and organ systems in terms of physiology and evolutionary adaptations

Basic microbiology of prokaryotes and eukaryotes; main topics include morphology, physiology, genetics, taxonomy, ecology, medically important species and immunology; mandatory laboratory designed to give hands-on experience and to reinforce basic principles. Prerequisites: BIOL 101, BIOL 107, BIOL 111, or BIOL 113; CHEM 119. May not be used for credit by biology, molecular and cell biology, microbiology, zoology, predentistry or premedicine majors.

Prerequisites, be able to:
1. Compare and contrast microorganisms and infectious particles in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
2. Describe the chemical composition and formation of the major biological macromolecules including proteins, carbohydrates, nucleic acids, and lipids
3. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes influence microbial growth and pathogenesis
4. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of diversity

Learning outcomes, be able to:
1. Compare and contrast bacteria, protists, fungi, viruses, and prions in terms of size, structural features, metabolism, replication, and habitats
2. Diagram DNA replication, transcription, and translation indicating the products and their influence on microbial growth and survival
1. Describe the importance and impact of microbes in environment, health, and biotechnology
2. Describe various morphological, physical, biochemical tests that are used for classifying and identifying various microorganisms
3. Explain how immune responses can be linked to pathogen recognition
4. Compare and contrast how microbial enzymes, toxins, adhesion factors, and antiphagocytic factors affect virulence
5. Outline various pathogenic factors and methods of virulence of different types of microorganisms
6. Identify the key targets and mechanisms of antimicrobials in treating infectious disease
7. Link the key concepts in bacterial metabolism to growth, survival, and virulence
8. Outline modes of action against microbes of chemical and physical microbial control agents
9. Analyze and interpret microbiology-related experimental data

A genetically-based introduction to the study of ecology and evolution; emphasis on the interactions of organisms with each other and with their environment. Prerequisite: BIOL 112.
285. Directed Studies. Credit 1-4. I, II, S

Prerequisites, be able to:
1. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
2. Sketch/explain the physical nature of a gene and mechanisms for regulating gene expression
3. Explain the relationship between genes/alleles and variation among organisms
4. Explain how genetic variation contributes to evolution
5. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of species diversity
6. Construct evidence-based phylogenies to describe diversity within an evolutionary framework
7. Define and give examples of natural selection, stabilizing selection, genetic drift, random mating, genetic bottleneck, homology, phylogeny
8. Calculate allele frequencies in a population
9. Describe examples of evolutionary adaptations in plants and animals in which structure fits function at the cellular and organismal levels
10. Describe plant and animal organs and organ systems in terms of physiology and evolutionary adaptations

Learning outcomes, be able to:
1. Describe the key events in the history of life on Earth, including the origins of photosynthesis, eukaryotic cells, and multicellularity
2. Classify the Earth’s major terrestrial and aquatic biomes/ecosystems, and describe their underlying geophysical and atmospheric causes
3. Explain the broad-scale ecological processes of energy flow, nutrient cycling, and succession
4. Evaluate population demographics using life history tables
5. Describe the evolutionary implications of biotic ecological interactions such as mutualism, competition, and commensalism
6. Explain the key requirements for evolution to occur via natural selection
7. Explain in quantitative terms how allele and/or genotypic frequencies are affected by gene flow, natural selection, genetic drift, mutation, recombination, and non-random mating
8. Describe the following key concepts of quantitative genetics: heritability, environment by genotype interaction, and response to selection
9. Describe the criteria that qualify traits as adaptations, including life-history and other evolutionary trade-offs
10. Compare and contrast sexual selection with natural selection
11. Interpret data in order to classify mechanisms of speciation (allopatric, sympatric, parapatric) within the framework of major species
12. Explain the relationships between molecular evolution processes (mutation, gene duplication, and horizontal gene transfer) and the origins of new genes, traits, and species
13. Describe the evolutionary implications of abiotic interactions such as phenotypic plasticity, avoidance, and tolerance
14. Interpret data/graphs related to evolution and ecology using quantitative methods

Selected topics in an identified area of biology. May be repeated for credit. Prerequisite: Approval of instructor.

Development of job search skills; utilization of career resources; self-assessment of career interests and career objectives; strategies for professional correspondence and networking; business etiquette and interviewing techniques; insight into life science career opportunities.

Prerequisites: Junior or senior classification; department of biology majors only; or approval of instructor.

Classification, phylogeny, comparative anatomy and biology of chordates; diversity, protochordates, vertebrate skeletons, shark and cat anatomy studied in laboratory. Prerequisite: BIOL 214.

Prerequisites, be able to:
1. Explain how animal diversity is the result of evolution
2. Define phylogeny
3. Describe the concept of phylogenetic trees
4. Define homology
5. Define homoplasy (analogy)
6. Define Cladistics
7. Explain taxonomy and classification
8. Distinguish the geological record

Learning outcomes, be able to:
1. Define homology (as applied to chordate anatomical characters)
2. Define characters and character states and their phylogenetic implications
3. List and describe the characters that define the Phylum Chordata
4. Describe the anatomy of protochordates (chephalochordates and urochordates)
5. Describe (draw) the currently accepted phylogenetic relationships of the major groups extant and extinct vertebrates
6. Describe chordate embryology (basic) up through the neurula stage
7. Describe the comparative anatomy of the chordate integumentary systems
8. Describe the comparative anatomy of the vertebrate skull, axial and appendicular skeletons
9. Describe the comparative anatomy of vertebrate respiratory systems
10. Describe the comparative anatomy of vertebrate circulatory systems
11. Visually recognize and identify the major groups of extant chordates
12. Identify the external and internal anatomical structures a shark
13. Identify the external and internal anatomical structures of a cat
14. Identify the skeletal structures representatives of the major groups of extant vertebrates

Integrated approach to cellular, neural, skeletal, muscular anatomy and physiology; includes some histology, histopathology, radiology and clinical correlations. Prerequisites: BIOL 111 and 112, or BIOL 107

Prerequisites, be able to:
1. Explain cell biology basics such as what the mitochondrion is and does, etc.
2. Explain chemistry basics such as enzymes, acid/base, pH, etc.
3. Explain the physics of physiology such as refraction of light, pressure gradients, forces for movement.
4. Write with proper grammar and use digital media
5. Demonstrate how to use a light microscope
6. Solve arithmetic and algebraic problems

Learning outcomes, be able to:
1. Identify tissues and relate their structure to their physiology
2. Articulate structure and function of skin
3. Describe bone anatomy including the Action/Origin/Insertions (AOIs) of the major muscles
4. Explain the growth and developmental physiology of bone
5. Identify major muscles (and respective AOIs) of the human body using human models and cat dissection specimens.
6. Describe the physiology of muscle at the cellular and organ level
7. Explain the anatomy and physiology of the central and peripheral nervous system

Continuation of BIOL 319. Integrated approach to endocrine, cardiovascular, respirtary, digestive, urinary, reproductive and developmental anatomy and physiology; includes some histology, histopathology, radiology and clinical correlations. Prerequisites: BIOL 319; or approval of instructor.

Prerequisites, be able to:
1. Identify tissues and relate their structure to their physiology
2. Explain the anatomy and physiology of the central and peripheral nervous system
3. Explain cell biology basics such as what the mitochondria is and does, etc.
4. Explain chemistry basics such as enzymes, acid/base, pH, etc.
5. Explain the physics of physiology such as refraction of light, pressure gradients, forces for movement
6. Demonstrate proper use of grammar and writing skills including the ability to professionally use digital communication
7. Demonstrate basic microscopy skills
8. Demonstrate proficiency in college level arithmetic
9. Explain the basics of system physiology, from cells up, including cell to cell communication, the respiratory system, excretory system, etc.
10. Explain the basic biochemistry, e.g., what an amino acid looks like, oxidative phosphorylation, etc.

Learning outcomes, be able to:
1. Explain, compare/contrast, and critically analyze body systems
2. Identify the major hormones produced by the human body and articulate their respective effects on homeostasis of physiological systems.
3. Characterize the tissue types learned in BIOL 319 and be able to explain their respective uses and functions in physiological systems
4. Identify all major structures of the special senses, endocrine, cardiovascular, respiratory, digestive, urinary and reproductive systems using human models and cat dissection specimens
5. Compare/contrast the structures of these systems with respect to their functions
6. Explain the physiology demonstrated by electrical recordings of special senses, brain, lung and heart activities

Morphology, taxonomy, natural history and phylogeny of invertebrate animals, with emphasis on biodiversity; class includes both lecture and lab. Labs include study of preserved material and demonstration of living animals in aquaria and terraria. Prerequisite: BIOL 214 or approval of instructor.

Prerequisites, be able to:
1. Classify organisms using the Linnean system (kingdom, phylum, class, order, genus, species)
2. Describe the characteristics of large animal phyla: Porifera, Cnidaria, Annelida, Mollusca, Arthropoda, Echinodermata, Chordata
3. Describe the basic animal systems: nervous, digestive, reproductive, excretory, skeleto-muscular, respiratory, circulatory, endocrine
4. Compare and contrast mitosis and meiosis
5. Describe the transitions in early embryonic development from fertilization to juvenile
6. Explain the differences between prokaryotes and eukaryotes, protists and Animalia
7. Explain why oxygen and water are essential for living organisms
8. Explain what an energy budget is

Learning outcomes, be able to:
1. Identify major groups of non-photosynthetic protists, know their habitats and which ones pose threats to human health
2. Explain how sponges differ from all other multicellular animals
3. Describe the features that enable cnidarians and other invertebrates to survive largely by diffusion
4. Identify embryonic germ layers, explain how they differ between phyla, and know why animals with mosaic development are particularly useful in studying cellular development
5. Compare/contrast the nervous systems of a medusa, flatworm, annelid, cephalopod, ancient versus derived arthropod, echinoderm, and vertebrate
6. Explain how colonies are derived and how they feed and reproduce, including differentiated individuals
7. Define parthenogenesis, describe the ecological situations in which it is likely to occur, and name animal groups in which it occurs
8. Describe the life cycles of common nematode and flatworm parasites
9. Describe the enormous diversity among the annelids, mollusks and arthropods, and give reasons for their success in so many habitats
10. Describe suspension, deposit, and indirect deposit feeding, and give examples of animals that use each strategy.
11. Explain which features (genetic, embryological, and anatomical) link the echinoderms, hemichordates, and chordates.
12. Describe the structure and function of the unique water-vascular system of echinoderms
13. Compare the non-vertebrate chordates in regard to their modes of feeding, motility, early development, and habitat
14. List common invertebrates that are important in ecosystem dynamics, as seafood, as pests, or as experimental subjects
15. List descriptive information for all of the animal phyla, especially those that occur in Texas and the Gulf of Mexico.

Hands-on approach to obtaining, organizing and analyzing genome-related data; emphasis on asking and answering biologically relevant questions by designing and performing experiments using computers; understanding biology from a computational perspective. Prerequisite: Junior or senior classification in life sciences, engineering, mathematics, chemistry.

Prerequisites, be able to:
1. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
2. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated
3. Explain the relationship between genes/alleles and variation among organisms
4. Explain how genetic variation contributes to evolution
5. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of species diversity
6. Apply Boolean operators (and, or, not, nesting) to combine/exclude data in a search
7. Apply fundamentals of logic (inference and arguments)

Learning outcomes, be able to:
1. Retrieve gene and genome data from databases
2. Assemble genome data tables
3. Perform genomic calculations, including comparisons at DNA, RNA, and protein levels
4. Distinguish the terms homology, orthology, and paralogy
5. Perform genome analyses using Galaxy
6. Perform genome analyses using Cyverse
7. Explain how sequence information is used for transcriptome analyses
8. Explain how genetic variation (SNPs) data are used to study populations and to uncover the basis of disease
9. Evaluate genomic data using R and Rstudio
10. Justify the use of different types of data display

Introduction to modern microbiology with emphasis on prokaryotes; includes microbial cell structure, function, and physiology; genetics, evolution, and taxonomy; bacteriophage and viruses; pathogenesis and immunity; and ecology and biotechnology; includes laboratory experience with microbial growth and identification. Prerequisites: BIOL 112; CHEM 227, and CHEM 237 or CHEM 231; or approval of instructor.

Prerequisites, be able to:
1. Compare and contrast prokaryotic and eukaryotic cells in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
2. Describe the chemical composition and formation of the major biological macromolecules including proteins, carbohydrates, nucleic acids, and lipids
3. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated
4. Apply chemical concepts of atomic structure, oxidation-reduction, thermodynamics, and kinetics to biological systems
5. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
6. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of diversity
7. Define and give examples of natural selection, stabilizing selection, genetic drift, random mating, genetic bottleneck, and homology
8. Explain how genetic variation contributes to evolution
9. Perform calculations to determine chemical concentrations and pH

Learning outcomes, be able to:
1. Compare and contrast bacteria, protists, fungi and viruses in terms of size, structural features, metabolism, replication, and habitats
2. Diagram DNA replication, transcription, and translation indicating the players involved in each
3. Describe the importance and impact of microbes in environment, health, and biotechnology
4. Explain key metabolic pathways in microbes
5. Describe microbial reproduction and growth, and the influence of metabolic and environmental factors on these processes
6. Compare and contrast mechanisms of horizontal gene transfer
7. Explain how immune responses can be linked to pathogen recognition
8. Compare and contrast virulence mechanisms
9. Link the key concepts in bacterial metabolism to virulence
10. Analyze and interpret microbiology-related experimental data
11. Identify structures and components in a prokaryotic cell

Analysis of ecosystems at organismal, population, interspecific and community levels. BIOL 358 is the laboratory for this lecture course. Prerequisite: BIOL 214 or approval of instructor.

Prerequisites, be able to:
1. List the conditions for evolution by natural selection
2. Describe other evolutionary phenomena, such as mutational processes (kinds, effects)
3. Explain major kinds of evolutionary patterns in the history of life (e.g., convergent evolution, speciation)
4. Define the kinetics of biological reaction rates and explain how they are influenced by temperature
5. Compare and contrast aerobic and anaerobic production of ATP, including details of the end products and the differences in efficiency
6. Summarize the phylogeny of life (including, distinguishing traits of the domains, patterns of relationships among the domains and among the animal phyla, especially with regard to major animal phyla and major classes (e.g., insecta).
7. Explain how PCR works and why it matters as a key tool in all areas of modern biology
8. Describe various types of DNA sequence variation, and how that variation is used in constructing phylogenies
9. Describe the structure and functional properties of eukaryotic cells, with special attention to the mitochondria (more generally how phospholipid bilayer membranes establish gradients and why that matters to function, and how these functions are accomplished in Archaea)
10. Explain the processes of DNA replication, including proofreading enzymes, and translation in both prokaryotes and eukaryotes.
11. Explain how the physicochemical properties of proteins are conferred by their amino acid composition and 3-dimensional structure

Learning outcomes, be able to:
1. Describe and apply the fundamental concepts of Ecology and ecological processes in a scientifically coherent manner
2. Explain the mathematical underpinnings of ecological theory
3. Apply a range of quantitative methods used in Ecology, including regression, allometry, statistical principles related to normal distributions, and principles of experimental design
4. Present a historical perspective on the development of the discipline and sub-disciplines of Ecology
5. Interpret quantitative findings from comparative and experimental analyses of ecological phenomena, including graphs and mathematical results from the primary literature
6. Describe earth’s climate system and its relationship to patterns in species distributions and other ecological properties
7. Explain the process of scientific discovery, and modern research approaches in Ecology based on numerous examples from the primary literature not described in the text
8. Describe how fundamental biological processes at the cellular and subcellular level (energetics phenomena) including how oxygen limitation constrains thermal tolerance relate to large-scale patterns in distribution and abundance
9. Explain how climatological variation may influence mutation rates and therefore explain latitudinal patterns in species diversity
10. Use phylogenetic tools to understand patterns in species diversity

Introduction to how animals function, including basics of neurophysiology, endocrinology, muscular, cardiovascular, respiratory, ormoregulartory, and metabolic physiology; broadly comparative in scope and encompassing adaptation of physiological systems to diverse environments; the laboratory stresses techniques used for monitoring and investigating physiological mechanisms and responses to environmental changes. Prerequisites: BIOL 214, CHEM 228 or approval of instructor.

Prerequisites, be able to:
1. Apply scientific reasoning to biological phenomena
2. Perform calculations to assess biological data
3. Describe the chemical composition of major biological macromolecules and the cellular composition of major biological tissues
4. Understand animal cells in terms of subcellular structures and relationships to tissue functions
5. Describe the composition, structure, and function of cellular membranes and their roles in simple diffusion, transport, membrane potential, and cell signaling, and homeostasis
6. Explain the relationships between DNA, RNA and proteins in animal cells
7. Explain how adaptations to different environmental conditions relate to survival, reproduction, and diversity of life histories
8. Describe examples of evolutionary adaptations in animals in which structure fits function at the cellular and organismal levels
9. Describe animal organs and organ systems in terms of physiology and evolutionary adaptations
10. Explain the concept of homeostasis and its relationship to cellular and organismal physiology

Learning outcomes, be able to:
1. Explain the fundamental principles of nervous, sensory and motor system physiology
2. Describe electrical and synaptic cellular signaling and demonstrate underlying principles using computational approaches
3. Explain the fundamental principles of cardiovascular and circulatory physiology
4. Explain the relationships of gases and their transport to respiratory physiology
5. Apply analytical chemistry knowledge to problems of metabolic physiology
6. Compare and contrast thermoregulatory physiology in endotherms and homeothermy and calculate impacts of temperature on physiological processes
7. Explain fundamental principles of digestive physiology and understand their neural and endocrine regulation
8. Compare and contrast osmoregulatory physiology of animals in aquatic vs. terrestrial environments, including renal and excretory function
9. Explain the connections between endocrine and neuroendocrine physiology and diversity of hormonal signaling mechanisms, including their regulation of animal reproduction
10. Develop hypotheses and design experiments to demonstrate principles of animal physiology

Basic principles of endocrinology including structure and functions of hormones in vertebrates; hormonal control of growth, metabolism, osmoregulation, and reproduction; endocrine techniques and mechanism of action of hormones. Prerequisite: BIOL 214 and CHEM 227; BIOL 320 or 388 strongly recommended.

Prerequisites, be able to:
1. Describe how the process of evolution by natural selection results in adaptation
2. Sketch a branching phylogeny (cladogram) describing how morphological characters are used to distinguish the major classes of chordates
3. Describe the basic function of the major cellular organelles (nucleus, mitochondrion, Golgi, ER, cytoskeleton, plasma membrane, endo- and exocytotic vesicles)
4. Explain how membranes function as permeability barriers and describe the basic transport mechanisms that enable solutes to cross (diffusion, channels, carrier-mediated, active transport)
5. Describe how information coded in DNA is transcribed and translated into proteins
6. Explain the basic mechanisms through which gene expression is regulated
7. Graphically represent quantitative data illustrating the relationship between independent and dependent variables
8. Recognize standard diagrammatic representations of biochemical structures of amino acids, proteins, lipids, and carbohydrates

Learning outcomes, be able to:
1. List the different chemical classes of hormonal molecules and distinguish them in terms of chemical structure, regulation of synthesis, and transport to targets
2. Contrast the mechanism of action of membrane permeable and impermeable hormones
3. Describe how receptor-ligand interactions result in activation of transduction pathways that regulate cell physiology and gene transcription
4. Provide examples of how hormone activation of targets can be modulated during blood and tissue transport to impact hormone action
5. Describe the conserved structure of the vertebrate hypophysis
6. Distinguish neurosecretion from other types of chemical communication
7. Describe the mechanisms suggested to have resulted in the appearance of orthologous and paralogous hormone families over evolutionary time
8. Explain how the neural control of kidney water conservation is responsive to changing osmotic environments
9. Explain how multiple hormone systems synergize to assure sufficient supplies of nutrients to power cellular metabolism under different physiological conditions
10. Provide a reasonable hypothesis for how thyroid regulation of metabolism evolved from invertebrate precursors
11. Explain how the adrenal gland can function both to sustain basal metabolism and respond to challenges to homeostasis
12. Contrast the function of the hypothalamic-pituitary-gonad axis in the regulation of female and male reproductive cyclicity

A problem oriented course surveying the manipulation and mechanisms of genetic systems in bacteria; recombination, structure and regulation of bacterial genes, plasmids and phages. Prerequisites: BIOL 351; GENE 302. Cross-listed with GENE 406.

Prerequisites, be able to:
1. Compare and contrast bacteria, protists, fungi and viruses in terms of size, structural features, metabolism, replication, and habitats
2. Diagram DNA replication, transcription, and translation indicating the players involved in each
3. Describe the importance and impact of microbes in environment, health, and biotechnology
4. Explain key metabolic pathways in microbes
5. Describe microbial reproduction and growth, and the influence of metabolic and environmental factors on these processes
6. Compare and contrast mechanisms of horizontal gene transfer
7. Explain how immune responses can be linked to pathogen recognition
8. Compare and contrast virulence mechanisms
9. Link the key concepts in bacterial metabolism to virulence
10. Analyze and interpret microbiology-related experimental data
11. Identify structures and components in a prokaryotic cell

Learning outcomes, be able to:
1. Diagram the mechanisms of prokaryotic gene regulation
2. Contrast the mechanisms of positive and negative regulation of the lactose, arabinose, galactose and tryptophan operons
3. Analyze the effects of DNA mutations (e.g., silent mutation, missense mutation, non-sense mutation or frameshift mutation) on gene expression / translation
4. Link the effects of DNA damage to the excision of a Lambda lysogen and the induction of the SOS response
5. Diagram the mechanisms of DNA repair and explain how DNA replication influences which system is used by the cell
6. Predict the outcome of specific mutations in a phage genome (e.g., Lambda phage, T7 phage or T4 phage) on the phage lifecycle
7. Analyze experiments in primary literature articles and provide criticisms of the articles’ findings.

Structure, function, and biogenesis of cells and their components; interpretation of dynamic processes of cells, including protein trafficking, motility, signaling and proliferation. Prerequisite: BIOL 213 and BICH 410.

Prerequisites, be able to:
1. Define energetics in terms of ∆G, distinguish hydrophilic and hydrophobic molecules, distinguish hydrogen, ionic, and covalent bonds, and define the chemical features and roles of biological macromolecules (nucleic acids, proteins, carbohydrates, lipids)
2. Compare and contrast prokaryotic/eukaryotic gene and genome structures
3. Interconvert DNA, RNA, and protein sequences, identify relevant polarity/direction of each process, and define the cellular location of each in eukaryotic cells
4. Describe the mechanisms and subcellular locations for energy generating processes in eukaryotic cells
5. List factors that influence membrane fluidity and explain how these factors exert their effect
6. Explain/sketch the molecular basis of DNA replication and recombination in eukaryotes
7. Predict the movement of molecules across a membrane via simple or facilitated diffusion based on electrochemical gradients
8. Identify the three types of cytoskeletal filaments and their corresponding subunits
9. Describe processes involved in intracellular trafficking of membranes and proteins
10. Describe what occurs in each phase of the cell cycle and meiosis, indicate amounts of DNA present at each step
11. Explain how PCR and restriction endonucleases are used for cloning/genetic engineering
12. Explain/sketch mechanisms by which gene expression may be regulated at levels of transcription, RNA processing, translation, and protein turnover in eukaryotic cells

Learning outcomes, be able to:
1. Interpret results from experimental approaches commonly used in the study of cells and cellular processes, including mutant screens, cell fractionation, microscopy, immunoblots, PCR/RT-PCR, RNA/DNA sequencing
2. Explain/sketch mechanisms by which gene expression may be regulated at levels of transcription, RNA processing, translation, and protein turnover in eukaryotic cells
3. Predict the outcomes and/or constraints for membrane transport processes
4. Predict the subcellular localization of proteins based on signal sequence information
5. Predict the topology of membrane proteins based on signal sequence information and biochemical properties, including interpretation of hydropathy plots and helical wheel projections
6. Distinguish mechanisms of endomembrane sorting and intracellular transport
7. Distinguish the molecules and mechanisms involved in common cell signaling pathways
8. Explain how cytoskeletal dynamics contribute to cell structure, organization, and directed movement
9. Explain how cell cycle regulation leads to accurate DNA replication and mitosis
10. Explain the relationship between cell adhesion and tissue development/function
11. Distinguish necrotic and programmed cell death in terms of molecular and cellular mechanisms
12. Explain the molecular/cellular mechanisms responsible for the onset of cancer and metastasis

Concepts of development in systems ranging from bacteriophage to the mammalian embryo; use of recombinant DNA technology and embryo engineering to unravel the relationships between growth and differentiation, morphogenesis and commitment, aging and cancer. Prerequisite: BIOL 413 or concurrent enrollment or approval of instructor.

Prerequisites, be able to:
1. Explain the central dogma of molecular biology, including a description of transcription and translation
2. Describe the general eukaryotic cell structure (nucleus, endomembrane system, cytoskeleton, etc.)
3. Explain the structure/function of eukaryotic genes (promoters, enhancers, coding region, exons and introns)
4. Describe general features of DNA and protein structure
5. Explain the concept of evolution by natural selection
6. Describe the stages eukaryotic cell cycle and mitosis
7. Define basic concepts of Mendelian genetics, including transmission, dominance, and linkage
8. Describe eukaryotic chromosome and nucleosome structure
9. Explain concepts of general chemistry: aqueous solutions/concentrations, pH, ionic vs. covalent bonds

Learning outcomes, be able to:
1. Describe cell signaling pathways
2. Explain mechanisms of cell differentiation, differential gene expression
3. Describe mechanisms of cell fate specification, including maternal cytoplasmic determinants, conditional specification via cell-cell interactions, and morphogen gradients
4. Describe mechanisms of morphogenesis, including general architecture of animal tissue, epithelial-mesenchymal transition, and cell migration
5. Describe mechanisms of gastrulation, generation of 3 primary germ layers, role of embryonic organizer
6. Explain mechanisms of establishing primary axes of the embryo in model organisms (worm, fly, frog, fish, chick, mouse)
7. Explain regulation of stem cells and progenitors
8. Describe common constituents of ECM, their role in cell fate, cell survival, cell migration
9. Describe conservation of developmental regulatory genes since the Cambrian explosion, “deep homology”
10. Explain concepts of eve-devo: co-option, fates of duplicated genes, canalization, genetic assimilation

Modern methods of study of cell structure and cell function. Prerequisites: BIOL 413 and BICH 412 or registration therein; approval of instructor.

Prerequisites, be able to:
1. Describe the central dogma of molecular biology
2. Describe gene silencing in plants and animals (VIGS, RNAi)
3. Describe the process of transcriptional regulation (cis and trans factors)
4. Interconnect the concepts of genetic master switches and evo-devo
5. List plant, animal, and bacterial responses to the environment (circadian rhythm, tropisms, and their signaling pathways)
6. Describe the general organization of the plant and animal cell
7. Describe the cell cycle
8. Calculate chemical concentrations in terms of molarity and percent weight to volume
9. Explain the processes of innate immunity in plants and animals
10. Explain the concept of phylogenetic relationships between organisms
11. Describe the following basic analytical techniques in biochemical and molecular biology: spectrophotometry, SDS-PAGE, Western blots, PCR, subcellular fractionation, enzyme kinetics, DNA sequencing
12. Explain the basic approaches to making transgenic plants, animals, fungi, and bacteria
13. Explain the structures and functions of plant and animal organ systems

Learning outcomes, be able to:
1. Compare and contrast the cell biology of plants to that of other organisms, such as fungi and animals
2. Describe the different levels of cellular organization in different cell types arising through differential gene expression
3. Sketch the mechanism by which fluorescent protein tags are incorporated into plant cells and are targeted to specific organelles or regions
4. Predict and explain how the cell cycle and nuclear changes accompany differentiation and cell maturation in plants
5. Describe how small molecules cross membranes, and, on that basis, predict the plasmolytic effects of various solutes
6. Compare and contrast how different endomembranes and cytoskeletal activities in different parts of the cell cycle produce different outcomes
7. Explain how different cytoskeletal elements provide the basis for different intracellular movements in cells
8. Calculate statistically meaningful summaries of the measurements made in the lab
9. Interpret the statistical summaries in light of predicted outcomes of the experiment
10. Explain positive and negative controls in experimental design
11. Predict the outcome of hypotheses that you formulate
12. Explain how correlation is different from causation

Still and video photography and photomicrography, computer-based digital image analysis and processing of biological images; theory and principles of light and electron microscopy including transmission and scanning electron microscopy; optical contrast methods for light microscopy including phase contrast, DIC, polarizing light and confocal laser scanning microscopy. Prerequisite: Junior classification or approval of instructor.

Prerequisites, be able to:
1. Describe the central dogma of molecular biology
2. Describe gene silencing in plants and animals (VIGS, RNAi)
3. Describe the process of transcriptional regulation (cis and trans factors)
4. Interconnect the concepts of genetic master switches and evo-devo
5. List plant, animal, and bacterial responses to the environment (circadian rhythm, tropisms, and their signaling pathways)
6. Describe the general organization of the plant and animal cell
7. Describe the cell cycle
8. Calculate chemical concentrations in terms of molarity and percent weight to volume
9. Explain the processes of innate immunity in plants and animals
10. Explain the concept of phylogenetic relationships between organisms
11. Describe the following basic analytical techniques in biochemical and molecular biology: spectrophotometry, SDS-PAGE, Western blots, PCR, subcellular fractionation, enzyme kinetics, DNA sequencing
12. Explain the basic approaches to making transgenic plants, animals, fungi, and bacteria
13. Explain the structures and functions of plant and animal organ systems

Learning outcomes, be able to:
1. Interpret the quality of images
2. Describe how image acquisition systems are used to produce and record images which address specific biological questions
3. Sketch the optical paths of microscopy image acquisition systems
4. Compare and contrast the utility of standard, commercial scientific image processing and visualization software
5. Demonstrate how to use commercial and open source software to address image acquisition, processing and analysis
6. Identify excellent images for high quality multimedia presentations

Cell biology and biophysics of neurons; functional organization of the vertebrate nervous system; physiological basis of behavior. Prerequisites: BIOL 213; BIOL 319, BIOL 320, BIOL 388, BIOL 413, NRSC 235/PSYC 235, or PSYC 235/NRSC 235, or approval of instructor.

Cross Listing: NRSC 434/BIOL 434.

Prerequisites, be able to:
1. Explain how membranes function as permeability barriers and describe the basic transport mechanisms (diffusion, channels, carrier-mediated, active transport)
2. Describe the basic function of the major cellular organelles (nucleus, mitochondrion, Golgi, ER, cytoskeleton, plasma membrane, endo- and exocytotic vesicles)
3. Describe how information coded in DNA is transcribed and translated into proteins
4. Explain the basic mechanisms through which gene expression is regulated
5. Describe the molecules and mechanisms of cellular energy conversion and management
6. Describe the general structure and function of the major organ systems of animals
7. Identify and contrast the major phyla of invertebrate and vertebrate animals
8. Explain what behavioral ecology has taught us about why animals behave differently
9. Explain how genetic variation contributes to evolution
10. Explain what is meant by an animal model

Learning outcomes, be able to:
1. Describe how membrane potentials are created and maintained
2. Relate the structure of the primary types of ion channels to their function
3. Describe how action potentials are created and regulated
4. Explain how action potentials encode and convey information in the nervous system
5. Name and describe the function of the cellular structures comprising the synapse
6. Explain what synaptic plasticity is and how it contributes to learning and memory
7. Describe the cellular transduction mechanisms for the major sensory systems
8. Describe the structure and function of motor pathways in the brain
9. Describe the structure and function of cognition and memory networks in the brain
10. Describe the cellular basis of major diseases of the nervous system

Study of modern methods and tools used to investigate nervous system structure and function. Prerequisite: Approval of instructor.

Prerequisites, be able to:
1. Explain fundamental aspects of cell biology, including membranes, proteins, and gene expression
2. Record data using a computer

Learning outcomes, be able to:
1. Apply standard tools and techniques for studying the nervous system.
2. Locate, measure and discriminate neurons and neural signals in live animals.
3. Justify current areas of emphasis in basic and translational neuroscience research.
4. Explain existing technological constraints and limitations for biomedical devices.

Structure and function of prokaryotic cells, with emphasis on evolutionary adaptations to different environmental, developmental, and pathogenic selections pressures; formation of teamsa and preparation of presentations on specific topics in microbiology.
Prerequisites: BIOL 351; BIOL 406/GENE 406 or concurrent enrollment; BICH 410, BICH 431/GENE 431 and GENE 302 strongly recommended.

Prerequisites, be able to:
1. Compare and contrast bacteria, protists, fungi and viruses in terms of size, structural features, metabolism, replication, and habitats
2. Diagram DNA replication, transcription, and translation indicating the players involved in each
3. Describe the importance and impact of microbes in environment, health, and biotechnology
4. Explain key metabolic pathways in microbes
5. Describe microbial reproduction and growth, and the influence of metabolic and environmental factors on these processes
6. Compare and contrast mechanisms of horizontal gene transfer
7. Explain how immune responses can be linked to pathogen recognition
8. Compare and contrast virulence mechanisms
9. Link the key concepts in bacterial metabolism to virulence
10. Analyze and interpret microbiology-related experimental data
11. Identify structures and components in a prokaryotic cell

Learning outcomes, be able to:
1. Diagram process of spore formation including the phosphotransfer systems involved.
2. Provide mechanistic detail of prokaryotic chemotaxis (e.g., mechanisms of chemoreception, mechanisms of flagellar rotation and tumbling).
3. Contrast the process of fermentation and respiration.
4. Link the generation of the proton motive force with other biological processes.
5. Diagram prokaryotic cell division including the regulation of Z-ring formation.

Introduction to biology of common organisms inhabiting bays, beaches and near-shore oceanic waters with special reference to Gulf of Mexico biota; emphasis on classification, distribution, history, ecology, physiology, mutualism, predation, major community types and economic aspects of marine organisms. Prerequisite: BIOL 214 or approval of instructor.

Prerequisites, be able to:
1. Explain the relationship between the molecular structure of water and its physical properties
2. Describe the coastline of the U.S.A. including Hawaii and Alaska
3. Define diffusion, osmosis, and osmoregulation.
4. Compare and contrast photosynthesis and respiration
5. Describe basic systems found in animals: nervous, digestive, reproductive, skeletal or equivalent, excretory, circulatory and endocrine
6. Compare and contrast mitosis and meiosis. Describe asexual reproduction in a sponge, coral or other common marine invertebrate
7. Describe and differentiate between common animal phyla: Porifera, Cnidaria, Annelida, Arthropoda, Echinodermata and Chordata
8. Classify animals using Linnean nomenclature
9. Distinguish between flowering and non-flowering plants, and between vascular and non-vascular plants
10. Define the following ecological terms: habitat, niche, competition, parasitism, symbiosis, disturbance, succession, geographic speciation

Learning outcomes, be able to:
1. Describe the different properties of marine versus fresh water
2. Describe how a constant marine environment can affect the body forms of marine photosynthetic organisms and animals
3. Differentiate between common reproductive strategies involving free-living larval stages versus common reproductive strategies of land animals
4. Describe the ocean current regimes of the Americas with special reference to the Gulf of Mexico
5. Describe the plate tectonics and major geologic events shaping the Gulf of Mexico, and how the input of major rivers has affected the nearshore habitats
6. Differentiate between phytoplankton-based versus detrital-based ecosystems, and explain why the latter are so common in the northern Gulf of Mexico
7. Describe the common habitats of the coast of Texas and their ecosystem services
8. Describe common tidal zonation on rocky and subtidal habitats, and the role of keystone species
9. Define symbioses and give examples from coral reefs, deep-sea ecosystems, and coastal habitats
10. Describe hermatypic corals and how their growth and structure define a coral reef
11. Name characteristic fishes of various ocean habitats and their adaptations to their habitats
12. Name the major groups of marine mammals and describe their behaviors and physiological and anatomical adaptations to the marine environment
13. Describe common methods of field study in marine environments, and how their data are analyzed
14. Explain how oil and gas exploitation, including remediation for spills, is conducted in the Gulf of Mexico, and what organisms associate with oil platforms
15. Name the major fisheries in the U.S.A. and explain how they are regulated, and describe basic economic and biological problems associated with aquaculture
16. Describe the effects of habitat destruction, global warming, pollution and acidification on marine life

Cellular and molecular mechanisms of nervous system development including neural induction and the basis of complex behaviors; use of a wide range of model organisms with a specific emphasis on vertebrate nervous system development.
Prerequisites: BIOL 213, BIOL 319, BIOL 320, BIOL 413, BIOL 388, NRSC 235/PSYC 235 or PSYC 235/NRSC 235.

Prerequisites, be able to:
1. Describe the structural and functional components of an animal cell.
2. Explain the general mechanisms of intracellular signal transduction (e.g., signaling pathways by which ligand binding to receptor can be transduced to modulate gene expression)
3. Explain major concepts of molecular genetics (i.e., transcription, translation, transcriptional regulation, post-translational modifications, epigenetics)
4. Identify the structural components of a neuron
5. Describe how synaptic transmission (action potentials) occurs; explain the functions of neurotransmitters and the differences between excitatory vs. inhibitory neurotransmission.
6. Explain general neuroanatomy and identify the different regions of the vertebrate nervous system

Learning outcomes, be able to:
1. Describe the major events involved in the early formation of the nervous system, from the single cell stage to gastrulation to neural tube closure
2. Discuss the role of molecular gradients in nervous system tissue patterning
3. Explain the role of transcription factors in formation of dorsal/ventral and anterior/posterior segments in the nervous system
4. Discuss how intracellular and intercellular signaling processes control specification of stem- and progenitor cells into mature neurons and glial cells
5. Describe the molecular events and cellular interactions that guide neuronal migration
6. Explain the molecular control of axon guidance and synaptic specificity
7. Discuss concepts of early synapse elimination and critical periods of plasticity in development
8. Describe the developmental events that are recapitulated in nervous system regeneration, and discuss current strategies for applying concepts of neural development to regenerative medicine

Structure, composition and life cycles of viruses; methods used to study viruses; their interaction with host cells; mechanisms of pathogenicity and cellular transformation; responses of the host to viral infection, and vaccine applications; in-depth study of the life cycles of the major classes of viruses and discussion of emerging viruses. Prerequisite: BIOL 213 or 351 or approval of instructor.

Prerequisites, be able to:
1. Compare and contrast prokaryotic and eukaryotic cells in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
2. Compare and contrast DNA replication, transcription, and translation in prokaryotic and eukaryotic cells
3. Explain the structure/function of genes (promoters, enhancers, coding region, exons, and introns)
4. Explain how molecules get in and out of cells (endocytosis, exocytosis, budding)
5. Explain how the processes of transcription and translation can be regulated in prokaryotic and eukaryotic cells
6. Describe what occurs in each phase of the cell cycle and mitosis
7. Describe the general mechanism of cell signaling pathways, from receptor/ligand interactions to a response

Learning outcomes, be able to:
1. Describe the molecular mechanisms of virus infection and spread in prokaryotic and eukaryotic cells for all 7 viral genome types.
2. Explain the molecular and cellular basis for viral disease (acute, persistent, latent)
3. Describe the host immune response to viral infection (innate and adaptive responses)
4. Define the mechanisms that viruses use to overcome the host immune response
5. Explain current approaches to treating or preventing (vaccines) viral disease
6. Describe the broad impact of viruses and disease on science and society
7. Predict how viruses emerge and the outcome on human health
8. Interpret results from experimental approaches commonly used in the study of viruses
9. Critically analyze a scientific paper related to the study of viruses

Introduction to the entire field of bioinformatics; theoretical background of computational algorithms, with an emphasis on application of computational tools related to modern molecular biological research. Prerequisite: BIOL 213, GENE 301, or GENE 302, or BIMS 320/GENE 320 or GENE 320/BIMS 320 and junior or senior classification, or approval of instructor.

Prerequisites, be able to:
1. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
2. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated
3. Explain the relationship between genes/alleles and variation among organisms
4. Explain how genetic variation contributes to evolution
5. Explain how adaptations to different environmental conditions relate to survival, reproduction, and broad patterns of species diversity
6. Sketch/explain the processes of DNA replication, repair, and recombination
7. Explain the relationship between gene expression and cellular differentiation

Learning outcomes, be able to:
1. Download DNA and protein sequences and ensure proper formatting for bioinformatics analysis
2. Analyze properties of DNA and protein sequences using web-based bioinformatics tools
3. Explain how high-throughput DNA sequencing is conducted
4. Compare and contrast RNAseq, DNAseq, and ChIPseq in terms of procedures and applications
5. Interpret phylogenetic and comparative genomics data
6. Explain how metabolomic studies are conducted and how the data are analyzed
7. Analyze protein structures
8. Describe tools and applications for large-scale image analyses

Introduction to basic immunological concepts and principles of serology. Prerequisite: BIOL 351 or equivalent or approval of instructor.

Prerequisites, be able to:
1. Compare and contrast prokaryotic and eukaryotic cells in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
2. Discuss the main elements of and distinctions between innate and adaptive immunity
3. Outline the function of all the cells produced by hematopoiesis in the immune process
4. Describe the various organs of the body that help make up the immune system
5. Understand the mechanisms and protective benefits of the humoral immune response- the B lymphocyte and antibody production
6. Discuss the mechanisms of cell mediated immunity – the T lymphocyte response
7. Discuss the mechanism of receptor diversity utilized by lymphocytes
8. Outline how antibodies can be used therapeutically and as tools in research

Learning outcomes, be able to:
1. Discuss the main elements of and distinctions between innate and adaptive immunity including timing, adaptability, and memory capabilities
2. Explain the cellular defenses of various leukocytes and the mechanisms of phagocytosis, antigen presentation, and soluble mediate release (cytokines)
3. Link why the innate immune system is necessary for the activation of the adaptive immune system
4. Outline how erythrocytes, platelets, and leukocytes are all produced during the hematopoietic process and how each play a role in the production of a robust, protective immune response
5. Understand the mechanisms and protective benefits provided by skin, mucous membranes, inflammation, fever, and the complement cascades of innate immunity
6. Outline the key structural elements of immunoglobulins and how the different classes of antibodies carry out different effector functions
7. Outline the main processes involved receptor diversification of B and T lymphocytes thus resulting in defense cells each displaying unique antigen specific receptors
8. Discuss how lymphocyte receptor diversification results in the ability of the specific immune response to protect against any type of invader
9. Understand the expression, mechanisms and functions of MHC molecules in antigen presentation to T cells in order to activate cell mediated immunity
10. Examine the effector functions of CD4 T cells in immune defense against infection
11. Outline why a robust humoral response depends on an accompanying T cell response
12. Examine the effector functions and killing mechanisms of CD8 T cells as part of specific immune responses against intracellular pathogens
13. Discuss the production and use of monoclonal antibodies as therapeutics and tools in scientific experiments

Practical application of serological principles which include precipitation, agglutination and blood banking principles; techniques in tissue culture and hybridoma technology also included.
Prerequisite: BIOL 454 or registration therein.

Prerequisites
1. Compare and contrast immune cells and organs in terms of size, organization, function of subcellular structures, and relationships to multicellular functions
2. Discuss the main elements of and distinctions between innate and adaptive immunity
3. Outline the function of all the cells produced by hematopoiesis in the immune process
4. Describe the various organs of the body that help make up the immune system
5. Outline how antibodies can be used therapeutically and as tools in research
6. Outline the Hybridoma technique for monoclonal antibody production
7. Explain antigen- antibody interaction outcomes based on antigen structure
8. Compare and contrast methods and purposes of the ELISA and immunoblotting tests
9. Demonstrate the use of animal models for immune response studies

Learning outcomes
1. Explain the cellular defenses of various leukocytes and the mechanisms of phagocytosis, antigen presentation, and soluble mediate release (cytokines)
2. Discuss and identify the functions of blood, spleen, and lymph nodes in terms of size, organization, function, and relationship to immune functions
3. Outline the key structural elements of immunoglobulins and how the different classes of antibodies carry out different effector functions
4. Examine the effector functions of CD4 T cells in immune defense against infection
5. Examine the effector functions and killing mechanisms of CD8 T cells as part of specific immune responses against intracellular pathogens
6. Discuss the production and use of monoclonal antibodies as therapeutics and tools in scientific experiments
7. Compare and contrast antigen- antibody interactions based on whether the antigen is soluble or cellular
8. Outline the purposes of the ELISA in diagnostic identification, detection, and quantification of various proteins including antigens and antibodies
9. Outline the purposes of the immunoblotting (western blotting) in identification of proteins (antigen or antibody) in complex mixtures such as serum
10. Demonstrate proficiency of antibody production and collection using the mouse model

Microbiology, epidemiology and pathology of human pathogens with an emphasis on bacterial agents. Prerequisite: BIOL 351 or approval of instructor.

Prerequisites, be able to:
1. Outline the structure and functions of the prokaryotic cell and how they differ from other pathogenic organisms
2. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes influence microbial growth and pathogenesis
3. Compare and contrast different antimicrobial control mechanisms
4. Discuss the main elements of and distinctions between innate and adaptive immunity
5. Understand the mechanisms and protective benefits of the humoral immune response- the B lymphocyte and antibody production
6. Discuss the mechanisms of cell mediated immunity – the T lymphocyte response
7. Explain how vaccines work and the target antigens involved in the process
8. Discuss the epidemiology of different types of pathogens based on mechanism of exposure, entry, and pathogenesis

Learning outcomes, be able to:
1. Compare and contrast bacteria in terms of their structure and pathogenic components to other pathogenic microorganism
2. Describe the importance and impact of microbes in health, infectious disease, and biofilm formation
3. Outline modes of action of chemical and physical microbial control agents
4. Understand the mechanisms and protective benefits provided by skin, mucous membranes, inflammation, fever, and the complement cascades of innate immunity
5. Understand the mechanisms and protective benefits provided by T and B lymphocytes of the specific immune response
6. Explain how immune responses can be linked to either the elimination or exacerbation of the disease process
7. Compare and contrast how microbial enzymes, toxins, adhesion factors, and anti-phagocytic factors affect virulence
8. Identify the key targets of potential vaccines for various infectious diseases and the accompanying problems associated with vaccine development especially against eukaryotic pathogens
9. Compare and contrast how intracellular and extracellular pathogens thwart the effectiveness of the immune response
10. Discuss why some pathogens can be used as potential bioterrorism agents based on virulence factors and growth capabilities
11. Compare and contrast microbial disease due to growth and metabolism of the infectious agent versus microbial toxemia due toxin production
12. Analyze pathogenesis mechanisms of historic diseases versus endemic diseases versus newly emerging diseases like Zika and Ebola

Understanding of antimicrobial agents, limitations of use, biosynthesis and regulation, and challenges in development as new therapeutics. Prerequisites: BICH 410 or BICH 440 and BIOL 351 or VTPB 405.

Prerequisites, be able to:
1. Demonstrate basic understanding of cell organization, genetics, and evolution
2. Demonstrate a basic understanding of gene regulation
3. Demonstrate a basic understanding of the chemical basis of life
4. Demonstrate a basic understanding of molecular biology
5. Demonstrate a basic understanding of interaction of organisms with their environment
6. Demonstrate a basic understanding of atomic structure and chemical bonding; chemical reactions; stoichiometry; states of matter; solutions; equilibrium; acids and bases; coordination chemistry
7. Demonstrate a basic understanding of theory and applications of oxidation-reductions systems; thermodynamics and kinetics; complex equilibria and solubility product; nuclear chemistry; descriptive inorganic and organic chemistry
8. Demonstrate a basic understanding of protein, carbohydrate, lipid and nucleotide chemistry

Learning outcomes, be able to:
1. Identify different classes of antimicrobial agents
2. Define mechanisms of action for antibiotics
3. Define mechanisms of antibiotic resistance
4. Analyze approaches used to overcome microbial resistance
5. Explain the complexity of the biosynthetic processes for antibiotic production
6. Analyze the challenges involved in developing new antibiotics
7. Explain how economic factors influence antibiotic development

Study Abroad, email Dr. Leslie Winemiller lesliew@bio.tamu.edu

Prerequisites, be able to:
1. Explain the role of genes in determining the form and function of animals
2. Explain how biodiversity is dependent on genetic changes occurring within populations (evolution)
3. Analyze the role of evolutionary mechanisms in the formation of new species
4. Recognize how evolutionary mechanisms shape biodiversity
5. Evaluate biological taxonomy by comparing and contrasting genetic, anatomical, physiological, behavioral, and ecological attributes
6. Illustrate biodiversity via evolutionary trees or phylogenies.
7. Describe how biogeographical distribution provides clues about the Earth’s past geological events
8. Explain the role of ecology in predicting the distribution and abundance of populations in the biosphere.
9. Articulate how an organism’s structure, function, and/or behavior is determined by cell-to-cell interactions and environmental influences.

Learning outcomes, be able to:
1. Describe and discuss the geography, natural history, and culture of the Brazilian Amazon
2. Articulate a basic understanding of tropical biology gained from both individual and collective group participation in field experiences in diverse ecosystems in the central Amazon River
3. Identify unique aspects of Brazilian Amazon culture and language (Portuguese).
4. Systematically observe, record, and analyze observations of flora, fauna, and geography
5. Identify local species with the assistance of field guides and texts
6. Develop and express ideas, thoughts, and reactions to observations through written journal entries
7. Demonstrate ability to measure environmental parameters using scientific data collection equipment
8. Effectively collaborate in groups to hypothesize, research, and interpret scientific principles
9. Independently research a topic in tropical biology, create a presentation, and effectively communicate the presentation to peers and evaluators
10. Critically analyze scientific research presentations through questioning and discussions

Evolutionary patterns, mechanisms and processes at the organismal, chromosomal and molecular levels; modes of adaptation and the behavior of genes in populations. Prerequisite: GENE 302 or approval of instructor.

Prerequisites, be able to:
1. Describe the structure of DNA, its replication, and error/repair
2. Explain the relationships between genetic code, codons, codon specificity, codon redundancy
3. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
4. Explain the relationship between genes/alleles and variation among organisms
5. Describe Mendelian inheritance and Mendel’s Laws
6. Describe meiosis and recombination
7. Differentiate exons vs introns
8. Describe evolution as a science
9. Define homology
10. Recognize the contributions of Charles Darwin to the science of evolution
11. Describe natural selection
12. Define phylogeny
13. Describe the concept of phylogenetic trees

Learning outcomes, be able to:
1. Describe Evolution as a science and philosophy
2. Describe the history of evolutionary thought
3. Differentiate phenetic, cladistic, and likelihood methods of phylogenetic reconstruction
4. Describe the evidence of evolution
5. Describe Natural Selection, Darwinian fitness, and explain how natural works and how it does not
6. Describe variation among individuals, its genetic/mutational basis and the origin of new genes
7. Describe (one-locus models) of how natural selection, mutation, migration, genetic drift, and nonrandom mating affect the evolution of a population; estimate coefficient of inbreeding
8. Compute and interpret the results of examples of the Hardy-Weinberg Theorem
9. Describe evolution at two loci; compute and evaluate linkage disequilibrium
10. Describe adaptation-based hypotheses for the evolution of sex
11. Describe evolution at multiple loci/quantitative traits including: selection gradient, selection differential and response to selection
12. Describe sexual selection and the Bateman gradient
13. Describe evolution of social behavior, inclusive fitness, kin selection and group selection
14. Describe Species and the processes of speciation

Examines how behavior contributes to survival and reproduction, and how evolutionary history and ecological circumstance interact to shape the expression of behavior; focus on integrative nature of behavior: how the interaction of evolutionary processes, mechanistic constraints, and ecological demands determine behavioral strategies. Prerequisite: Any one of the following: BIOL 214, BIOL 357, BIOL 388, BIOL 405, BIOL 434/NRSC 434, BIOL 466, or approval of instructor.

Prerequisites, be able to:
1. Perform basic algebra
2. Perform literature searches
3. Interpret and explain the basis for Mendelian inheritance data
4. Explain processes underlying evolutionary biology

Learning outcomes, be able to:
1. Critically interpret a scientific paper
2. Apply quantitative reasoning to a verbal scientific problem
3. Construct a written argument about a scientific question
4. Explain the role of constraints in adaptive evolution
5. Explain the mechanistic basis of decision making
6. Apply quantitative theory to test biological predictions

Active research of basic nature under the supervision of a Department of Biology faculty member. May be taken two times. Registration in multiple sections of this course is possible within a given semester provided that the per semester credit hour limit is not exceeded. Prerequisite: Approval of departmental faculty member.

Learn more on our Undergraduate Research Page.

Basic aspects of the biotechnology business; includes key aspects of biotechnology patents, the main steps in preclinical drug development and company structure and funding.
Prerequisites: BIOL 213 or equivalent; CHEM 227 and CHEM 228.

Prerequisites, be able to:
1. Sketch/explain the structures and functions of the major biological macromolecules and their subunits; perform calculations to determine chemical concentrations and pH
2. Predict the outcomes of biochemical reactions based on thermodynamic principles and enzyme kinetics
3. Describe the molecules and mechanisms of cellular energy conversion and management
4. Compare and contrast passive and active membrane transport
5. Sketch/explain the processes of DNA replication, repair, and recombination
6. Sketch/explain the physical nature of a gene and mechanisms for regulating gene expression
7. Explain the relationship between gene expression and cellular differentiation
8. Describe the processes of protein sorting and vesicular transport within a cell
9. Describe the structures, functions, and components of the cytoskeleton
10. Describe the molecular components and mechanisms of cellular signal transduction
11. Explain the processes that control the cell cycle and their relationships to cell death and cancer
12. Interpret data/graphs related to biological experiments and use appropriate statistical approaches to infer significance

Learning outcomes, be able to:
1. Define the following key terms used in the biotechnology business: Indefiniteness, Inherency, Markman hearing, NDA, Rochester ruling, Supreme Court AMP v Myriad ruling, ADME, Pharmacokinetics & Pharmodynamics, Bioavailabiity, Delivery, IND, Phase 1, 2, 3, GMP, GLP, CRO, Elevator pitch, CEO, CSO
2. Evaluate biotechnology patents and related patents
3. Explain risks commonly involved in biotechnology
4. Explain scientific and regulatory steps involved in drug development
5. Compare and contrast different ways to finance a project
6. Evaluate a new biotechnology project

Fraud in science, how to recognize it, and how to avoid committing fraud; includes the basis of ethics and plagiarism, negotiation techniques and conflict management, the regulations and ethics covering animal and human experiments, record-keeping, data management and peer review.
Prerequisites: BIOL 491, NRSC, 491, BICH 491, GENE 491, BIMS 491, or CHEM 491, or concurrent enrollment, or approval of instructor.

Prerequisites, be able to:
1. Formulate a hypothesis to explain a biological problem or observation then design experiments with controls that could be used to test it
2. Interpret data/graphs related to biological experiments and use appropriate statistical approaches to infer significance
3. Explain the theoretical basis and application of techniques/technology used in one area of biological research

Learning outcomes, be able to:
1. Define what constitutes fraud in science, how to recognize it, and how to avoid it
2. Explain what constitutes plagiarism
3. Describe ethics and federal regulations covering animal and human experiments, record-keeping, data management, and peer review
4. Apply the mirroring technique, difficult conversations technique, cognitive therapy (on self, and ability to explain to others), and ethical negotiations
5. Explain the key components of patent law

Prerequisites, be able to:
1. Describe general features of DNA structure
2. Explain the relationships between DNA, genes, and chromosomes in the determination and inheritance of traits
3. Explain how the information in genes flows from DNA to proteins through the processes of transcription and translation and how these processes can be regulated
4. Describe typical modes of DNA manipulation – restriction digests, gene cloning, PCR, DNA sequencing

Learning outcomes, be able to:
1. Design synthetic biology applications for bacteria
2. Cite multiple examples of synthetic biology applications
3. Describe the tools and approaches used in modern synthetic biology
4. Explain approaches to create and direct variability in gene sequences
5. Discuss ethical and regulatory issues in synthetic biology