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2.0: Introduction - Biology

2.0: Introduction - Biology


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In which we consider what biology is all about, namely organisms and their diversity. We discover that organisms are built of one or more, sometimes many cells that act in a coordinated (social) manner. We consider the origins of organisms, their basic properties, and their relationships to one another.

Biology is the science of organisms, how organisms function, behave, interact, adapt, and, as populations, have and can evolve. As we will see, organisms are discrete, highly organized, bounded but open, non-equilibrium, physicochemical systems. Now that is a lot of words, so the question is what do they mean? How is a rock different from a mushroom that looks like a rock? What exactly, for example, is a bounded, non-equilibrium system? The answers are not simple; they assume a working knowledge of thermodynamics, a complex topic that we address in Chapter 5. For the moment, when we talk about a non-equilibrium system, we mean a system that can do various forms of work. Of course that means we have to define what we mean by work. For simplicity, we will start by defining work as some outcome that takes the input of energy to achieve. In the context of biological systems, work ranges from generating and maintaining molecular gradients and driving other unfavorable, that is energy-requiring reactions, such as the synthesis of a wide range of biomolecules, including nucleic acids, proteins, lipids, and carbohydrates, required for growth, reproduction, the generation of movement, and so on.

We will focus on what is known as free energy, which is energy available to make things happen. When a system is at equilibrium, its free energy is 0, which means that there are no macroscopic (visible) or net changes. The system is essentially static, even though at the molecular level there are still movements due to the presence of heat. Organisms maintain their non-equilibrium state (their free energy is much greater than zero) by importing energy in various forms form the external world. Organisms are different from other non-equilibrium systems in that they contain a genetic (heritable) component. While other types of non-equilibrium systems occur in nature – hurricanes and tornados are non-equilibrium systems – they differ from organisms in that they are transient. They arise de novo and when they dissipate they leave no offspring, no baby hurricanes. In contrast, each organism alive today arose from one or more pre-existing organisms (its parent(s)) and each organism, with some special exceptions, has the ability to produce offspring. As we see, the available evidence indicates that each and every organism, past, present, and future, has (or will have) an uninterrupted history stretching back billions of years. This is a remarkable conclusion, given the obvious fragility of life, and makes organisms unique among physiochemical systems.

Biology has only a few over arching theories. One of these, the Cell Theory of Life, explains the historic continuity of organisms, while the Theory of Evolution by Natural Selection (and other processes), explains both the diversity of organisms and how populations of organisms can change over time. Finally, the Physicochemical Theory of Life explains how it is that organisms can display their remarkable properties without violating the laws that govern all physical and chemical systems.


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UG Courses

UB 102 (JAN)
INTRODUCTORY BIOLOGY II (MICROBIOLOGY, CELL BIOLOGY AND GENETICS)
Introduction to the microbial world and its diversity importance of microbes in exploration of basic principles of biology bacterial growth and its modulation by nutrient availability in the medium structure and function of a bacterial cell structure of cell wall isolation of auxotrophs introduction to viruses – life cycles of temperate and lytic bacteriophages, structure and function of extra-chromosomal elements and their applications in molecular microbiology.
Introduction to cell biology, eukaryotic cells and their intracellular organization introduction to the light microscopes and other methods of studying intracellular organelles further studies on endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondria, nucleus (organization and function), plasma membrane structure and its function, the cytoskeleton, the cell cycle.
Mendelian genetics (segregation and independent assortment) sex determination and sex linkage in diploids cytoplasmic inheritance pedigrees, markers, mapping and genetic disorders gene frequencies and Hardy- Weinberg principle.
Light microscopy, identification of microorganisms, staining techniques (Gram’s, acid fast), bacterial plating, tests for antibiotic resistance, cell media and tissue culture cell counting, immunostanining for actin, microtubules, DNA and identifying interphase and various mitotic phases Drosophilcrosses using red eye and white eye mutants, observation of Barr body in buccal mucosa cells, preparation of mitotic/polytene chromosomes from Drosophila larvae and karyotyping using human metaphase plate photos.
Dipshikha Chakravortty, Sachin Kotak and Arun Kumar
References:

  • Berg, J. M., Tymoczko, J. L. and Styrer, L., Biochemistry, W. H. Freeman & Co., 6th Edition, 2006.
  • Stanier, R. Y., Adelberg, E. A. and Ingraham, J. L., General Microbiology, MacMillan Press, 5th Edition, 2007.
  • Alberts, B., Molecular Biology of the Cell, Garland Science, 5th Edition, 2008.
  • Strickberger, M. W., Genetics, Prentice-Hall, India, 3rd Edition, 2008.
  • Daniel, H., Essential Genetics: A genomics perspective, Jones & Bartlett, 3rd Edition, 2002.
  • Strachan, T. and Read, A. P., Human Molecular Genetics, Garland Science, 3rd Edition, 2004.

UB 201(AUG)
INTRODUCTORY BIOLOGY III (MOLECULAR BIOLOGY, IMMUNOLOGY AND NEUROBIOLOGY)
Molecular biology (central dogma, DNA repair, replication, transcription, genetic code and translation) examples of post-transcriptional and post-translational modifications genetic methods of gene transfer in bacteria.
Introduction to the immune system – the players and mechanisms, innate immunity, adaptive responses, B cell receptor and immunoglobulins, T cell activation and differentiation and Major Histocompatibility Complex encoded molecules.
Overview of the nervous system, ionic basis of resting membrane potential and action potentials, neurodevelopment, neurotransmitters, sensory systems, motor systems, learning and memory, attention and decision making.
UB 201L
M13 infection, plaque assay, preparation of bacterial competent cells, transformation, transduction, conjugation, β -galactosidase assay. Immune organs and isolation of cells from lymph node, spleen and thymus lymphocyte and macrophage activation studies, nitrite detection, ELISA and cell cycle analysis gross anatomy of the human brain staining of mouse brain sections generation of action- potential psychophysical and cognitive neurobiology experiments.
Umesh Varshney, Dipankar Nandi, Kavita Babu and Sridharan Devarajan
References:

  • Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., Ploegh, H. and Matsudai-
  • Kindt, T., Goldsby, R. and Osborne, B. A., Kuby Immunology, W. H. Freeman Publishers, 6th Edi- tion, 2006.
  • Bear, M., Connors, B. and Paradiso, M., Neuroscience: Exploring the Brain, Lippincott Williams & Wilkins, 3rd Edition, 2006.

UB 205(JAN)
INTRODUCTORY PHYSIOLOGY
Mammalian Physiology: Introduction to physiology, internal environment, control of internal environment by feedback systems, renal physiology, body fluids and kidneys, urine formation by the kidneys, principles of membrane transport, transporters, pumps and ion channels, cell signalling and endocrine regulation, hormonal regulation of energy metabolism, hormonal regulation of calcium metabolism, hormonal control of reproduction in males and females, pregnancy and lactation structure of heart, cardiac muscle contraction, cardiac cycle, electric conductivity of heart, regulation of cardiac homeostasis, structure and function of arteries and vein, blood pressure, blood flow, capillary exchange, physiology of lymphatic system.
Plant Physiology: Plant cell structure and cell wall, water uptake, photosynthesis and photorespiration, secondary metabolites, phytochrome and light signalling, hormone signalling in plants, control of flowering, stress physiology.
N. Ravi Sundaresan and C. Jayabhaskaran
References:

  • Hall, J. E., Guyton and Hall Textbook of Medical Physiology, Elsevier, 12th Edition, 2011.
  • Jameson, J. L. and De Groot, L. J., Endocrinology, Elsevier, 6th Edition, 2010.
  • Taiz, L. and Zeiger, E., Plant Physiology, Sinauer Associates, 5th Edition, 2010.

UB 301L (AUG)
EXPERIMENTS IN MICROBIOLOGY AND ECOLOGY
There are two sets of practical experiments for Biology majors:
In the first part, students will get a hands-on experience in understanding the basic concepts of microbiology. The topics include the microbial growth curve, microbial nutritional requirements, genetic engineering techniques, plasmid isolation, creation of genetic knock out in bacteria, bacterial infection in cell culture system, estimation of infection by colony forming unit (CFU) analysis and fluorescence technique.
In the second part, students will explore key concepts in Ecology, Evolution and Behavior using field methods, laboratory manipulations and computer simulations. Students will design many of their own experiments and will utilize different modes of scientific communication, including oral presentations and documentaries. Topics include niche and population dynamics, competition and predation, trophic interactions, evolution and adaptation, natural and sexual selection, and conservation. This module also includes a mandatory field trip where students develop an independent research project.
Dipshikha Chakravortty, Maria Thaker and Kartik Shanker

UB 302 (JAN):
DEVELOPMENTAL BIOLOGY

Introduction, history and concepts of developmental biology the current understanding on the mechanisms of development using model organisms including invertebrates, vertebrates and plants general principles for the making of a complex, multicellular organismfrom a single cell the creation of multi-cellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), cell type determination creation of specific organs, (organogenesis) molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development fundamental differences between animal and plant development embryogenesis in plant – classical and modern views axis specification and pattern formation in angiosperm embryos organization and homeostasis in the shoot and root meristems patterning in vegetative and flower meristems growth and tissue differentiation in plants stem cells and regeneration evolution of developmental mechanisms
Usha Vijayraghavan, Ramray Bhat, and Utpal Nath
References:


2.0: Introduction - Biology

Three lecture hours and three laboratory hours a week. Introduction to fundamental concepts in biology, with an emphasis on evolution, inheritance, anatomy and physiology, metabolism and ecology. Application of these concepts to issues affecting society. This course does not fulfill the requirements for a major in biology.

Three lecture hours and three laboratory hours a week. Introduction to fundamental concepts in biology, with an emphasis on anatomy, physiology, classification and ecological relationships. Application of these concepts to issues affecting society. This course does not fulfill the requirements for a major in biology.

Three lecture and three laboratory hours a week. Recent course work in biology or chemistry is recommended. Survey of the major organ systems in the human body. Chemical principles related to physiology are included.

Three lecture and three laboratory hours a week. Survey of the major organ systems in the human body. Chemical principles as related to physiology are included.

(Same as PSYC 2050.) Provides an introduction to the effects of drugs on behavior. Topics include how drugs affect the brain and, consequently, behavior the underlying brain and environmental factors thought to be responsible for drug addiction, tolerance and sensitivity treatment of major psychological disorders (e.g., depression, mania, anxiety) with drug therapy and the classification of common psychoactive drugs.

Two lecture hours per week. Orientation to the degree in Biology. Topics will include methods of scientific inquiry, critical thinking skills, evaluation of biomedical research, literature review, scientific writing, and experimental design. Class discussion and in-class labs will be included. Recommended for biology majors with less than two years of high school biology. Also appropriate for K-12 science education and health sciences students.

Two lecture hours a week. Introduction to evolutionary theory, plant, animal, microbial diversity, evolutionary history, and ecology.

Three lecture and three laboratory hours a week. Introduction to scientific method, theory and experimentation, cell chemistry, enzymes, metabolism, photosynthesis, genetics, ecology, and evolution. Fulfills Biology Major requirement.

Three lecture and three laboratory hours a week. Animal and plant biology with emphasis on structure, physiology, ecology, and evolution. Fulfills Biology Major requirement.

Three lecture hours a week. Major organ systems with emphasis on homeostatic mechanisms in health and disease.

Three laboratory hours a week. Exercises dealing with major organ systems. Recommended for health sciences students.

Three lecture hours a week. An introduction to infectious disease agents of significance in individual and community health settings. The characteristics, symptoms, diagnosis, control, and treatment of infectious diseases will be considered.

Three laboratory hours a week. Basic laboratory techniques for culture and identification of bacteria.

Two lecture hours a week. Basic principles of biotechnology with emphasis on genetic engineering and its application to problems of medical, agricultural, and social importance.

Two lecture hours a week. An introduction to the neural basis of behavior in animals. The emphasis will be on the evolutionary connectedness of all nervous systems, including that of humans, and on demystifying how the brain works, using both reductionist and systems-level approaches.

Introduction to understanding DNA structure and replication, transcription, and translation, and the regulation of these processes with an emphasis on improving students’ critical thinking and problem solving skills.

A comprehensive overview of the marine environment and the characteristics of marine organisms and their distinctive communities, such as coral reefs, kelp forests, seagrass beds, and the deep ocean.

A consideration of the role played by infectious diseases in shaping civilization and society. The focus will be on HIV/AIDS, but sexually transmitted infections such as syphilis, gonorrhea, genital herpes, and genital warts will be discussed as well. HIV/AIDS will also be compared with other infectious diseases of historical importance including the Black Death, leprosy, smallpox, tuberculosis, influenza, and poliomyelitis.

Three lecture hours a week. Integrative physiology of major organ systems, with emphasis on homeostatic mechanisms in health and disease.

Three laboratory hours a week. Exercises dealing with the physiology of the major organ systems.

Three lecture hours a week. Fundamental principles of biotechnology. Topics include genetic engineering of bacteria, plants and animals molecular and cellular cloning the human genome project forensics and DNA typing cloning of organisms and gene therapy. Bioethical implications are also considered.

Three lecture hours a week. Mechanisms of evolution, from the molecular to the population level. Topics include population genetics, adaptation, natural selection, speciation, systematics, coevolution, history of life, the geological record, and evolution of humans. This course is also recommended for middle and high school biology teachers.

Discussion and readings on selected topics.

Three lecture hours a week. A survey of biochemistry, molecular genetics, and cell biology including cell structure and chemistry, macromolecular structure and synthesis, protein trafficking, cell motility, signaling, and division. A student may take this class for a grade a maximum of two times.

Experiments demonstrating techniques and concepts in molecular cell biology with an emphasis on learning critical thinking through writing. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors. A student may take this class for a grade a maximum of two times.

Three lecture hours a week. Dynamic aspects of plant function, structure, and growth.

Three lecture hours a week. Comparative analysis of the behavior, physiology, anatomy, phylogeny, evolution, and ecology of animals.

Three laboratory hours a week. Comparative structure and function of representative animal types.

Three lecture hours a week. Functional anatomy, metabolism, cultivation, growth, and control of microorganisms with emphasis on the prokaryotes relationships of these organisms to their environment.

Three laboratory hours a week. Techniques of cultivation, quantitation, isolation, and identification of microorganisms with emphasis on bacteria effects of physical and chemical agents.

CHEM 2400 recommended. Three lecture hours a week. Introduction to classical and molecular genetics including Mendelian genetics, gene mapping, and molecular biology.

Three laboratory hours a week. Experiments demonstrating concepts in genetics.

Students will read and review primary literature in the field of biology. Students will discuss the readings with the instructor and/or write papers. Topics may vary. Course may be repeated for credit a maximum of two times.

(Same as MATH 4010.) This course provides an introduction to the use of continuous and discrete differential equations in the biological sciences. Biological topics will include single species and interacting population dynamics, modeling infectious and dynamic diseases, regulation of cell function, molecular interactions and receptor-ligand binding, biological oscillators, and an introduction to biological pattern formation. There will also be discussions of current topics of interest such as Tumor Growth and Angiogenesis, HIV and AIDS, and Control of the Mitotic Clock. Mathematical tools such as phase portraits, bifurcation diagrams, perturbation theory, and parameter estimation techniques that are necessary to analyze and interpret biological models will also be covered.

Three lecture and three laboratory hours a week. An introduction to the principles of paleontology including taphonomy, taxonomy, evolution, and extinction by examination of the fossil record. Study of commonly preserved organisms and their use in paleoecology, paleoenvironmental reconstruction, biostratigraphic correlation, and conservation paleobiology will be stressed as well.

Three lecture and three laboratory hours a week. Structure, function, distribution, and taxonomic relationships of invertebrate animals.

Three lecture and three laboratory hours a week. Diversity, taxonomy, structure, function, distribution, and ecology of living and extinct vertebrates.

BIOL 3820 recommended. Three lecture and two laboratory hours per week. Principles governing distribution and abundance of organisms and their interactions. Experiments, data collection and analysis of ecological processes with an emphasis on critical thinking through writing. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

Three lecture hours a week with a one day weekend lab every other weekend. Georgia is a state with great a diversity of natural communities, in large part because of the many different landscapes present in the state. Through readings, discussions, tests, field outings, projects and in-class exercises, students will become familiar with the principles involved in the structure and function of Georgia’s dwindling, but diverse, ecosystems. There will be an emphasis on plant communities and the physical environment, but animal communities and landscape management strategies will also be covered. Locations, diversity, and plant indicator species (especially trees) will be examined in the classroom and in the field, and experiential learning is emphasized.

Four lecture hours a week. Introduction to developmental biology emphasizing cellular, genetic, and molecular aspects and mechanisms of development.

Four lecture hours per week. Introduction to the development of the nervous system. Covers the field of developmental neurobiology from neural induction to the modification of neuronal connections in the adult nervous system and uses a variety of model organisms to demonstrate the rules by which nervous systems develop.

Comprehensive basis for understanding brain research, major discoveries in neuroscience, and the methods employed for those achievements. Topics include the neural basis of learning and memory, sensory perception, motor control, neurological diseases, drug action, and behavior.

Four lecture hours a week. Historical background as well as current issues and developments in zoos. Topics include conservation, SSPs (Species Survival Plans), behavioral enrichment, studbook management, and planning/economics of major exhibits. Course instruction will be on-site at Zoo Atlanta. Students will work directly with animal curators and keepers.

Four lecture hours per week. Human brain and spinal cord functional neuroanatomy and associated pathologies.

(Same as PSYC 4130.) Three lecture hours a week. Experimental analysis of sensory and perceptual processes at both a physiological and a psychophysical level. The five primary sensory systems will be covered: vision, audition, touch, taste, and smell.

This course discusses the cell cycle, and how misregulation of this well orchestrated process results in cancer. Current research in cell cycle and cancer biology will be utilized to stimulate critical thinking and communication about the complex biological processes that go awry in cancer and form the basis for intervention with chemotherapeutic drugs.

Four lecture hours a week. Basic biochemistry and physiology of the endocrine system, including synthesis and secretion of steroid and protein hormones, mechanisms of hormone action, and endocrinology of reproduction.

(Same as PSYC 4630.) Four lecture hours per week. Interaction of nervous and endocrine systems in the control of animal behavior, including humans, with emphasis on the mechanisms that adapt behavior to the changing physical and social environments.

Functional and physiological aspects of biological timekeeping, with special emphasis on circadian timing. Significant student participation is expected with required essential and timely reading assignments.

The circulatory, respiratory, gastrointestinal, and renal physiological systems will be emphasized.

CHEM 4600 is recommended. Four lecture hours a week. Mechanisms of cell and organelle function at the molecular level.

This course discusses the cell cycle and how misregulation of this well orchestrated process results in cancer. Strong emphasis will be placed on stimulating critical thinking and developing scientific writing skills to effectively comprehend and communicate scientific knowledge in the field of cell cycle and cancer. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

Four lecture hours a week. Principles of immunobiology with emphasis on humoral and cellular immunity, immunochemical methods for detection, quantitation and study of humoral antibodies and immune cells.

Four lecture hours a week. Principles of immunobiology focusing on human innate and adaptive immune responses and mechanisms that coordinate these responses to protect from infection. Over-reactions of the immune system and principles underlying efficacy of vaccines for infectious diseases. Analysis of research articles to explore recent advances in immunology research with an emphasis on critical thinking through writing. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

This course discusses the molecular basis of tumorigenesis and the interactions between the immune system and tumors/cancer cells. Topics covered include: basic tumorigenesis of common solid tumors, basic immunology, tumor antigen expression, types of immune responses to tumors, mechanisms by which tumors escape/suppress the immune response and novel approaches for immunotherapy of advanced cancers. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

Four lecture hours per week. An overview of significant human and animal pathogens, including aspects of bacterial, viral, protozoan, and helminthic infections and pathogenesis. Pathogen characteristics and features, epidemiology, immunity, and treatment.

Four lecture hours per week. Principles of microbial diversity with emphasis on the phylogeny, metabolism, interactions of microorganisms with the environment and molecular mechanisms generating diversity and the impact on modern methods of bioprospecting.

Four lecture hours a week. Microbiology of industrial processes, including quality control, fermentations, biotransformations, strain selection, and maintenance.

(Same as CHEM 4450.) Use of molecular mechanics methods to solve structural problems in organic, bioorganic, and biophysical chemistry. May be repeated if topics are different.

CHEM 2400 recommended. Four lecture hours per week. Comprehensive introduction to water pollution (including relevant methods and techniques) and its relationship to public health.

Four lecture hours a week. Microbial communities and the interrelationships of microorganisms and environment. Particular emphasis on metabolic activities and their measurement and applications to environmental problems (bioremediation).

A survey of the important parasites of humans and domestic animals. Emphasis will be placed on medically important parasitic protozoa, helminthes, and arthropods clinical effects of infection, epidemiology, methods for detection and identification as well as global impact of parasitic diseases in today’s world.

CHEM 4600 is recommended. Four lecture hours a week. Studies of the absorption, distribution, and excretion of toxicants, their detoxification and bioactivation, and their adverse effects.

One lecture and six laboratory hours a week. Techniques and procedures for isolation, characterization, and identification of microorganisms of practical significance model ecosystems and biofilms sampling and enumeration of microorganisms metabolism and analysis of microbial growth.

Four lecture hours a week. Principles of human heredity, with emphasis on the molecular basis of heredity, detection and treatment of genetic diseases, and genetic counseling.

Four lecture hours a week. Advanced topics and techniques in prokaryotic and eukaryotic genetic systems, including gene mapping, molecular techniques, regulation of gene expression, genomics, and population genetics.

Four lecture hours a week. Etiology, pathology, mechanisms of metastasis and treatment of cancer. Students will also analyze current primary literature in the field.

Four lecture hours per week. Introduction to viruses, including structure and replication of viruses virus isolation and classification pathogenesis and epidemiology of virus disease.

Following an introduction to basic neuroanatomy and neuroimmunology, individual lectures will focus on the diagnosis, treatment, and pathogenesis of several neurologic diseases of virus origin. These include encephalitis, meningitis, chronic inflammatory and demyelinating diseases, HIV/AIDS-associated dementia, peripheral neuropathies, retinitis, and transmissible spongiform encephalopathies caused by prions. The concept of virus latency within the nervous system will be emphasized, as will the possible contributions of viruses or prions toward the onset of Alzheimer?s disease.

Four lecture hours a week. This course integrates material from pathogenic microbiology, molecular biology and immunology into an overview of bacterium-host interactions including bacterial attributes, virulence factors, and several paradigms of bacterial-host interactions focusing on molecular and genetic approaches.

CHEM 4600 recommended. Four lecture hours a week. Molecular biology of bacteria and their viruses, with an emphasis on the use of microbes as model systems for studying molecular processes. Topics include microbial physiology, genetic exchange, gene expression, recombinant DNA technology, and the molecular basis for microbial pathogenesis.

Examination of the histories of different scientific disciplines, their methodologies, practices, forms of knowledge and interrelations, integrating transformations in the sciences with broader historical changes. Topics include the histories of scientific revolutions, the relationship between science and technology, the social and political uses of science, and criticisms of science.

(Same as CHEM 4630.) Introduction to enzyme catalysis, with emphasis on the general concepts of enzyme kinetics and the common tools for studying enzymes.

(Same as CHEM 4640 and CSC 4640.) Four lecture hours per week. A “hands-on” approach to bioinformatics using PCs, the internet, and computer graphics to analyze, correlate, and extract information from biological databases, emphasizing sequence and structure databases for proteins and nucleic acids, and introducing the computer skills necessary for bioinformatics. Topics include: sequences and three-dimensional structures of proteins and nucleic acids, the major databases, algorithms for sequence comparison, data mining, and prediction of structure and function.

Spatial variations, processes, and environmental constraints influencing the distribution of life.

[Same as CHEM 4670]. A comprehensive and integrated review of principles and modern techniques found in day-to-day biochemical research laboratories. Topics include, but are not limited to: general principles of biochemical investigations, molecular biology and basic techniques, molecular cloning and gene analysis, protein structure, purification and characterization, biomolecular interactions, basic enzyme analysis, spectroscopic techniques, mass spectrometric techniques, centrifugation, electrophoretic, chromatographic, radioisotope and electrochemical techniques.

Four lecture hours per week. An introduction to the theory of microscopy and various types of microscopes and their applications to biological research. Topics include: microscopes, basic specimen preparation, and staining techniques.

Four lecture hours per week. Topics include preparation and basic staining of tissues, special stains, identification of tissue features and classification. The course will correlate tissue form and function by incorporating concepts of cell, tissue, and organ physiology. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

Clinical case studies will be used to teach the principles and processes behind adult and childhood diseases. Students will learn basic diagnostic skills in hematology and blood chemistry, histopathology, ECG, spirometry, radiology, and urology.

Four lecture hours per week. The discussion of pathogenic agents and their associated occupational and public health risks. Topics include emerging biosafety issues such as bioterrorism, human gene therapy, and federal and state regulations guiding use of pathogenic organisms.

CHEM 4600 recommended. One lecture and six laboratory hours a week. Isolation and characterization of nucleic acids and proteins. Topics include molecular cloning, isolation, characterization and sequence analysis of chromosomal and plasmid DNA, PCR mediated gene amplification, and protein purification.

(Same as MATH 4544.) Three lecture hours a week. Principles and methods of statistics as applied to biology and medicine.

(Same as CHEM 4780.) This is an introductory self-contained course on the application of molecular dynamics and related methodologies by which student with a relatively limited background in chemistry, biology, and computer literacy can learn the fundamentals of research in these areas. In this course, students will learn to do computer calculations that quantify biomolecular interaction concepts discussed in lectures in biology, biochemistry, and biophysics.

Four lecture hours a week. Survey of cellular components and processes in different cell types as they relate to the function of the cell. Includes signal transduction, photoreceptors, neurons, muscle, blood cells, cells of the immune system, and cell biology of infection.

Readings or research preparatory to honors thesis or project.

Writing or production of honors thesis or project.

One lecture hour and one discussion hour per week. Student learning of experimental strategies and procedures through laboratory group meetings and individual discussion with faculty laboratory director.

Students will work in small groups to develop specific biological hypotheses, design and carry out experiments to test these hypotheses, and analyze the results they obtain. May be repeated for credit if topic is different.

One lecture and six laboratory hours a week. Students will work in small groups to develop specific biological hypotheses, design and carry out experiments to test these hypotheses, and analyze the results they obtain. May be repeated for credit if topic is different.

Independent laboratory investigation of common interest to student and instructor. May be repeated once.

Admission by permission of instructor. Nine lab hours per week. Students will directly participate in ongoing primary research at the zoo. This will be under the direction of animal curators and keepers at the zoo and will provide specific research opportunities with the living collections at Zoo Atlanta.

Admission by permission of instructor. Nine lab hours per week. Supervised hands-on experience with the practical aspects of managing a wide range of exotic animals in a captive setting. Students will work directly with animal curators and keepers.

Students will participate in the education programs at the Georgia Aquarium one morning a week for about three hours, depending on Aquarium requirements, and under the supervision of Aquarium staff. The primary goal is to train interns to be able to deliver education programs at the Georgia Aquarium.

This is the second part of the Georgia Aquarium internship program. Students will participate in the education programs at the Georgia Aquarium one morning a week for about three hours, depending on Aquarium requirements, and under the supervision of Aquarium staff. The interns will deliver education programs to visiting student groups and train interns in first part of the Intern program (BIOL 4913 or BIOL 6913).

Students engage in off-campus internship training arranged through collaboration with biology faculty members. May be taken for credit a maximum of two times.

Students receive hands-on experience in activities that require knowledge and skills related to the field of biology. Specific topics available each semester will vary. May be taken for credit a maximum of two times.

Three or four lecture hours a week. Detailed examination of a selected area in biological sciences. May be repeated for credit if topic is different.

Speakers from different biology-related fields will discuss their jobs from the perspective of helping Biology majors with their career planning. Topics will include graduate training at GSU, health and teaching-related careers, other biology-related careers, and job search strategies. (May be repeated for credit a maximum of two times.

Current research topics in biology. May be repeated for credit a maximum of two times.

Critical analysis of research in biology using primary literature and seminars in biology. Serves as one of the two Critical Thinking Through Writing (CTW) courses required of all biology majors.

Directed Readings designed for Bachelor of Interdisciplinary Studies students. This course may satisfy the junior and/or senior-level Critical Thinking Through Writing requirements.


BIOL * 1020 – Introduction to Biology F (3-2) [0.50]

This course will introduce important concepts concerning the organization of life, from cells to ecosystems. The dynamic and interactive nature of all living systems will be emphasized. This course will be valuable for students without Grade 12 or 4U Biology who are interested in environmental issues, medicine, advances in biotechnology and related topics. Department of Molecular and Cellular Biology.

Is the textbook recommended by the student? Yes
Did the student enjoy the professor? Yes
Professor : Anneth Nassuth

Is the textbook recommended by the student? No
Did the student enjoy the professor? Yes
Professor : Not specified


Biology (BIOL)

Provides a broad introduction of biology, including our molecular-organismic-ecological heritage and the role of humans within the biosphere. Not intended for biology or biochemistry majors. When combined with BIOL�L, this course is equivalent to the previously offered BIOL 100. Students may not receive credit for both. Satisfies GE Category B2.

BIOL�L. Introduction to Biology Lab. Unit: 1

Semester Corequisite: BIOL� or instructor consent
Introductory level hands-on observation and experimentation on biological specimens, materials, and models. Not intended for biology and biochemistry majors. Materials fee required. When combined with BIOL�, this course is equivalent to the previously offered BIOL 100. Students may not receive credit for both. Satisfies GE Category B3.

BIOL�. Biology for Teachers. Units: 4

Survey of major areas of biology including cell biology, genetics, evolution, plant and animal anatomy and physiology, ecology, and behavior. Course content and practices are aligned with the Next Generation Science Standards (NGSS). Specially designed for students interested in teaching grades K-8. Three hours lecture and three hours lab. Materials fee required. Satisfies GE Category B2 B3.

BIOL�. Principles of Biology I. Units: 5

Semester Prerequisite: CHEM� with a grade of C (2) or higher. Quarter Prerequisite: CHEM 215 with a grade of C (2) or better, or consent of department
Provides a foundational understanding of the process of life and the universality of life processes at the molecular and cellular level. Introduces diversity, structure and function of Bacteria, Archaea, protists, and plants. Four hours lecture and three hours laboratory. Materials fee required. When combined with BIOL�, this course is equivalent to the previously offered BIOL 200, 201, and 202. Satisfies GE category B2 and B3 this course is not recommended as a GE course for non-STEM majors.

BIOL�. Principles of Biology II. Units: 5

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 200 and BIOL 201 with a grade of C or better
Provides a foundational understanding of the principles of genetics, evolution and ecology of organisms, populations, and communities. Introduces diversity, structure and function of animals and fungi. Four hours lecture and three hours laboratory. Materials fee required. When combined with BIOL�, this course is equivalent to the previously offered BIOL 200, 201, and 202.

BIOL�. Genetics and Society. Units: 3

Technological advances in genetics and their impact on society. Biological and ethical perspectives of the application of genetic research. Previously offered as BIOL 216. Satisfies GE category B2.

BIOL�. Biology of Diseases. Units: 3

The biology, pathogenicity, epidemiology, diagnosis, and treatment of prominent and emerging infectious diseases. Impact of current biotechnology in relation to vaccine development, experimental treatments, and improved diagnostics and screening. Previously offered as BIOL 217. Satisfies GE Category B2.

BIOL�. Sustainable Agriculture. Units: 3

Evidence-based comparison of traditional, modern, and sustainable agricultural practices, including plant health, pests and diseases, crop types and yields, food distribution, and food insecurity. Examination of food-related choices in a scientific, ethical, and social context. Satisfies GE category B2.

BIOL�. Microbiology for Allied Health Majors. Units: 4

Semester Prerequisite: BIOL� strongly recommended. Quarter Prerequisite: one lower-division biology course
Structure, physiology, and classification of bacteria, microbial eukaryotes, and viruses. Rudiments of infection and immunity, and overview of pathogenic microbes. Laboratory training in microscopy, cultivation, and identification of microorganisms. Three hours lecture and three hours laboratory. Materials fee required. Students enrolling in this course for a third time may do so only with the consent of instructor. Formerly BIOL 220 students may not receive credit for both.

BIOL�. Human Anatomy and Physiology I for Allied Health Majors. Units: 4

Semester Prerequisite: Be declared in one of the following degree options: BS in Nursing, BS in Nutritional Science and Dietetics, or BS in Kinesiology, or Minor in Kinesiology or consent of instructor. Quarter Prerequisite: BIOL 100 and be declared in one of the following degree options: BS in Nursing, or BS in Health Science, or BS in Nutrition and Food Science, or BS in Kinesiology, or Minor in Kinesiology or consent of instructor
Covers living chemistry, cells, tissues, integumentary, skeletal, muscular, and nervous systems. Three hours lecture and three hours laboratory. Materials fee required. Previously offered as BIOL 223. Students may not receive credit for both courses. Students enrolling in this course for a third time may do so only with the consent of instructor.

BIOL�. Human Anatomy and Physiology II for Allied Health Majors. Units: 4

Semester Prerequisite: BIOL 223 or BIOL�, and be declared in one of the following degree options, BS in Nursing, BS in Nutritional Science and Dietetics, BS in Kinesiology, Minor in Kinesiology, or consent of instructor. Quarter Prerequisite: BIOL 223, BS in Nursing, BS in Health Science, BS in Nutrition and Food Science, BS in Kinesiology, Minor in Kinesiology, or consent of instructor
Covers digestive, nervous, respiratory, cardiovascular, urinary, endocrine, and reproductive systems. Three hours lectures and three hours laboratory. Materials fee required. Previously offered as BIOL 224. Students may not receive credit for both courses. Satisfies GE category B2 and B3.

BIOL�. Human Ecology. Units: 3

Semester Prerequisite: Junior or senior standing. Quarter Prerequisite: junior or senior standing
Environmental and ecological impacts of the growing human population, taking into consideration the effects of science, technology, and our societal attitudes. Satisfies GE Category B5. Formerly offered as NSCI 310. Students may not receive credit for both courses. Satisfies Environmental Sustainability Pathway.

BIOL�. History of Life on Earth. Units: 3

Semester Prerequisite: Junior or senior standing. Quarter Prerequisite: Junior or senior standing
History of life on earth and the processes that govern its genesis, evolution, extinction, ecology, and preservation. Offered as BIOL� and GEOL�. Satisfies GE Category B5. Formerly offered as NSCI 360. Students may only receive credit for one of these courses.

BIOL�. Special Studies in Biology. Unit: 1

Investigation, research, or study of a selected topic, the topic title to be specified in advance. May repeat for credit as topics change for a total of 2 units. Instructor consent required. This course does not satisfy any requirements for the undergraduate major in Biology. Formerly BIOL 295A.

BIOL�. Special Studies in Biology. Units: 2

Investigation, research, or study of a selected topic, the topic title to be specified in advance. May repeat for credit as topics change, for a total of 4 units. Instructor consent required. This course does not satisfy any requirements for the undergraduate major in Biology. Formerly BIOL 295B.

BIOL�. Cell Biology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better, and one of CHEM� with a C (2.0) or better, CHEM� with a C (2.0), or better or CHEM� with a C (2.0) or better. Quarter Prerequisite: BIOL 200, BIOL 201 and BIOL 202 with grades of C (2.0) or better CHEM 215 and CHEM 216
Structure and function of eukaryotic cells and organelles, and their physiological processes at the molecular level, including metabolism, signal transduction, gene regulation, and cell cycle control. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 300 students may not earn credit for both courses. Satisfies GE designation WI.

BIOL�. Molecular Biology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better and one of the following: CHEM�, CHEM� or CHEM� with a C (2.0) or better. Quarter Prerequisite: BIOL 300 with a grade of C or better and CHEM 223 or CHEM 323
Informational macromolecules, and how they direct molecular processes in both eukaryotic and bacterial cells. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 400 students may not receive credit for both courses.

BIOL�. Biology of Stem Cells. Units: 2

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM�
Examination of fundamental concepts and themes in stem cell-based regenerative medicine: pluripotency and reprogramming, cell types, organ systems, stem cells and therapeutics an ethics. Experimental approaches and emerging areas in stem cell research addressed in seminars from visiting scholars/scientists and with readings from the primary literature. Formerly offered as BIOL 413 students may not receive credit for both courses.

BIOL�. Microbiology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM�
The structure and function, metabolism, and genetics of microorganisms with an introduction to bacterial, viral, fungal, and protozoan pathogens. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 320 students may not receive credit for both courses.

BIOL�. Genetics. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM�
Principles of heredity and genetic analysis, including underlying molecular mechanisms. Includes current concepts of the organization, function, and regulation of genes. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 423 students may not receive credit for both courses.

BIOL�. Comparative Embryology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM� and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
Descriptive survey of developmental patterns of tissue and organ formation to include studies of insects, echinoderms, and amphibian, avian, reptilian, marsupial plus placental mammalian vertebrate embryology. Two hours lecture and three hours laboratory. Materials fee required. BIOL� strongly recommended. Formerly offered as BIOL 340 students may not receive credit for both courses.

BIOL�. Biology of Invertebrates. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM3400
Survey of the major groups of invertebrates, with emphasis on taxonomy, structure, function, reproduction, and evolution. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 331 students may not receive credit for both courses.

BIOL�. Comparative Biology of the Vertebrates. Units: 5

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM�
Structural, developmental and ecological changes in the evolution of the chordates and their ancestors, with an emphasis on comparative vertebrate anatomy. Three hours lecture and six hours laboratory. Materials fee required. Formerly offered as BIOL 342 students may not receive credit for both courses.

BIOL�. Mammalogy. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM� , CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with grade C (2.0) or better
Semester Corequisite: CHEM�, CHEM�, or CHEM�, and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
Systematics, evolution, morphology, physiology, ecology and behavior of mammals. Two hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 343 students may not receive credit for both courses.

BIOL�. Herpetology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with grad of C (2.0) or better
Semester Corequisite: CHEM�, CHEM�, or CHEM3400, and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
Diversity, evolution, morphology, physiology, behavior and ecology of amphibians and reptiles. Two hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 344 students may not receive credit for both courses.

BIOL�. Ornithology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with grade C (2.0) or better
Semester Corequisite: CHEM�, CHEM� or CHEM�, and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
Introduction to the biology of birds. Course includes study of the functional morphology, ecology and behavior, and the evolutionary relationships among extant taxa. Laboratory exercises will focus on identification and museum studies, coupled with field observations of avian species diversity and associated habitats with an emphasis on resident and migratory species of southern California. Two hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 345 students may not receive credit for both courses.

BIOL�. Entomology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: Completion of or concurrent enrollment in CHEM�, CHEM� or CHEM3400, and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
A survey of the anatomy, classification, physiology, ecology, and evolution of the insects. Two hours lecture and three hours laboratory/field studies. Materials fee required. Formerly offered as BIOL 335 students may not receive credit for both courses.

BIOL�. Vertebrate Paleontology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: one lower-division biology course
Semester Corequisite: CHEM�, CHEM�, or CHEM�, and one of the following courses: BIOL�, BIOL�, BIOL�, BIOL�, or BIOL� or consent of instructor
Survey of the origins, evolution, and diversity of major lineages of fossil vertebrates, with emphasis on the use of fossil examples to elucidate patterns of form and function, origins of major groups, development of key structural innovations, and patterns of change and extinction over time. Two hours lecture and three hours laboratory. Formerly offered as BIOL 305 students may not receive credit for both courses.

BIOL�. Local Flora. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better, or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better or consent of instructor
Identification of the flora and ecological communities of southern California with a consideration of taxonomic principles. One hour lecture, one hour discussion, and three hours laboratory including field collections. Materials fee required. Formerly offered as BIOL 319 students may not receive credit for both courses.

BIOL�. Plant Biology and Diversity. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM�, or CHEM�
Comparative plant morphology, anatomy, and development, with emphasis on ecological consequences of variation in anatomical traits. Three hours lecture and three hours laboratory. Materials fee required. 2000-level physics course (or equivalent) recommended. Formerly offered as BIOL 354 students may not receive credit for both courses.

BIOL�. Comparative Animal Physiology I. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 300 with a grade of C or better
A comparative analysis of the physiologic mechanisms and performance in animals, with emphasis on evolutionary trends in neuronal and musculoskeletal functions. Three hours lecture and three hours laboratory. Materials fee required. 2000-level physics course (or equivalent) recommended. Together BIOL� and BIOL� are equivalent to BIOL 424 students may not earn credit for both BIOL 424 and BIOL�. Satisfies GE designation WI.

BIOL�. Comparative Animal Physiology II. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better. Prerequisite: BIOL 300 with a grade of C or better
A comparative analysis of the physiologic mechanisms and performance in animals, with emphasis on evolutionary trends in cardiorespiratory, osmotic and thermoregulatory functions. Three hours lecture and three hours laboratory. Materials fee required. 2000-level physics course (or equivalent) recommended. Together BIOL� and BIOL� are equivalent to BIOL 424, students may not earn credit for both BIOL 424 and BIOL�. Satisfies GE designation WI.

BIOL�. Evolution. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: CHEM�, CHEM�, or CHEM�
A broad survey of evolutionary biology. Topics include natural selection and adaptation, population genetics, speciation, and the historical patterns in the diversity of life that arise from the evolutionary process. Three hours lecture and one hour of discussion. Formerly offered as BIOL 321 students may not receive credit for both courses.

BIOL�. Ecology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better, MATH� with a grade of C (2.0) or better, and Pre- or Co-requisite one of the following: CHEM� ,CHEM�, or CHEM� or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better and MATH 120, MATH 192 or MATH 211 or consent of instructor
Semester Corequisite: Completion of or concurrent enrollment in CHEM�, CHEM� or CHEM�
Analysis of the interrelationships of organisms and their physical and biotic environment with a consideration of the role of the environment in natural selection. Three hours lecture and three hours laboratory/field studies. Materials fee required. Formerly offered as BIOL 450 students may not receive credit for both courses.

BIOL�. Microbial Ecology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2) or better. Quarter Prerequisite: BIOL 202 with a grade of C (2) or better completion of CHEM 221 or CHEM 321
Semester Corequisite: CHEM�, CHEM�, or CHEM�
An overview of interactions between microorganisms and their environments, and classical and modern methods used to study microbial communities and their ecology. Particular focus will be placed on important roles that microbes play in carbon and nitrogen cycling, and human-microbe interactions. Three hours lecture and three hours lab. Materials fee required.

BIOL�. Invasion Biology. Units: 3

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM�. Prerequisite: BIOL 300 with a grade of C (2.0) or better
Semester Corequisite: Completion of or concurrent enrollment in CHEM�, CHEM�, or CHEM�
The study of how exotic species are introduced into a new environment and the impact that they have on that new environment. More specifically, it involves the exploration of the ecology and evolution of invasive species. Through a combination of lectures, discussion and hands-on, research-based approaches, students will: 1) understand how invasive species are being introduced 2) evaluate and predict under which ecological and evolutionary conditions a species might become invasive 3) diagnose the impact of invasive species on the surrounding biotic and abiotic environment 4) collect and analyze data and create a visual representation of species spread and 5) design a plan for prevention, control and/or eradication of targeted invasive species. Two hours lecture and three hours laboratory/ field studies. Materials fee required.

BIOL�. Conservation Biology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better completion of or concurrent enrollment in CHEM� or CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of "C" (2.0) or better, and BIOL 321 or 450
Semester Corequisite: CHEM� or CHEM� or CHEM�
An examination of factors influencing biological diversity including habitat loss and fragmentation, global climate change, and species extinction. The science of conservation biology is interdisciplinary and has a focus that ranges from genes and populations through ecosystems and global levels of biodiversity. The maintenance and restoration of biodiversity necessarily overlaps with other disciplines including wildlife and resource management, law, economics, and ethics. Formerly offered as BIOL 514 or BIOL 5840 students may not earn credit for both courses. Three hours lecture, one hour discussion.

BIOL�. Marine Biology. Units: 4

Semester Prerequisite: BIOL� with a grade of C (2.0) or better Pre- or Co-requisite one of the following: CHEM�, CHEM�, or CHEM� or consent of instructor. Prerequisite: BIOL 300 with a grade of C (2.0) or better or consent of instructor
Semester Corequisite: Completion of or concurrent enrollment in CHEM�, CHEM�, or CHEM�
This course provides students with comprehensive knowledge in marine biology. This course covers taxonomy, ecology, evolution and conservation of marine fauna and flora. During this course, students will obtain training in taxonomical identification, field ecology and management of marine resources. Three hours lecture and three hours laboratory/ field studies. Materials fee required.

BIOL�. Directed Study. Unit: 1

Reading and library research in an area of biology conducted under the direction of a faculty member in the Department of Biology. Consent of instructor and departmental approval of a written proposal submitted on a standard application form filed in advance of the semester in which the course is to be taken. No more than two units of BIOL� or BIOL� may be applied toward a biology elective for graduation. Graded credit/no credit. Formerly BIOL 396A.

BIOL�. Directed Study. Units: 2

Reading and library research in an area of biology conducted under the direction of a faculty member in the Department of Biology. Consent of instructor and departmental approval of a written proposal submitted on a standard application form filed in advance of the semester in which the course is to be taken. No more than two units of BIOL� or BIOL� may be applied toward a biology elective for graduation. Graded credit/no credit. Formerly BIOL 396B.

BIOL�. Medical Microbiology. Units: 5

Semester Prerequisite: BIOL�. Quarter Prerequisite: BIOL 300 with a grade of C or better, and BIOL 320 or consent of instructor
An overview of topics and lab techniques in medial microbiology, emphasizing the biology of medically relevant bacteria, viruses, fungi and protozoa. The course will focus on the host-pathogen interaction, including the actions of the pathogenic microorganism and the immune response, as well as the overall host microbiome as an ecosystem perturbed by infection. Three hours of lecture, one hour of discussion, and three hours laboratory. Materials fee required. Formerly offered as BIOL 420 students may not receive credit for both courses.

BIOL�. Functional Microbial Genomics. Units: 5

Semester Prerequisite: BIOL� with a grade of C or better, or BIOL� with a grade of C or better
Training in microbiology and molecular biology laboratory skills, biotechnology research, and the broader concepts of genomics and genome database/bioinformatics/cyber infrastructure applications. Students will participate in authentic/original research- attempting to duplicate that in faculty labs but in a classroom setting. Mastering the process of science will be stressed. This will include an emphasis on experimental design, research material preparation, critical thinking, data analysis, real-life research problem solving, and iterative learning. BIOL� recommended. Three hours lecture and six hours laboratory. Materials fee required. Formerly offered as BIOL 427 students may not receive credit for both courses.

BIOL�. Developmental Biology. Units: 4

Semester Prerequisite: BIOL� or BIOL� or BIOL� or BIOL�. Quarter Prerequisite: BIOL 300 with a grade of C or better, and CHEM 223 or 323
Comparative analysis of patterns and processes of development of organisms, with emphasis on the role of genetic and biochemical mechanisms. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 440 students may not receive credit for both courses.

BIOL�. Plant Physiology. Units: 5

Semester Prerequisite: BIOL� with a grade of C (2.0) or better, and one of the following with a grade of C (2.0) or better: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better, and CHEM 223, or CHEM 323
Comparative analysis of physiological activity in plants at the various levels of cells, tissues, organs and organisms. Three hours lecture and six hours laboratory. Materials fee required. Formerly offered as BIOL 431 students may not receive credit for both courses.

BIOL�. Medical and Economic Botany. Units: 3

Semester Prerequisite: One of the following: BIOL�, BIOL�, or BIOL� and one of the following: CHEM�, CHEM�, or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better
Survey of medically and economically important plant species and families. Includes plants harmful and beneficial to humans, with emphasis on vascular species. Formerly offered as BIOL 380 students may not earn credit for both courses.

BIOL�. Human Anatomy and Physiology I. Units: 5

Semester Prerequisite: One of the following with a grade of C or better: BIOL�, BIOL�, or BIOL�. Quarter Prerequisite: BIOL 300 with a grade of C or better
Comprehensive study of the human form and function in the broader context of vertebrate animals, and select case studies of human pathologies. Course covers early development and the anatomy and physiology of the integumentary, skeletal, muscular, and nervous systems, and the special senses. Four hours lecture and three hours laboratory. Materials fee required. When combined with BIOL�, this course is equivalent to the previously offered BIOL 323 and BIOL 324. Students may not receive credit for both this course and either BIOL 323 or BIOL 324.

BIOL�. Human Anatomy and Physiology II. Units: 5

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 300 with a grade of C or better
Comprehensive study of the human form and function in the broader context of vertebrate animals, and select case studies of human pathologies. Course covers early development and the anatomy and physiology of the digestive, respiratory, cardiovascular, excretory, reproductive, and endocrine systems. Four hours lecture and three hours laboratory. Materials fee required. When combined with BIOL�, this course is equivalent to the previously offered BIOL 323 and 324. Students may not receive credit for both this course and either BIOL 323 or BIOL 324.

BIOL�. Special Topics. Unit: 1

Semester Prerequisite: BIOL� with a grade of C (2) or better. Quarter Prerequisite: BIOL 300 with a grade of C (2) or better
Semester Corequisite: CHEM� or CHEM� or CHEM�
Group study of a selected topic, the title to be specified in advance. May be repeated up to four times for credit as topics change. Can be taken a maximum of four times for a total of four units. Formerly 490A.

BIOL�. Special Topics. Units: 2

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 300 with a grade of C or better
Semester Corequisite: CHEM� or CHEM� or CHEM�
Group study of a selected topic, the title to be specified in advance. May be repeated up to four times for credit as topics change. Can be taken a maximum of four times for a total of eight units. Formerly BIOL 490B.

BIOL�. Special Topics. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better completion of or concurrent enrollment in CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C or better
Group study of a selected topic, the title to be specified in advance. May be repeated up to four times for credit as topics change. Formerly BIOL 490C.

BIOL�. Special Laboratory Topics. Unit: 1

Semester Prerequisite: BIOL� with a grade of C (2.0) or better completion of or concurrent enrollment in CHEM� or CHEM� or CHEM�. Quarter Prerequisite: BIOL 300 with a grade of C (2.0) or better and 15 units of upper-division biology course work
Semester Corequisite: CHEM� or CHEM� or CHEM�
Group laboratory study of a selected topic, the title to be specified in advance. May be repeated up to four times for credit as topics change. Materials fee required. Can be taken a maximum of four times for a total of four units. Formerly BIOL 491A.

BIOL�. Special Laboratory Topics. Units: 2

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 300 with a grade of C or better and 15 units of upper-division biology course work
Semester Corequisite: CHEM� or CHEM� or CHEM�
Group laboratory study of a selected topic, the title to be specified in advance. May be repeated up to four times for credit as topics change. Materials fee required. Can be taken a maximum of four times for a total of eight units. Formerly BIOL 491B.

BIOL�. Readings in Biology. Unit: 1

Semester Prerequisite: BIOL� with a grade of C or better. Quarter Prerequisite: BIOL 200, 201, 202 and 300
Group study of topics of current biological interest, involving analysis of the primary literature and presentations by students. May be taken up to four times but students may only earn credit toward the major once. Instructor consent required. Graded credit/no credit. Formerly BIOL 391.

BIOL�. Biology Seminar. Unit: 1

Semester Prerequisite: BIOL� with a grade of C or better, or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better
Topics of current biological interest, presented by students, faculty, and guest speakers. Discussion of primary research associated with presentation topics, including how the research relates to broader topics in Biology. May be taken once for credit toward the B.S. in Biology may be taken twice for credit toward the elective requirement of the Master of Science in Biology. Formerly offered as BIOL 390 or BIOL 591 students may not earn credit for either of these previous courses and this course. Graded credit/no credit.

BIOL�. Ethics in Biological Research. Unit: 1

Quarter Prerequisite: Graduate or senior standing in Biology
Ethical issues related to biological research. Covers use of animals and humans as research subjects, conservation and cultural issues, intellectual property, authorship, and research misconduct. It includes basic Research Ethics, also known as Responsible Conduct of Research, and meets the Responsible Conduct of Research training requirements for NIH and NSF grants.

BIOL�. Biostatistics and Experimental Design. Units: 4

Semester Prerequisite: MATH�, BIOL� with a grade of C or better, and consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of "C" or better, MATH 192 or 211, and consent of instructor
Provides an understanding of the design of biological experiments and analysis of data. Topics will include experimental design and sampling protocols, techniques for displaying and describing data, probability, and hypothesis testing. The course surveys statistical approaches to the analysis of proportions and frequencies, comparisons of means among numerical variables, regression, correlation, analysis of variance, as well as non-parametric approaches. Three hours lecture and three hours laboratory. Formerly offered as BIOL 505, students may not receive credit for both.

BIOL�. Experimental Cellular Analysis. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better or graduate standing in Biology or consent of instructor
Laboratory techniques for examining and manipulating cells, including genetic, biochemical, imaging, and viability assays. This course will integrate core principles of cell biology and biochemistry with an emphasis on experimental design, execution, interpretation, and presentation. Two hours lecture and six hours laboratory. Materials fee required.

BIOL�. Animal Tissue Culture. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better, or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better
Theory and concepts of animal tissue culture including fundamentals of tissue culture techniques, sub-culturing and maintenance of cell lines. Strong emphasis on stem cell technology. One hour lecture and four hours laboratory. Materials fee required. Formerly offered as BIOL 513 students may not earn credit for both courses.

BIOL�. Neurobiology. Units: 3

Semester Prerequisite: One of the following courses with a grade of C or better: BIOL�, BIOL�, BIOL�, or BIOL� or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better
Study of the structure, physiology, and pharmacology of the nervous system. Mechanisms of cellular communication, perception of sensory information, endocrine function, motor control, development, and learning and memory in the nervous system will be examined. Formerly offered as BIOL 580 students may not receive credit for both courses.

BIOL�. Introduction to Regulatory Affairs in the Life Sciences. Units: 2

Semester Prerequisite: BIOL�. Quarter Prerequisite: BIOL 300 with a grade of "C" or better and consent of the instructor
Introduces the pharmaceutical, biotechnology, and biologics industries and the laws and regulations related to these products. Discussion of company organization, product development, and commercialization-associated activities. Consent of Instructor required. Formerly offered as BIOL 516 students may not earn credit for both courses.

BIOL�. Human Embryonic Stem Cell Culture Methods. Units: 2

Semester Prerequisite: BIOL�. Quarter Prerequisite: BIOL 300 with a grade of "C" or better and consent of instructor
Advanced laboratory training in plating and passaging of human embryonic stem cells and human induced pluripotent stem cells. Mastery of a variety of cell culture techniques including isolation and culturing techniques including isolation and culturing of mouse embryonic fibroblasts, PCR and flow cytometry and immunohistochemistry on human embryonic stem cells and embryoid bodies. One hour of lecture and three hours of lab. Consent of Instructor required. Materials fee required. Formerly offered as BIOL 517 students may not earn credit for both courses.

BIOL�. Genomics. Units: 4

Semester Prerequisite: Graduate standing in Biology, or one of the following courses with a grade of C or better: BIOL�, BIOL�, or BIOL�. Prerequisite: BIOL 300 with a grade of C or better
Overview of modern genomics methods. Topics covered will include genome sequencing, assembly, annotation, and analysis transcriptomics and proteomics and metagenomics and single-cell genomics. Three hours lecture and three hours lab. Materials fee required.

BIOL�. Advanced Molecular Genetics. Units: 3

Semester Prerequisite: One of the following courses with a grade of C or better: BIOL�, BIOL�, BIOL�, or BIOL� or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better, BIOL 400, 423, and CHEM 223 or 323
Examination of modern molecular techniques applied to genetics research in common model organisms, including transgenesis, gene targeting/replacement, temporal-spatial control of gene expression, and in situ and genome-wide expression analysis. Formerly offered as BIOL 528 students may not receive credit for both courses.

BIOL�. Microscopy. Units: 3

Semester Prerequisite: senior standing or consent of instructor. Quarter Prerequisite: senior standing and consent of instructor
Theory and techniques of modern microscopy. Lectures on theory of optics and imaging for several types of microscopes (Light microscope, fluorescence microscope, confocal microscope, scanning probe microscope, and electron microscope). Laboratory includes hands-on training in the technical aspects of specimen preparation and microscope use. Two hours lecture and three hours laboratory. Formerly offered as BIOL/GEOL 530, students may not receive credit for both courses. Offered as GEOL� and BIOL�. Students may not receive credit for both. Materials fee required.

BIOL�. Advanced Molecular Techniques. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better, or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better and BIOL 400
Techniques utilized in molecular research and biotechnology. Methods for isolating and analyzing molecules of life, including DNA, RNA, and protein will be carried out in the context of an advanced molecular research project. A final research report will be required from the student. Two hours lecture and six hours laboratory. Materials fee required. This course incorporates portions of BIOL 502 and BIOL 592 students may not receive credit both BIOL 592 and BIOL�.

BIOL�. Virology. Units: 4

Semester Prerequisite: One of the following courses with a grade of C (2.0) or better: BIOL�, BIOL�, BIOL�, or BIOL�. Quarter Prerequisite: BIOL 400 with a grade of "C" (2.0) or better
Examination of the structure, genetics and modes of replication of viruses, viroids, and other related sub-cellular entities their implications in medicine and their use in scientific research. Virological methods such as infection and plaque assays will be carried out in the context of an advanced virology research project. Three hours lecture and three hours laboratory. Formerly offered as BIOL 572 students may not receive credit for both courses. Materials fee required.

BIOL�. Biotechnology Practicum. Units: 5

Semester Prerequisite: BIOL� with a grade of C (2.0) or better and either BIOL�, BIOL� with grades of C (2.0) or better or CHEM�/4100L or graduate standing or permission of instructor. Prerequisite: BIOL 300 with grade of C (2.0) or better, plus 15 additional units of upper-division Biology or permission of instructor
Laboratory principles and procedures useful to students interested in a research or industry career. Laboratory exercises will emphasize preparation of useful biotechnological products, including cells and purified enzymes. Students will take an active role in planning experiments, including preparing required solutions, reagents, and materials. Students will evaluate and report the quality of products they produce, measuring abundance, purity, and potency. Three hours lecture and six hours laboratory. Materials fee required.

BIOL�. Immunology. Units: 5

Semester Prerequisite: BIOL� and either BIOL� or BIOL� or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 400 with a grade of "C" or better
Foundations of immunology and current advances in the study of the immunological response. Laboratory examination of immunological assays applied in both research and clinical diagnostics. Three hours lecture, one hour discussion, and three hours laboratory. Materials fee required. Formerly offered as BIOL 573 students may not receive credit for both courses.

BIOL�. Advanced Vertebrate Morphology. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better, or graduate standing in Biology. Quarter Prerequisite: BIOL 342, BIOL 424 and consent of instructor
Advanced techniques in the study of vertebrates, including dissection and specimen preparation. Lecture sessions on advanced topics in vertebrate anatomy and recent research advances. Lab activities include construction of animal skeletal materials, detailed study and dissection of vertebrate organ systems, and individual student designed projects. Projects consist of both laboratory projects under the guidance of instructor and problem-based learning activities that are conducted both in the laboratory and in open activity time with small student groups. (Highly recommended to students planning on applying to PBL veterinary professional programs.) Two hours lecture and three hours laboratory. Materials fee required. BIOL� or BIOL� recommended. Formerly offered as BIOL 524 students may not receive credit for both courses.

BIOL�. Comparative Biomechanics. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better and PHYS� or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with grade of C or better, PHYS 121, PHYS 122, or consent of instructor
Examination and quantitative analysis of structure and function of animals and plants using physical principles. Application of fluid and solid mechanics in the study of biologic materials. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 555 students may not receive credit for both courses.

BIOL�. Endocrinology. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better
Endocrine systems with emphasis on mechanisms for regulating the biosynthesis, secretion, transport, and actions of hormones. Formerly offered as BIOL 576 students may not receive credit for both courses.

BIOL�. Population Genetics. Units: 4

Semester Prerequisite: Math 2110 with a grade of C or better and either BIOL� with a grade of C or better or BIOL� with a grade of C or better or graduate standing in Biology. Quarter Prerequisite: BIOL 423 and MATH 192 or 211
Focuses on evolution at the genetic level including the description of genetic variation within and among populations and the evolutionary forces that can act on this variation over time. Three hours lecture, one hour discussion. Formerly offered as BIOL 522 students may not earn credit for both courses.

BIOL�. Internship in Biology. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575A.

BIOL�B. Internship in Biology: Pre-Health. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575B.

BIOL�C. Internship in Biology: Biotechnology. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575C.

BIOL�D. Internship in Biology: Wildlife Biology. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575D.

BIOL�E. Internship in Biology: Botany. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575E.

BIOL�F. Internship in Biology: Science Education. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575F.

BIOL�G. Internship in Biology: Museum Science. Units: 2

Supervised work and study in work situations involving biological research and technical skills. May be repeated for a total of six units. Only two units of internship courses (BIOL�-5752G) may be applied towards the biology major requirements. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 575G.

BIOL�. Vertebrate Field Biology. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better, or BIOL� with a grade of C or better, or graduate standing in Biology, or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, BIOL 450
Field study of the ecology and natural history of the vertebrate fauna of southern California. One hour lecture and six hours laboratory/field work. Materials fee required. Formerly offered as BIOL 525 students may not receive credit for both courses.

BIOL�. Global Change Biology. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better, or graduate standing in Biology, or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of "C" or better, and an upper-division lab course in ecology (BIOL 349, BIOL 450, or BIOL 455) or consent of instructor
An examination of changing ecological and biogeochemical processes at selected times in the earth's history including, but not limited to, the modern era. Exploration of causes and consequences of contemporary global change for biological systems including displaced populations, disrupted ecological interactions, and altered epidemiological patterns. Formerly offered as BIOL 515 students may not earn credit for both courses.

BIOL�. Physiological Ecology. Units: 4

Semester Prerequisite: One of the following with a grade of C or better: BIOL�, BIOL�, or BIOL� or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 354 and 424 or 431 and either 331 or 342 and 450
Study of physiological, morphological, and behavioral responses of organisms to physical environmental factors such as temperature, light, salinity, and altitude. Three hours lecture and three hours laboratory. Materials fee required. Formerly offered as BIOL 565 students may not receive credit for both courses.

BIOL�. Senior Seminar: Molecular Biology. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in molecular biology. Formerly BIOL 590A.

BIOL�. Senior Seminar: Biosystematics. Units: 2

Semester Prerequisite: At least 90 semester units and either BIOL� with a C or better or BIOL� with a C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in biosystematics. Formerly BIOL 590B.

BIOL�. Senior Seminar: Cell Biology. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in cell biology. Formerly BIOL 590C.

BIOL�. Senior Seminar: Physiology. Units: 2

Semester Prerequisite: At least 90 semester units or graduate standing in Biology, or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in physiology. Formerly BIOL 590D.

BIOL�. Senior Seminar: Ecology. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in ecology. Formerly BIOL 590E.

BIOL�. Senior Seminar: Genetics. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a graded of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in genetics. Formerly BIOL 590G.

BIOL�. Senior Seminar: Evolution. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in evolution. Formerly BIOL 590H.

BIOL�. Senior Seminar: Microbiology. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in microbiology. Formerly BIOL 590I.

BIOL�. Senior Seminar: Zoology. Units: 2

Semester Prerequisite: At least 90 semester units or graduate standing in Biology, or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in zoology. Formerly BIOL 590J.

BIOL�. Senior Seminar: Botany. Units: 2

Semester Prerequisite: At least 90 semester units and one of the following courses with a grade of C or better: BIOL�, BIOL�, BIOL�, or BIOL� or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in botany. Formerly BIOL 590K.

BIOL�. Senior Seminar: History of Biology. Units: 2

Semester Prerequisite: At least 90 semester units and BIOL� with a grade of C or better or graduate standing in Biology. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Investigation into the history of different branches of biology. Formerly BIOL 590L.

BIOL�. Senior Seminar: Conservation Biology. Units: 2

Semester Prerequisite: At least 90 semester units and either BIOL� with a grade of C or better or BIOL� with a grade of C or better or graduate standing in Biology or consent of instructor. Quarter Prerequisite: BIOL 300 with a grade of C or better, and a minimum of 15 upper-division units in biology courses and at least 135 quarter units
Survey of current literature, methods and ethics of scientific inquiry in conservation biology. Formerly BIOL 590M.

BIOL�. Independent Research. Unit: 1

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of 3 or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of 3 or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the major requirements of the B.S. in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596A.

BIOL�. Independent Research. Units: 2

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of B or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of B or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the major requirements of the B.S. in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596B.

BIOL�. Independent Research. Units: 3

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of B or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of B or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the major requirements of the B.S. in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596C.

BIOL�. Independent Research. Units: 4

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of B or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of B or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the major requirements of the B.S. in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596D.

BIOL�. Independent Research. Units: 5

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of 3 or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of 3 or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the undergraduate degree in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596E.

BIOL�. Independent Research. Units: 6

Semester Prerequisite: BIOL� with a grade of C or better and a minimum overall GPA of 3 or better. Quarter Prerequisite: BIOL 202 with a grade of C or better and a minimum overall GPA of 3 or better
Laboratory and/or field research in selected areas in biology conducted under the direction of a faculty member. A total of four units of Independent Research (BIOL�-5956) may be applied toward the undergraduate degree in Biology. Students must present research findings at least once per academic year at the Biology Department colloquium, and must attend the Biology Department colloquium every semester until their projects are complete. Department approval of a written project proposal submitted on a standard application is required. The project proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Materials fee required. Consent of Instructor required. Graded credit/no credit. Formerly BIOL 596F.

BIOL�. Directed Study in Science Education. Unit: 1

Readings and library research on pedagogical content knowledge of specific content areas in biology. This course should be taken concurrently with or shortly after taking an upper division course in the relevant area of biology. Graded credit/no credit. May be repeated up to four times for credit. No more than two units may be applied toward degree requirements for the BS in Biology. Department approval of a written proposal submitted on a standard application is required. The proposal must be submitted for Departmental review in advance of the semester in which the course is to be taken. Consent of Instructor required. Formerly BIOL 597.

BIOL�. Effective Teaching Strategies for Graduate TAs. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: Graduate standing in Biology
Course explores multiple perspectives and strategies for effective teaching. Covers the diversity of students and learning needs, effective presentations, professional behaviors, assessment of student progress and learning, and how to adapt class content or teaching approach as needed. Includes classroom visitations and peer observations. This course is required of all graduate students prior to or concurrent with their first assignment as a teaching assistant. Formerly offered as BIOL 601 students may not receive credit for both courses.

BIOL�. Professional Writing in the Biological Sciences. Units: 2

Semester Prerequisite: Graduate standing in Biology
Writing skills appropriate to scientific works (journal articles, meeting abstracts, proposals, technical writing for general audiences, etc.). Includes formatting conventions, peer review, and ethical issues in scientific writing. Graduate students should take this course early in their program.

BIOL�. Presentation in Biological Sciences. Unit: 1

Semester Prerequisite: Graduate standing in Biology
Methods of effective presentation in biological research. Covers structure of oral presentations, effective data presentation, and audience engagement. Completion of course requires presentation of original laboratory and/or field research. Students will work closely with their thesis mentor to develop, carry out, analyze, prepare, and present their first research talk at the Biology Department Student Research Colloquium or other venue approved by the student's thesis committee. Graded credit/no credit.

BIOL�L. Graduate Biostatistics and Experimental Design Laboratory. Unit: 1

Semester Prerequisite: BIOL� and consent of instructor
Provides experience in using various computer programs and techniques to address problems in statistical analysis and presentation of data related to a student's thesis project, including analysis of proportions and frequencies, comparisons of means among numerical variables, regression, correlation, analysis of variance, as well as non-parametric approaches. Graded credit/no credit.

BIOL�. Primary Literature in Biology. Unit: 1

Semester Prerequisite: Graduate standing in Biology
Faculty supervised discussion in journal club format. Students will learn how to interpret, evaluate, present, and critique published research articles in various subfields of biology. Formerly BIOL 691. May be repeated up to three times for credit. Graded credit/no credit.

BIOL�. Advanced Topics in Molecular Biology. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected research areas in molecular biology. May be repeated for credit as topics change. Formerly BIOL 600.

BIOL�. Advanced Topics in Cell Biology. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected research areas in cell biology. May be repeated for credit as topics change. Formerly BIOL 605.

BIOL�. Advanced Topics in Plant Biology. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected areas of current study in plant biology. May be repeated for credit as topics change. Formerly BIOL 620.

BIOL�. Advanced Topics in Zoology. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected research areas in zoology. May be repeated for credit as topics change. Formerly BIOL 622.

BIOL�. Advanced Topics in Physiology. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected research areas in physiology. May be repeated for credit as topics change. Formerly BIOL 624.

BIOL�. Advanced Topics in Immunology. Units: 2

Quarter Prerequisite: BIOL 573
An in-depth examination of current research in cellular and molecular immunology. May be repeated for credit as topics change. Formerly BIOL 677.

BIOL�. Advanced Topics in Microbiology. Units: 2

Semester Prerequisite: BIOL� or BIOL� and graduate standing in Biology. Quarter Prerequisite: BIOL 220 or BIOL 320
An in-depth examination of current research in microbiology. May be repeated for credit as topics change. Formerly BIOL 678.

BIOL�. Advanced Topics in Ecology. Units: 2

Semester Prerequisite: BIOL� or equivalent, and graduate standing in Biology. Quarter Prerequisite: BIOL 450 or equivalent
Literature survey of specific topics related to community or ecosystem dynamics. May be repeated for credit as topics change. Formerly BIOL 670.

BIOL�. Advanced Topics in Evolution. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
Topics of current research interest in plant or animal evolution. May be repeated for credit as topics change. Formerly BIOL 680.

BIOL�. Advanced Topics in Genetics. Units: 2

Semester Prerequisite: Graduate standing in Biology. Quarter Prerequisite: consent of instructor
An in-depth consideration of selected research areas in genetics. May be repeated for credit as topics change. Formerly BIOL 650.

BIOL�. Advanced Topics in Biosystematics. Units: 2

Semester Prerequisite: Graduate standing in Biology, BIOL�, and one taxonomy-based course eg BIOL�, 3410, 3460, 3420, or 3540. Quarter Prerequisite: BIOL 423 and one taxonomy-based course eg BIOL 319, 331, 335, 342, 353, or 354
Fundamental concepts of classification systems, biometric and experimental taxonomic procedures, nomenclature and systematic literature, both plant and animal materials used. Formerly BIOL 664.

BIOL�. Advanced Topics in Biology. Units: 2

Semester Prerequisite: Graduate standing in Biology
Selected topics and reviews of current investigations in the fields of biology. May be repeated for credit as topics change. Formerly BIOL 690.

BIOL�. Supervised Graduate Research in Biology. Unit: 1

Semester Prerequisite: Classified graduate standing in Biology. Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Laboratory and/or field research methods in biology. Instruction in methods and techniques in the student's subfield of biology, focusing on developing methods and direction for the thesis research. Students should take this course early in their graduate program. Formerly BIOL 692 students may not receive credit for both. Consent of instructor required. Graded credit/no credit.

BIOL�. Thesis proposal. Units: 3

Semester Prerequisite: BIOL�, BIOL�, and completion of at least 6 additional units toward the graduate degree
Research proposal development conducted under direction of the student's thesis mentor. To complete the course, students must successfully defend their thesis proposal. The written thesis proposal should explicitly state the research objectives, review the body of literature that motivates and justifies the research, describe appropriate research methods, and present preliminary data. The student will defend the thesis proposal with an oral presentation open to the public, followed by a private question and answer period with the thesis committee. Successful completion allows student to advance to candidacy. Consent of instructor required. Graded credit/no credit.

BIOL�. Independent Graduate Research in Biology. Unit: 1

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Consent of instructor required. Formerly BIOL 696A. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit.

BIOL�. Independent Graduate Research in Biology. Units: 2

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Consent of instructor required. Formerly BIOL 696B. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit.

BIOL�. Independent Graduate Research in Biology. Units: 3

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Consent of instructor required. Formerly BIOL 696C. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit.

BIOL�. Independent Graduate Research in Biology. Units: 4

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Formerly BIOL 696D. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit. Consent of instructor required.

BIOL�. Independent Graduate Research in Biology. Units: 5

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Formerly BIOL 696E. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit. Consent of instructor required.

BIOL�. Independent Graduate Research in Biology. Units: 6

Quarter Prerequisite: classified standing in Masters Degree Program and consent of instructor
Original individual research in biology to be conducted under the supervision of a faculty member. Formerly BIOL 696F. May be repeated twice for credit. No more than six units of Independent Graduate Research (BIOL�-6956) may be applied toward degree requirements. Graded credit/no credit. Consent of instructor required.

BIOL�. Graduate Thesis. Units: 3

Semester Prerequisite: BIOL�
Preparation of the thesis for the Master of Science in Biology under the direction of a faculty member from the student's committee. Requirements: successful completion and defense of the thesis. Formerly offered as the combination of BIOL 699A, BIOL 699B and BIOL 699C. Consent of instructor required. Graded credit/no credit.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 0

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Unit: 1

Quarter Prerequisite: Advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 2

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 3

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 4

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 5

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.

BIOL�. Continuous Enrollment for Graduate Candidacy Standing. Units: 6

Quarter Prerequisite: advancement to candidacy and approval of program graduate coordinator or, if an interdisciplinary studies major, consent of the Dean of Graduate Studies
Independent study leading to completion of requirements (other than course work) for the master's degree. To retain classified standing in the master's program, a student must enroll in a Continuous Enrollment for Graduate Candidacy Standing course each quarter until the project or thesis is accepted or the comprehensive examination passed. Students who enroll through the university have full use of all university facilities. See Culminating Experience: Exam, Thesis, or Project in Graduate Degree and Program Requirements section of the Bulletin of Courses. Continuous Enrollment for Graduate Candidacy Standing is a variable unit course, see fee schedule in the Financial Information section of the Bulletin of Courses. Earned units are not degree-applicable nor will they qualify for financial aid.


Materials and Methods

Reagents and Tools table

Reagent/Resource Reference or Source Identifier or Catalog Number
Software
MCL Version: 14-137 https://micans.org/mcl/ (Enright et al, 2002 )
ClusterOne Version: 1.0 https://paccanarolab.org/cluster-one/ (Nepusz et al, 2012 )
LibSVM Version: 321 https://www.csie.ntu.edu.tw/

Methods and Protocols

Mass spectrometry dataset collection

Mass spectrometry data and features based on those data used as input into the machine learning classifier were collected from various publications. Specifically, protein interaction features for datasets used in hu.MAP 1.0 (Drew et al, 2017 ), e.g., Wan et al, Hein et al, Huttlin et al, were downloaded from http://hu1.proteincomplexes.org/static/downloads/feature_matrix.txt.gz. Four vector comparison measures were used for co-fractionation data from Wan et al including Poisson noise Pearson correlation coefficient, weighted cross-correlation, co-apex score, and MS1 ion intensity distance metric. All four vector comparison measures were applied to each of the 55 fractionation experiments, totaling 220 features. Pairs of proteins were filtered to ensure co-fractionation measures were > 0.5 in at least two species. AP-MS data from (Guruharsha et al, 2011 ) mapped onto human orthologs using InParanoid (Sonnhammer & Östlund, 2015 ) were represented using the HGSCore value originally downloaded from supplemental table S3 in Guruharsha et al AP-MS data from (Malovannaya et al, 2011 ) were represented by the MEMOs (core modules) certainty assignments “approved”, “provisional”, and “temporary” originally downloaded from supplemental file S1, assigning the scores 10, 3, and 1, respectively. Bioplex 1.0 (Huttlin et al, 2015 ) features were used as originally downloaded from http://wren.hms.harvard.edu/bioplex/data/cdf/150408_CDF_STAR_GRAPH_Ver2594.cdf including NWD Score, Z Score, Plate Z Score, Entropy, Unique Peptide Bins, Ratio, Total PSMs, Ratio Total PSMs, and Unique:Total Peptide Ratio. For the Hein AP-MS data, the features prey.bait.correlation, valid.values, log10.prey.bait.ratio, and log10.prey.bait.expression.ratio were taken from supplemental table S2 in (Hein et al, 2015 ). The mean value was used across the experiments in the case of multiple entries for a given protein pair. Note, all HumanNet (Lee et al, 2011 ) features were excluded from all model training.

New datasets added for hu.MAP 2.0 were downloaded from original publications or associated dataset web resources as shown in Table 1. The same measures used for Bioplex1.0 were also used for Bioplex2.0 features specifically NWD Score, Z Score, Plate Z Score, Entropy, Unique Peptide Bins, Ratio, Total PSMs, Ratio Total PSMs, Unique:Total Peptide Ratio and Average Assembled Peptide Spectral Matches. We used the measures from the proximity labeling dataset, Gupta et al, for both the ciliated condition and nonciliated condition, specifically Average Spectra, Average Saint probability, Max Saint probability, Fold Change, and Bayesian FDR estimate. The same measures were used for the proximity labeling Youn et al data but only for the single condition. Measures used for Boldt et al data were socioaffinity index (SAij) and individual terms based on the spoke model for where protein i is the bait (Sij) and where protein j is the bait (Sji). The matrix model term for the socioaffinity index was also used (Mij). Mass spectrometry data from (Treiber et al, 2017 ) were downloaded from the Pride web resource (Perez-Riverol et al, 2019 ) (PXD004193) and reprocessed using the MSBlender pipeline (Kwon et al, 2011 ). Full details are described in (Mallam et al, 2019 ). Only WMM features, described below, were calculated for Treiber et al.

Bioplex 2.0 (Huttlin et al, 2017 )

HuRI dataset (Luck et al, 2020 ), which was not included in training but was included for evaluation, was downloaded from http://interactome.baderlab.org/data/HuRI.tsv. HuRI protein interactions were ranked based on the number of assays the interaction was identified in.

Weighted matrix model

Our implementation of the WMM is based on presence or absence of proteins in individual experiments (e.g., one pull-down). Due to the nature of high-throughput experiments, noise arises in the form of spurious identifications leading to a protein being erroneously called present in the experiment. To deal with this noise, we set arbitrary but sensible cutoffs of the quality of identification required for a protein to be considered present in the experiment. WMM for Bioplex2.0 was calculated only considering experiments for a given protein where the protein had > 2.0 Bioplex2.0 Z score and > 4.0 Bioplex2.0 Z score. WMM based on Gupta et al were calculated considering all experiments, > 2 average spectral counts, and > 4 average spectral counts. WMM based on Boldt et al were calculated considering all experiments and > 4 spectral counts. WMM based on Treiber et al were calculated considering > 2 spectral counts and > 4 spectral counts. WMM based on Youn et al were calculated considering all experiments, > 2 spectral counts and > 4 spectral counts. For each calculation, we generate a feature in the form of the negative natural log P-value of Equation (1) and the total number of experiments the pair of proteins is observed together (i.e., pair count).

All features, precalculated from original publications and WMM, were combined into 17,564,755 protein pairs × 292 features matrix. Since not all features cover all protein pairs, missing values were filled with 0.0. The final feature matrix can be found in the Data availability section.

Gold standard test and training set

To create a test and training set of literature-curated protein complexes, we downloaded the complete set of CORUM complexes (Giurgiu et al, 2019 ) version 2017_07_02 (http://mips.helmholtz-muenchen.de/corum/download/corum_2017_07_02.zip) and filtered out all non-human proteins. Complexes were merged to eliminate redundancy, so no two complexes had > 0.6 Jaccard coefficient. Complexes were then randomly split into test and training sets. A complex was removed from the test or training sets if any pairs of proteins overlapped in the other set. Large complexes > 30 subunits were removed from the test and training complexes. Test and training sets were also generated for pairs of proteins for training the SVM classifier. A pair of proteins was labeled “positive” if both proteins were in the same complex. A pair was labeled “negative” if proteins were in separate complexes. All other pairs were left unlabeled. For test and training pairs, only 10% of pairs from large complexes were considered. Below is the command line used to generate the test and training sets:

./protein_complex_maps/preprocessing_util/complexes/split_complexes.py --input_complexes allComplexes_20170702_geneids_human.txt --random_seed 1234 --size_threshold 30 --subsample_large_complexes 0.1 --remove_large_complexes --remove_largest --merge_threshold 0.6

Additionally, the full test and training sets used in this study can be found in the Data availability section.

Support vector machine model selection and evaluation

We trained a SVM classifier using Libsvm (Chang & Lin, 2011 ) to classify pairs of proteins as co-complex protein interactions. We first generated a feature matrix using the features described above where rows are pairs of proteins and columns are features. The feature matrix was further labeled using the gold standard training set described above. We used fivefold cross-validation using only the training set when training to select SVM parameters C and gamma. We evaluated a range of C values (2, 8, 32, 128, 512) and gamma values (0.00048828125, 0.001953125, 0.0078125, 0.03125). As an evaluation metric, we used Area Under the Precision-Recall Curve (AUPRC) averaging across the five cross-validation sets. We identified C = 512 and gamma = 001953125 with the highest cross-validated AUPRC. We retrained a full model using all training data using these parameters. We used this final model to predict on all pairs in the feature matrix. The final result is a list of pairs with a corresponding score generated by model.

We evaluated the final model using a precision-recall framework as shown in Fig 2A. We used the scikit-learn python package (preprint: Buitinck et al, 2013 ) to calculate precision and recall for the leave-out gold standard test protein pairs.

For comparisons between datasets as shown in Fig 2A, we generated additional models restricting the features to just those generated from the given dataset keeping the parameters C and gamma fixed. Note, the HuRI dataset was evaluated using the dataset directly as described above.

We additionally evaluated the SVM confidence score for its fidelity to the test set precision value. We observed that the test set precision is consistently higher than the confidence score (Fig EV4). For example, a confidence score as low as 0.02 has

Figure EV4. SVM confidence score versus test set precision

The line plot shows the relationship between the SVM confidence score, and the empirical precision value calculated from the test set of protein interactions. The relationship shows the precision value is consistently higher than the confidence score.

Two-stage clustering and parameter set selection

We next used a two-stage clustering approach to identify clusters within the protein interaction network generated by the classification step described above (Fig 2B). First, the network was thresholded based on the SVM score. We then applied the ClusterOne (Nepusz et al, 2012 ) algorithm to identify dense regions in the thresholded network. Further, for each dense region produced by ClusterOne, we applied the MCL (Enright et al, 2002 ) algorithm to identify clusters. To identify optimal parameters for the score threshold, ClusterOne parameters density and overlap as well as MCL inflation parameter, we generated clusters for various parameter combinations. Specifically, we evaluated a range of parameters: SVM score threshold (1.0, 0.99, 0.97, 0.95, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 0.00005, 0.00001), ClusterOne max overlap (0.6, 0.7, 0.8), density (0.1, 0.2, 0.3, 0.35, 0.4), and MCL inflation (1.2, 2, 3, 4, 5, 7, 9, 11, 15). We also compared using an unweighted graph as input into ClusterOne versus a weighted graph and observed the unweighted graph had superior performance. A weighted graph was used for the MCL stage clustering. We additionally applied a post-clustering filter that removed nodes from a cluster that lacked edges that scored greater than the SVM score threshold.

To evaluate the clusterings as shown in Fig 2C and D, we used the k-cliques method, specifically weighted recall (R_weighted), and weighted precision (P_weighted), which we described previously (Drew et al, 2017 ). Briefly, the k-cliques method globally compares a set of clusters to a set of gold standard complexes by comparing cliques derived from the clusters to cliques derived from gold standard complexes. This comparison is done for all clique sizes from size 2 (i.e., pairs) to size n (i.e., the size of the largest complex or cluster). A precision and recall value are calculated for all clique sizes. A weighted average is then calculated for both precision and recall across all clique sizes, weighted by the number of clusters with size >= to the clique size. This is to limit the bias effect that larger clusters will have on the final precision or recall value.

We evaluated all clusterings using the k-cliques method, comparing to the training set of gold standard complexes. We selected five clusterings that optimize the trade-off between precision and recall as shown in Fig 2C. These five clusterings were then combined into a union set. Table 2 shows the clustering parameters used for the selected clusterings.

Clustering Confidence Score threshold ClusterOne density ClusterOne overlap MCL inflation
1 Extremely high 1.0 0.4 0.6 9
2 Very high 0.7 0.4 0.6 9
3 High 0.5 0.4 0.7 4
4 Medium high 0.04 0.4 0.7 2
5 Medium 0.02 0.1 0.6 2

We finally evaluated the individual selected clusterings and the union of the selected clusterings using the k-clique method by comparing to the leave-out set of gold standard test complexes (Fig 2D). In addition, we compare to previously published complex maps from (Wan et al, 2015 ), Bioplex 1.0 (Huttlin et al, 2015 ), Bioplex 2.0 (Huttlin et al, 2017 ), and our original hu.MAP 1.0 (Drew et al, 2017 ).

Identification of promiscuous proteins

Calculation of protein age enrichment for promiscuous proteins

Protein ages were mapped using ‘modeAge’ in the main_HUMAN.csv file from (Liebeskind et al, 2016 ) Z-scores for each age group were determined by comparing the number of promiscuous proteins to a background distribution. The background distribution was calculated by counting the number of randomly sampled non-promiscuous proteins (i.e., proteins that participate in only one complex) in each age group.

Annotation enrichment, tissue specificity, and overall expression

Annotation enrichment was calculated for GO, Reactome, CORUM, KEGG, and Human Phenotype Ontology (HP) terms using gProfiler (Reimand et al, 2016 ) for each individual complex. All proteins observed in the 15,000 mass spectrometry experiments were used as the background set. Annotations inferred by electronic transfer were ignored.

To evaluate annotation enrichment for all complexes, we first generated a set of shuffled complexes where protein ids were reassigned to new cluster ids. This has the effect of keeping both the number of clusters and the size distribution of clusters the same as the final set of hu.MAP 2.0 complexes. In addition, this also has the effect of keeping the distribution of complexes per protein constant with the final hu.MAP 2.0 complexes as well. Annotation enrichment for the shuffled set of clusters was done as described above. Using this background annotation enrichment from all categories, we calculated a 0.05 false discovery rate threshold.

We used the Human Protein Atlas (HPA) (Uhlén et al, 2015 ) to compare tissue specificity between the full human proteome, hu.MAP 1.0, and hu.MAP 2.0. RNA tissue distribution data were downloaded from: https://www.proteinatlas.org/download/proteinatlas.tsv.zip and mapped to proteins through genenames.

Comparison of overall expression levels between promiscuous and non-promiscuous proteins shown in Fig EV1 was done using HPA using the same proteinatlas.tsv.zip file described above. The median value was calculated for all “Tissue RNA” columns for each individual promiscuous and non-promiscuous protein, and the resulting distribution was plotted.


Existing technologies

The feasibly of de-extinction varies among organisms, and not all organisms face the same technical challenges in their resurrection [5]. For recently extinct species, it may be possible to use ‘standard’ cloning technology (such as the nuclear transfer followed by cellular reprogramming technique that most famously resulted in the birth of ‘Dolly the Sheep’ in 1996 [6]) and a closely related species as a surrogate maternal host. Cloning via nuclear transfer has been accomplished for a wide range of mammalian species, including several examples in which a species other than that of the developing embryo is used as a surrogate mother [7]. This inter-species nuclear transfer approach is being used to resurrect the bucardo, a subspecies of mountain goat that was endemic to the Pyrenees and went extinct in 2000 [8]. If extinction occurred before living tissues could be collected and preserved, however, cloning is not possible because DNA decay begins immediately after death. The first step to resurrecting long-extinct species is therefore to sequence and assemble a genome from the preserved remains of that extinct species. The past decade has seen enormous advances in technologies for ancient DNA isolation and genome assembly [9], and high-quality genomes are now available for several extinct species, including mammoths and passenger pigeons, while this work is in progress for many other species. Once genome sequences are known, genome-wide scans can be used to create lists of genetic differences between the extinct species and their closest living relatives (see [10], for example), which then become the initial targets for genome editing.

The successes of the Church lab and other groups demonstrate that genome editing using CRISPR/cas9 is feasible and efficient across a wide range of taxa [11]. The number of edits that would be required to turn, for example, an Asian elephant genome into a mammoth genome is not small it is estimated that there are around 1.5 million nucleotide-level differences between these two species [10]. However, the number of edits can be minimized by replacing large pieces of the genome in a single edit or by focusing on changing only those genes that are phenotypically relevant. As links between genotype and phenotype remain largely unknown, in particular for non-model organisms, the capacity to engineer every change is likely to exist before we understand the function of every gene.


PROGRAM DESCRIPTION

Bachelor of Science in Biology is a four-year program that provides its students the opportunity to integrate, interpret, and translate biological phenomena through scientific observations and environmental observations, and use this information to make meaningful decisions, with emphasis on its applications in the environment, medical field, and the industry.

The BS Biology program has three majors / specializations: (1) Medical Biology, (2) Industrial Biology, and (3) Environmental Biology.

The Industrial Biology curriculum provides a firm background in biology with emphasis on various molecular approaches in understanding biological phenomena, of culturing organisms for various industrial, pharmaceutical, and biotechnological uses, and of applying these in agriculture, industry, and the environment.


2.0: Introduction - Biology

Bi 1. Principles of Biology—The great theories of biology and their influence in the modern world. 9 units (4-0-5) third term. There are three overarching theories in biology: the theory of the cell, the theory of the gene, and the theory of evolution. Each of them has had major impacts on our lives—for example the concept of the gene has led to treatments for inherited diseases, personalized and genomic medicine, forensic DNA testing, and modern agriculture. Each theory will be discussed from its 19th century origin to its standing in the 21st century, and the scientific understanding and societal impact of each will be sampled. The course will also ask if there is yet a theory of the brain, and if not, how one might be framed. The course is designed to teach what technically adept members of society should know about biology. Instructors: Meyerowitz, Zinn.

Bi 1 x. The Great Ideas of Biology: Exploration through Experimentation. 9 units (0-6-3) third term. Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology. This course is intended for nonbiology majors and will satisfy the freshman biology course requirement. Limited enrollment. Instructor: Bois.

Bi 2. Current Research in Biology. 3 units (1-0-2) first term. Intended for students considering the biology option open to freshmen. Current research in biology will be discussed, on the basis of reading assigned in advance of the discussions, with members of the divisional faculty. Graded pass/fail. Instructor: Elowitz.

Bi 8. Introduction to Molecular Biology: Regulation of Gene Expression. 9 units (3-0-6) second term. This course and its sequel, Bi 9, cover biology at the molecular and cellular levels. Bi 8 emphasizes genomic structure and mechanisms involved in the organization and regulated expression of genetic information. The focus is on the ways that the information content of the genome is translated into distinctive, cell type specific patterns of gene expression and protein function. Assignments will include critical dissections of papers from classical and current research literature and problem sets. Instructors: Guttman, Hong.

Bi 9. Cell Biology. 9 units (3-0-6) third term. Prerequisites: Bi 8. Continues coverage of biology at the cellular level, begun in Bi 8. Topics: cytoplasmic structure, membrane structure and function, cell motility, and cell-cell recognition. Emphasis on both the ultrastructural and biochemical approaches to these topics. Instructors: Chan, Prober.

Bi 10. Introductory Biology Laboratory. 6 units (1-3-2) third term. Prerequisites: Bi 8 designed to be taken concurrently with Bi 9. An introduction to molecular, cellular, and biochemical techniques that are commonly used in studies of biological systems at the molecular level. Instructor: Staff.

Bi 21. Undergraduate Research with Presentation. Minimum 12 units per term (0-11-1) first, second, third terms. Special problems involving laboratory research in biology to be arranged with instructors before registration. Must give a public presentation reporting results of work. May be counted as advanced lab credit. May be repeated for credit. Instructor: Staff.

Bi 22. Undergraduate Research. Units to be arranged first, second, third terms. Special problems involving laboratory research in biology to be arranged with instructors before registration. Graded pass/fail. Instructor: Staff.

Bi 23. Biology Tutorials. 3 or 6 units second term. Small group study and discussion in depth of special areas or problems in biology or biological engineering, involving regular tutorial sections with instructors drawn from the divisional postdoctoral staff and others. Usually given winter term. To be arranged with instructors before registration. Graded pass/fail. Instructor: Huang.

Bi/BE 24. Scientific Communication for Biological Scientists and Engineers. 6 units (3-0-3) first, third terms. This course offers instruction and practice in writing and speaking relevant to professional biological scientists and engineers working in research, teaching, and/or medical careers. Students will write a paper for a scientific or engineering journal, either based on their previous research or written as a review paper of current work in their field. A Caltech faculty member, a postdoctoral scholar, or a technical staff member serves as a technical mentor for each student, to provide feedback on the content and style of the paper. Oral presentations will be based on selected scientific topics, with feedback from instructors and peers. Fulfills the Institute scientific writing requirement. Instructor: MacLean.

Bi 90 abc. Undergraduate Thesis. 12 or more units per term first, second, third terms. Prerequisites: 18 units of Bi 22 (or equivalent research experience) in the research area proposed for the thesis, and instructor's permission. Intended to extend opportunities for research provided by Bi 22 into a coherent individual research project, carried out under the supervision of a member of the biology faculty. Normally involves three or more consecutive terms of work in the junior and senior years. The student will formulate a research problem based in part on work already carried out, evaluate previously published work in the field, and present new results in a thesis format. First two terms graded pass/fail final term graded by letter on the basis of the completed thesis. Instructor: Bjorkman.

BE/Bi 101. Order of Magnitude Biology. 6 units (3-0-3). For course description, see Bioengineering.

CNS/Psy/Bi 102 ab. Brains, Minds, and Society. 9 units (3-0-6). For course description, see Computation and Neural Systems.

BE/Bi 103 a. Introduction to Data Analysis in the Biological Sciences. 9 units (1-3-5). For course description, see Bioengineering.

BE/Bi 103 b. Statistical Inference in the Biological Sciences. 9 units (1-3-5). For course description, see Bioengineering.

Bi/Ge/ESE 105. Evolution. 12 units (3-4-5) second term. Prerequisites: Completion of Core Curriculum Courses. Maximum enrollment: 15, by application only. The theory of evolution is arguably biology's greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Instructors: Phillips, Orphan. Given in alternate years offered 2019–20.

BE/Bi 106. Comparative Biomechanics. 9 units (3-0-6) second term. For course description, see Bioengineering.

Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8) first term. Prerequisite: Ch 41 abc or instructor's permission. Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, and the intermediary metabolism that provides energy to an organism. Instructor: Clemons.

Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8) second term. Prerequisites: Bi/Ch 110 Bi 8 and Bi 122 recommended. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and protein synthesis. Instructors: Campbell, Parker.

Bi 114. Immunology. 9 units (3-0-6) second term. Prerequisites: Bi 8, Bi 9, Bi 122 or equivalent, and Bi/Ch 110 recommended. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, gene rearrangement of lymphocyte receptors, cytokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. The course will present an integrated view of how the immune system interacts with viral and bacterial pathogens and commensal bacteria. Instructors: Bjorkman, Yui.

Bi/BE/BMB 115. Viruses and Applications to Biological Systems. 9 units (3-2-4) third term. Learn about viruses as fascinating biological machines, focusing on naturally-occurring and evolved variants, in silico viral vector engineering, and computational methods that include structure visualization and machine learning. This course will introduce the fundamentals in the chemistry and biology of viruses, emphasizing their engineerable properties for use in basic research and translational applications. Topics include: viruses by the numbers, mammalian and non-mammalian (plant, bacteria) viruses, enveloped vs. non-enveloped viruses, host-virus interactions, viral life cycles (replication vs. dormancy), immune responses to viruses, zoonosis, diverse mechanisms of entry and replication, the application of viruses as gene-delivery vehicles (with a focus on adeno-associated viruses or AAVs, lentiviruses, and rabies), and how to engineer viral properties for applications in basic research and gene therapy. The lectures will be complemented by short lab exercises in AAV preparation, bioinformatics and machine learning, and structure visualization. Instructors: Bjorkman, Gradinaru, Van Valen, Bjorkman. Given in alternate years offered 2019–20.

Bi 116. Microbial Genetics. 9 units (3-0-6) second term. Prerequisites: Bi 1, 8, 9 (or equivalent), and ESE/Bi 166. A course on microbial genetics, emphasizing the history of the discipline as well as modern approaches. Students will be exposed to different ways of manipulating microbial genomes (primarily bacterial, but we will also cover archaea and microbial eukaryotes). The power of microbial genetics to shed light on diverse process will be discussed in a variety of contexts, ranging from environmental science to the mammalian microbiome. Instructors: Mazmanian, Newman. Given in alternate years offered 2019–20.

Bi 117. Developmental Biology. 9 units (3-0-6) second term. Prerequisites: Bi 8 and Bi 9. A survey of the development of multicellular organisms. Topics will include the beginning of a new organism (fertilization), the creation of multicellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), induction of the nervous system (neurulation), and creation of specific organs (organogenesis). Emphasis will be placed on the molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development, covering both classical and modern approaches to studying these processes. Instructor: Bronner.

Bi 118. Morphogenesis of Developmental Systems. 9 units (3-0-6) second term. Prerequisites: Bi 8 and Bi 9, or instructor's permission. Lectures on and discussion of how cells, tissues, and organs take shape: the influence of force on cell shape change cell migration including chemotaxis and collective cell movement adhesion/deadhesion during migration the relationship between cell migration and metastasis and a review/overview of general signaling principles and embryonic development of invertebrate and vertebrate animals. Students will choose term project involving writing a grant proposal or quantitative analysis of available datasets relating to lecture topics. Instructor: Stathopoulos. Given in alternate years not offered 2019–20.

Bi 122. Genetics. 9 units (3-0-6) first term.Prerequisite: Bi 8 or Bi 9, or instructor's permission. Lecture and discussion course covering basic principles of genetics. Not open to freshmen. Instructors: Hay, Sternberg, Staff.

Bi/BE 129. The Biology and Treatment of Cancer. 9 units (3-0-6) second term. The first part of the course will concern the basic biology of cancer, covering oncogenes, tumor suppressors, tumor cell biology, metastasis, tumor angiogenesis, and other topics. The second part will concern newer information on cancer genetics and other topics, taught from the primary research literature. The last part of the course will concern treatments, including chemotherapy, anti-angiogenic therapy, and immunotherapy. Textbook: The Biology of Cancer, 2nd edition, by Robert Weinberg. Instructors: Zinn, Campbell. Given in alternate years not offered 2019–20.

CNS/Psy/Bi 131. The Psychology of Learning and Motivation. 9 units (3-0-6). For course description, see Computation and Neural Systems.

Bi 145 a. Tissue and Organ Physiology. 9 units (3-0-6) first term. Prerequisites: Bi 8, 9, Bi/Ch 110. Bi/Ch 110 may be taken concurrently. Reviews of anatomy and histology, as well as in-depth discussion of cellular physiology. Building from cell function to tissues, the course explores human physiology in an organ-based fashion. First term topics include endocrine physiology, the autonomic nervous system, urinary physiology, and the cardiovascular system. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.

Bi 145 b. Tissue and Organ Physiology. 9 units (3-0-6) second term. Prerequisites: Bi 145a. Building on the foundations of Bi 145a, Bi 145b will continue the exploration of human physiology incorporating anatomy and cellular physiology. Topics include muscle physiology, the skeletal system, digestive and hepatic physiology, nutrition, the respiratory system and reproductive physiology. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.

Bi/CNS/NB/Psy 150. Introduction to Neuroscience. 10 units (4-0-6) third term. Prerequisites: Bi 8, 9, or instructor's permission. General principles of the function and organization of nervous systems, providing both an overview of the subject and a foundation for advanced courses. Topics include the physical and chemical bases for action potentials, synaptic transmission, and sensory transduction anatomy development sensory and motor pathways memory and learning at the molecular, cellular, and systems level and the neuroscience of brain diseases. Letter grades only. Instructors: Adolphs, Lester.

Bi/CNS/NB 152. Neural Circuits and Physiology of Appetite and Body Homeostasis. 6 units (2-0-4) third term. Prerequisites: Graduate standing or Bi/CNS/NB/Psy 150, or equivalent. An advanced course of lectures, readings, and student presentations focusing on neural basis of appetites such as hunger and thirst. This course will cover the mechanisms that control appetites both at peripheral and central level. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on the logic of how the body and the brain cooperate to maintain homeostasis. Instructor: Oka. Given in alternate years not offered 2019–20.

Bi/CNS/NB 154. Principles of Neuroscience. 9 units (3-0-6) first term. Prerequisites: Bi/CNS/NB/Psy 150 or equivalent. This course aims to distill the fundamental tenets of brain science, unlike the voluminous textbook with a similar title. What are the essential facts and ways of understanding in this discipline? How does neuroscience connect to other parts of life science, physics, and mathematics? Lectures and guided reading will touch on a broad range of phenomena from evolution, development, biophysics, computation, behavior, and psychology. Students will benefit from prior exposure to at least some of these domains. Instructor: Meister. Given in alternate years not offered 2019–20.

Bi/NB/BE 155. Neuropharmacology. 6 units (3-0-3) second term. Prerequisites: Bi/CNS/NB/Psy 150. The neuroscience of drugs for therapy, for prevention, and for recreation. Students learn the prospects for new generations of medications in neurology, psychiatry, aging, and treatment of substance abuse. Topics: Types of drug molecules. Drug receptors. Electrophysiology. Drugs activate ion channels. Drugs block ion channels. Drugs activate and block G protein pathways. Drugs block neurotransmitter transporters. Pharmacokinetics. Recreational drugs. Nicotine Addiction. Opiate Addiction. Drugs for neurodegenerative diseases: Alzheimer's disease, Parkinson's disease. Drugs for epilepsy and migraine. Psychiatric diseases: Nosology and drugs. The course is taught at the research level. Instructor: Lester. Given in alternate years not offered 2019–20.

Bi/CNS/NB 157. Comparative Nervous Systems. 9 units (2-3-4) third term. Prerequisites: instructor's permission. An introduction to the comparative study of the gross and microscopic structure of nervous systems. Emphasis on the vertebrate nervous system also, the highly developed central nervous systems found in arthropods and cephalopods. Variation in nervous system structure with function and with behavioral and ecological specializations and the evolution of the vertebrate brain. Letter grades only. Instructor: Allman. Given in alternate years not offered 2019–20.

Bi/CNS 158. Vertebrate Evolution. 9 units (3-0-6) third term. Prerequisites: Bi 1, Bi 8, or instructor's permission. An integrative approach to the study of vertebrate evolution combining comparative anatomical, behavioral, embryological, genetic, paleontological, and physiological findings. Special emphasis will be given to: (1) the modification of developmental programs in evolution (2) homeostatic systems for temperature regulation (3) changes in the life cycle governing longevity and death (4) the evolution of brain and behavior. Letter grades only. Instructor: Allman. Given in alternate years offered 2019–20.

Bi 160. Molecular Basis of Animal Evolution. 9 units (3-3-3) third term. Prerequisites: Bi 8 and/or Bi 9 recommended. We share the planet with well over 1.5 million other animal species. This course covers how the staggering diversity of the animal kingdom came about through underlying molecular evolutionary phenomena, including gene and protein sequence evolution, gene family and genome evolution, the evolution of developmental processes, neural circuit evolution and behavior, and molecular mechanisms that physiologically adapt animals to their environment. Molecular processes involved in speciation will be explained, together with an analysis of constraints and catalysts on the production of selectable variation that have shaped the evolution of animal life. Participants will undertake a laboratory project on evolutionary genomics, involving fieldwork, genome sequencing and comparative genome analysis. The course focuses on the >99.9% of animals that lack backbones. Instructor: Parker.

Pl/CNS/NB/Bi/Psy 161. Consciousness. 9 units (3-0-6). For course description, see Philosophy.

Bi/CNS/NB 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-4-6) second term. Prerequisites: Bi/CNS/NB/Psy 150 or instructor's permission. A laboratory-based introduction to experimental methods used for electrophysiological studies of the central nervous system. Through the term, students investigate the physiological response properties of neurons in vertebrate and invertebrate brains, using extra- and intracellular recording techniques. Students are instructed in all aspects of experimental procedures, including proper surgical techniques, electrode fabrication, and data analysis. The class also includes a brain dissection and independent student projects that utilize modern digital neuroscience resources. Instructor: Bremner.

NB/Bi/CNS 163. The Biological Basis of Neural Disorders. 6 units (3-0-3) second term. For course description, see Neurobiology.

Bi/CNS/NB 164. Tools of Neurobiology. 9 units (3-0-6) first term. Prerequisites: Bi/CNS/NB/Psy 150 or equivalent. Offers a broad survey of methods and approaches to understanding in modern neurobiology. The focus is on understanding the tools of the discipline, and their use will be illustrated with current research results. Topics include: molecular genetics, disease models, transgenic and knock-in technology, virus tools, tracing methods, gene profiling, light and electron microscopy, optogenetics, optical and electrical recording, neural coding, quantitative behavior, modeling and theory. Instructor: Meister.

Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1) first term. The course will serve to introduce graduate students to 1) the process of writing fellowships to train students in preparing effective funding applications 2) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities as well as projects in other fields and 3) presentation of research and asking questions in research presentations. The first half of the class will involve training in grant writing by drafting an NSF-GRFP proposal. The second half of the class will involve giving chalk talk research presentations. Students can apply from all departments priority will be given to those in microbiology. Enrollment is limited to instructor approval. Instructor: Hoy.

ESE/Bi 166. Microbial Physiology. 9 units (3-1-5). For course description, see Environmental Science and Engineering.

ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6). For course description, see Environmental Science and Engineering.

BMB/Bi/Ch 170. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-0-6). For course description, see Biochemistry and Molecular Biophysics.

BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6). For course description, see Biochemistry and Molecular Biophysics.

BMB/Bi/Ch 174. Advanced Topics in Biochemistry. 6 units (3-0-3). For course description, see Biochemistry and Molecular Biophysics.

CNS/Bi/Psy/NB 176. Cognition. 9 units (4-0-5). For course description, see Computation and Neural Systems.

Bi/BE 177. Principles of Modern Microscopy. 9 units (3-0-6) second term. Lectures and discussions on the underlying principles behind digital, video, differential interference contrast, phase contrast, confocal, and two-photon microscopy. The course will begin with basic geometric optics and characteristics of lenses and microscopes. Specific attention will be given to how different imaging elements such as filters, detectors, and objective lenses contribute to the final image. Course work will include critical evaluation of published images and design strategies for simple optical systems and the analysis and presentation of two- and three-dimensional images. The role of light microscopy in the history of science will be an underlying theme. No prior knowledge of microscopy will be assumed. Instructor: Collazo. Given in alternate years not offered 2019–20.

Ge/ESE/Bi 178. Microbial Ecology. 9 units (3-2-4). For course description, see Geological and Planetary Sciences.

Bi/BE 182. Animal Development and Genomic Regulatory Network Design. 9 units (3-0-6) second term. Prerequisites: Bi 8 and at least one of the following: Bi/Ch 111, Bi 114, or Bi 122 (or equivalents). This course is focused on the genomic control circuitry of the encoded programs that direct developmental processes. The initial module of the course is devoted to general principles of development, with emphasis on transcriptional regulatory control and general properties of gene regulatory networks (GRNs). The second module provides mechanistic analyses of spatial control functions in multiple embryonic systems, and the third treats the explanatory and predictive power of the GRNs that control body plan development in mammalian, sea urchin, and Drosophila systems. Grades or pass/fail. Instructors: Stathopoulos, Peter. Given in alternate years offered 2019–20.

Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics. 9 units (3-0-6) second term. Prerequisites: Bi 8, CS 2, Ma 3 or BE/Bi 103a or instructor's permission. Biology is becoming an increasingly data-intensive science. Many of the data challenges in the biological sciences are distinct from other scientific disciplines because of the complexity involved. This course will introduce key computational, probabilistic, and statistical methods that are common in computational biology and bioinformatics. We will integrate these theoretical aspects to discuss solutions to common challenges that reoccur throughout bioinformatics including algorithms and heuristics for tackling DNA sequence alignments, phylogenetic reconstructions, evolutionary analysis, and population and human genetics. We will discuss these topics in conjunction with common applications including the analysis of high throughput DNA sequencing data sets and analysis of gene expression from RNA-Seq data sets. Instructors: Pachter, Thomson.

Bi/CNS/NB 184. The Primate Visual System. 9 units (3-1-5) third term. This class focuses on the primate visual system, investigating it from an experimental, psychophysical, and computational perspective. The course will focus on two essential problems: 3-D vision and object recognition. We will examine how a visual stimulus is represented starting in the retina, and ending in the frontal lobe, with a special emphasis placed on mechanisms for high-level vision in the parietal and temporal lobes. An important aspect of the course is the lab component in which students design and analyze their own fMRI experiment. Instructor: Tsao. Given in alternate years not offered 2019–20.

Bi/CNS/NB 185. Large Scale Brain Networks. 6 units (2-0-4) third term. This class will focus on understanding what is known about the large-scale organization of the brain, focusing on the mammalian brain. What large scale brain networks exist and what are their principles of function? How is information flexibly routed from one area to another? What is the function of thalamocortical loops? We will examine large scale networks revealed by anatomical tracing, functional connectivity studies, and mRNA expression analyses, and explore the brain circuits mediating complex behaviors such as attention, memory, sleep, multisensory integration, decision making, and object vision. While each of these topics could cover an entire course in itself, our focus will be on understanding the master plan­—how the components of each of these systems are put together and function as a whole. A key question we will delve into, from both a biological and a theoretical perspective, is: how is information flexibly routed from one brain area to another? We will discuss the communication through coherence hypothesis, small world networks, and sparse coding. Instructor: Tsao. Given in alternate years, not offered 2019–20.

CNS/Bi/EE/CS/NB 186. Vision: From Computational Theory to Neuronal Mechanisms. 12 units (4-4-4). For course description, see Computation and Neural Systems.

CNS/Bi/Ph/CS/NB 187. Neural Computation. 9 units (3-0-6). For course description, see Computation and Neural Systems.

Bi 188. Human Genetics and Genomics. 6 units (2-0-4) third term. Prerequisite: Bi 122 or graduate standing and instructor's permission. Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution. Instructor: Wold. Given in alternate years offered 2019–20.

Bi 189. The Cell Cycle. 6 units (2-0-4) third term. Prerequisites: Bi 8 and Bi 9. The course covers the mechanisms by which eukaryotic cells control their duplication. Emphasis will be placed on the biochemical processes that ensure that cells undergo the key events of the cell cycle in a properly regulated manner. Instructor: Dunphy.

Bi 190. Systems Genetics. 6 units (2-0-4) first term. Prerequisites: Bi 122. Lectures covering how genetic and genomic analyses are used to understand biological systems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Instructor: Sternberg. Given in alternate years not offered 2019–20.

BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6). For course description, see Bioengineering.

Bi 192. Introduction to Systems Biology. 6 units (2-0-4) first term. Prerequisites: Ma 1abc, and either Bi 8, CS1, or ACM 95 or instructor's permission. The course will explore what it means to analyze biology from a systems-level point of view. Given what biological systems must do and the constraints they face, what general properties must biological systems have? Students will explore design principles in biology, including plasticity, exploratory behavior, weak-linkage, constrains that deconstrain, robustness, optimality, and evolvability. The class will read the equivalent of 2-3 scientific papers every week. The format will be a seminar with active discussion from all students. Students from multiple backgrounds are welcome: non-biology or biology students interested in learning systems-level questions in biology. Limited enrollment. Instructor: Goentoro.

Bi/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6) first term. Prerequisites: calculus.This course develops the mathematical methods needed for a quantitative understanding of biological phenomena, including data analysis, formulation of simple models, and the framing of quantitative questions. Topics include: probability and stochastic processes, linear algebra and transforms, dynamical systems, scientific programming. Instructor: Meister.

BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units. For course description, see Bioengineering.

Bi 206. Biochemical and Genetic Methods in Biological Research. 6 units (2-0-4) third term. Prerequisites: graduate standing. This course will comprise discussions of selected methods in molecular biology and related fields. Instructor: Varshavsky. Given in alternate years offered 2019–20.

Bi 214. Stem Cells and Hematopoiesis. 9 units (3-0-6) third term. Prerequisites: Graduate standing, or at least one of Bi 114, Bi 117, Bi/Be 182, plus molecular biology. An advanced course with classes based on active discussion, lectures, and seminar presentations. Development from embryos and development from stem cells are distinct paradigms for understanding and manipulating the emergence of ordered biological complexity from simplicity. This course focuses on the distinguishing features of stem-cell based systems, ranging from the natural physiological stem cells that are responsible for life-long hematopoiesis in vertebrates (hematopoietic stem cells) to the artificial stem cells, ES and iPS cells, that have now been created for experimental manipulation. Key questions will be how the stem cells encode multipotency, how they can enter long-term self-renewal by separating themselves from the developmental clock that controls development of the rest of the organism, and how the self-renewal programs of different stem cell types can be dismantled again to allow differentiation. Does "stem-ness" have common elements in different systems? The course will also cover the lineage relationships among diverse differentiated cell types emerging from common stem cells, the role of cytokines and cytokine receptors in shaping differentiation output, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Instructor: Rothenberg.

Bi/CNS/NB 216. Behavior of Mammals. 6 units (2-0-4) first term. A course of lectures, readings, and discussions focused on the genetic, physiological, and ecological bases of behavior in mammals. A basic knowledge of neuroanatomy and neurophysiology is desirable. Instructor: Allman. Given in alternate years offered 2019–20.

Bi/CNS/NB 217. Central Mechanisms in Perception. 6 units (2-0-4) first term. Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Instructor: Allman. Given in alternate years not offered 2019–20.

Bi/CNS/NB 220. Genetic Dissection of Neural Circuit Function. 6 units (2-0-4) second term. Prerequisites: Bi/CNS/NB/Psy 150 or equivalent. Open to advanced (junior or senior) undergraduates only and with instructor permission. This advanced course will discuss the emerging science of neural "circuit breaking" through the application of molecular genetic tools. These include optogenetic and pharmacogenetic manipulations of neuronal activity, genetically based tracing of neuronal connectivity, and genetically based indicators of neuronal activity. Both viral and transgenic approaches will be covered, and examples will be drawn from both the invertebrate and vertebrate literature. Interested CNS or other graduate students who have little or no familiarity with molecular biology will be supplied with the necessary background information. Lectures and student presentations from the current literature. Instructor: Anderson. Not offered 2019–20.

Bi/BE 222. The Structure of the Cytosol. 6 units (2-0-4) third term. Prerequisites: Bi 9, Bi/Ch 110-111 or graduate standing in a biological discipline. The cytosol, and fluid spaces within the nucleus, were once envisioned as a concentrated soup of proteins, RNA, and small molecules, all diffusing, mixing freely, and interacting randomly. We now know that proteins in the cytosol frequently undergo only restricted diffusion and become concentrated in specialized portions of the cytosol to carry out particular cellular functions. This course consists of lectures, reading, student presentations, and discussion about newly recognized biochemical mechanisms that confer local structure and reaction specificity within the cytosol, including protein scaffolds and "liquid-liquid phase separations that form "membraneless compartments." Instructor: Kennedy.

Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4) second term. Prerequisites: Bi/BE 177 or a course in microscopy. Discussion and laboratory-based course covering the practical use of the confocal microscope, with special attention to the dynamic analysis of living cells and embryos. Course will begin with basic optics, microscope design, Koehler illumination, and the principles of confocal microscopy as well as other techniques for optical sectioning such as light sheet fluorescence microscopy (also called single plane illumination microscopy, SPIM). During the class students will construct a light sheet microscope based on the openSPIM design. Alongside the building of a light sheet microscope, the course will consist of semi-independent modules organized around different imaging challenges using confocal microscopes. Early modules will include a lab using lenses to build a cloaking device. Most of the early modules will focus on three-dimensional reconstruction of fixed cells and tissues. Later modules will include time-lapse confocal analysis of living cells and embryos. Students will also utilize the microscopes in the Beckman Institute Biological Imaging Facility to learn more advanced techniques such as spectral unmixing and fluorescence correlation spectroscopy. Enrollment is limited. Instructor: Collazo. Given in alternate years offered 2019–20.

Bi/CNS/BE/NB 230. Optogenetic and CLARITY Methods in Experimental Neuroscience. 9 units (3-2-4) third term. Prerequisites: Graduate standing or Bi/CNS/NB/Psy 150 or equivalent or instructor's permission. The class covers the theoretical and practical aspects of using (1) optogenetic sensors and actuators to visualize and modulate the activity of neuronal ensembles and (2) CLARITY approaches for anatomical mapping and phenotyping using tissue-hydrogel hybrids. The class offers weekly hands-on LAB exposure for opsin viral production and delivery to neurons, recording of light-modulated activity, and tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Lecture topics include: opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics), compatible readout modalities (electrophysiology, imaging) design and use of methods for tissue clearing (tissue stabilization by polymers/hydrogels and selective extractions, such as of lipids for increased tissue transparency and macromolecule access). Class will discuss applications of these methods to neuronal circuits (case studies based on recent literature). Instructor: Gradinaru. Given in alternate years offered 2020-21.

Ge/Bi 244. Paleobiology Seminar. 6 units (3-0-3). For course description, see Geological and Planetary Sciences.

Ge/Bi/ESE 246. Molecular Geobiology Seminar. 6 units (2-0-4). For course description, see Geological and Planetary Sciences.

CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4). For course description, see Computation and Neural Systems.

Bi 250 a. Topics in Molecular and Cellular Biology. 9 units (3-0-6) first term. Prerequisites: graduate standing. Lectures and literature-based discussions covering research methods, scientific concepts and logic, research strategies and general principles of modern biology. Students will learn to critique papers in a wide range of fields, including molecular biology, developmental biology, genetics and neuroscience. Graded pass/fail. Instructors: Aravin, Voorhees.

Bi 250 b. Topics in Systems Biology. 9 units (3-0-6) third term. Prerequisites: Bi 1, Bi 8, or equivalent Ma 2, Bi/CNS/NB 195, or equivalent or instructor's permission.Quantitative studies of cellular and developmental systems in biology, including the architecture of specific circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties, such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical, and computational perspectives. Instructors: Elowitz, Bois.

Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6) third term. Prerequisite: graduate standing. The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley's landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components. Instructor: Siapas.

Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit. Prerequisite: graduate standing. Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.

Bi 252. Responsible Conduct of Research. 4 units (2-0-2) third term. This lecture and discussion course covers relevant aspects of the responsible conduct of biomedical and biological research. Topics include guidelines and regulations, ethical and moral issues, research misconduct, data management and analysis, research with animal or human subjects, publication, conflicts of interest, mentoring, and professional advancement. This course is required of all trainees supported on the NIH training grants in cellular and molecular biology and neuroscience, and is recommended for other graduate students in labs in the Division of Biology and Biological Engineering labs. Undergraduate students require advance instructor's permission. Graded pass/fail. Instructors: Meyerowitz, Sternberg, Staff.

Bi 253. Reading, Writing, Reviewing, Experimental Design and Reproducibility. 6 units (2-0-4) second term. This course will consider scholarly communication in molecular and cellular biology, broadly defined. Students will learn about data standards, the minimal information required to describe an experiment and computer code. Discussion will include long term storage of data and informatics workflows. Appropriate citation of other article and resources will be considered. We will discuss evaluation of scientific premise, rigorous experimental design and interpretation, appropriate statistical power, authentication of key biological and chemical resources, data and material sharing, record keeping, and transparency in reporting data and observations. Students will learn to read papers critically and practice reviewing short articles from Micropublication: biology, which are short enough to allow a thorough analysis of methods necessary to ensure reproducibility. Graded Pass/Fail. Instructors: Sternberg, Hay, Meister, Staff.

Ch/Bi 253. Advanced Topics in Biochemistry. 6 units (2-0-4). For course description, see Chemistry.

Psy/Bi/CNS 255. Topics in Emotion and Social Cognition. 9 units (3-0-6). For course description, see Psychology.

CNS/Bi/NB 256. Decision Making. 6 units (2-0-4). For course description, see Computation and Neural Systems.

Bi/BE/Ch/ChE/Ge 269. Integrative Projects in Microbial Science and Engineering. 6 units (3-0-3) second term. A project-based course designed to train students to integrate biological, chemical, physical and engineering tools into innovative microbiology research. Students and faculty will brainstorm to identify several "grand challenges" in microbiology. Small teams, comprised of students from different graduate programs and disciplinary backgrounds (e.g. a chemical engineer, a computer scientist and a biologist) and a faculty member, will work to compose a project proposal addressing one of the grand challenges, integrating tools and concepts from across disciplines. Student groups will present draft proposals and receive questions and critiques from other members of the class at check-in points during the academic term. While there will not be an experimental laboratory component, project teams may tour facilities or take field trips to help define the aims and approaches of their projects. At the end of the course, teams will deliver written proposals and presentations that will be critiqued by students and faculty. Instructor: CEMI Faculty.

Bi 270 abc. Special Topics in Biology. Units to be arranged each term first, second, third. Students may register with permission of the responsible faculty member.

CNS/Bi 286 abc. Special Topics in Computation and Neural Systems. Units to be arranged. For course description, see Computation and Neural Systems.

Bi 299. Graduate Research. Units to be arranged first, second, third terms. Students may register for research units after consultation with their adviser.


Watch the video: Episode 1 - Introduction to Biology (June 2022).