May 03, 2024

2014-2015 Catalog

2014-2015 Catalog [ARCHIVED CATALOG]

Course Descriptions

UNDERGRADUATE COURSES
Lower Division Courses numbered 1–99 are designed primarily for freshmen and sophomores but are open to all students for lower division credit. (Graduate students requesting to enroll in lower-division undergraduate courses will not receive unit credit nor will the course fulfill degree requirements.) Upper Division Courses courses numbered 100–199 are open to all students who have met the necessary prerequisites as indicated in the catalog course description. Preparation should generally include completion of one lower division course in the given subject or completion of two years of college work.

GRADUATE COURSES
Courses numbered 200–299 are open to graduate students. (Undergraduate students must obtain the signature of the instructor, School Dean, and the Dean of Graduate Studies. Graduate level units will count towards the required 120 units for graduation; however students are urged to meet with their academic advisor in order to determine if graduate course units may be used to fulfill a graduation requirement.)

CROSS-LISTED/CONJOINED COURSES
Cross-listed Courses are the same course offered under different course subjects at the same level (either undergraduate or graduate) that share the same meeting time, requirements, units, etc. Conjoined Courses are the same course but one is undergraduate and one is graduate.

COREQUISITE COURSE
A corequisite course is a course that must be taken at the same time as another course.

PREREQUISITES
Prerequisites for courses should be followed carefully; the responsibility for meeting these requirements rests on the student. If you can demonstrate that your preparation is equivalent to that specified by the prerequisites, the instructor may waive these requirements for you. The instructor also may request that a student who has not completed the prerequisites be dropped from the course. Note: For all courses a “C-” or better grade is required for a course to be used as a prerequisite for another course. If a course was taken for a “P/NP” grade then a “P” grade is required. If the prerequisite for a course is not satisfied, students must obtain the approval of the instructor (or school designee) of the course they wish to take.

FOREIGN LANGUAGES
No credit is allowed for completing a less advanced course after successful completion (C-or better) of a more advanced course in the foreign languages. This applies only to lower division foreign language courses, not upper division courses.

More information about Course Substitutions , Grading Options , and Course Materials and Services Fees can be found in alternate areas of the catalog.

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Quantitative and Systems Biology
	QSB 200: Molecular Cell Biology [3 units] Focus on molecular aspects of cellular processes, including signal transduction, cell division, differentiation, protein synthesis and degradation, and regulation of gene expression. Each topic is accompanied by critical evaluation of classic papers and recent publications. Upper division undergraduate courses in cell and molecular biology should have been completed as course requisites for this course. Letter grade only. View course scheduling information
	QSB 200: Molecular Cell Biology [3 units] A graduate-level course focusing on molecular aspects of cellular processes, including signal transduction, cell division, differentiation, protein synthesis and degradation, and regulation of gene expression. Each topic is accompanied by critical evaluation of classic papers and recent publications. Upper division undergraduate courses in cell and molecular biology should have been completed as course requisites for this course. Normal Letter Grade only. View course scheduling information
	QSB 201: Teaching and Learning in the Sciences [1.0 unit] Students are introduced to ‘scientific teaching’ - an approach to teaching science that uses many of the same skills applied in research. Topics include how people learn, active learning, designing, organizing and facilitating teachable units, classroom management, diversity in the classroom and assessment design. Satisfactory/Unsatisfactory only. Discussion included. View course scheduling information
	QSB 202: Graduate Level Biochemistry [3.0 units] The overall objective of QSB 202 is to teach students fundamental principles and concepts of biochemistry as a scientific discipline at the graduate level. The emphasis will be on the relationship between macromolecular structure and function. Prerequisite: BIO 101 and BIO 102 , or their equivalents. Normal Letter Grade only. View course scheduling information
	QSB 207: Physical Biochemistry [3.0 units] Physical Biochemistry is the study of properties such as macromolecular folding, multimerization, structure, and ligand binding. This course will instruct students on these, and on the experimental techniques that can quantitatively probe these properties, including hands-on work with multidimensional NMR data. Also included is in-depth discussion of recent biophysical literature. Normal Letter Grade only. View course scheduling information
	QSB 212: Advanced Signal Transduction and Growth Control [4.0 units] Signal transduction in mammalian cells with emphasis on molecular and genetic regulation of these processes and their role in cell function. Graduate requirement includes an advanced discussion section involving research methodology and data interpretation led by the instructor. Prerequisite: An undergraduate biochemistry course or consent of instructor. View course scheduling information
	QSB 214: Tissue Engineering Design [3.0 units] Fundamental topics include: issues related to the cell source (including stem cells, plasticity, transdifferentiation, therapeutic cloning vs. reproductive cloning, bone marrow transplants, and cell differentiation and purification), cell culture and tissue organization, gene therapy delivery methods, cell adhesion and migration, issues in construct design, tissue preservation, and immunoisolation and/or modulation. Current case studies and issues for FDA approval of tissue engineered products are also covered. Prerequisite: MATH 021 and PHYS 008 or equivalent. View course scheduling information
	QSB 215: Principles of Biological Technologies [3.0 units] The principles underlying commonly used and cutting-edge technical procedures in biological research. Lectures and primary literature critiques on biochemical, molecular, cellular, bioengineering and computational techniques. Prerequisite: QSB 290 or consent of instructor. Discussion included. View course scheduling information
	QSB 217: Lab on a Chip: Developing 3rd World Diagnostics for Global Health [3.0 units] This is the first-ever four campus course between UC San Francisco, UC Berkeley, UC Santa Cruz, and UC Merced which aims to 1) raise awareness and knowledge about global health issues 2) teach students critical engineering skills such as nano/micro-fabrication 3) enable students to design, build, and test their own diagnostics and 4) develop entrepreneurial skills. Students learn about tuberculosis from leading experts at UCSF and then address the dearth of sensitive diagnostics by designing and testing their own nano/micro-systems. Taught at UC Merced with tele-conferencing to the other campuses and two field trips. Funded in part by QB3. Normal Letter Grade only. Laboratory included. View course scheduling information
	QSB 220: Cellular Microbiology [3.0 units] Emphasizes the molecular basis of interaction between microbial pathogens (bacteria, viruses and protozoan parasites) and host cells. We also include discussion of the immune response to infection. Student-led presentations and discussion of reading assignments from the current scientific literature. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 223: Human Parasitology [4 units] Covers the biology, parasitism and pathogenesis of parasites that cause significant human disease—the parasitic helminthes and the protozoan parasites. How each parasite establishes infection in their hosts, how it spreads between hosts, and the pathogenesis of disease. Current approaches to control parasitic disease will be addressed. Cutting edge science with a focus on new molecular concepts will be addressed during an additional one hour lecture/discussion session specifically for graduate students. Prerequisite: Quantitative and Systems Biology majors only. Normal Letter Grade only. Discussion Included. View course scheduling information
	QSB 227: Virology [3.0 units] Overview of viruses, focusing on structure, infecting cycle, interactions with host, transmission and methods of detection and control. Discussion included. View course scheduling information
	QSB 241: Advanced Genomic Biology [4.0 units] Comprehensive introduction to the language of genes and genomes, including genotype to phenotype relationships, gene regulation of development and disease, sources of phenotypic variation, and organization of genomes across the domains of life. Graduate requirements include advanced discussion section led by instructor and genome informatics project. View course scheduling information
	QSB 242: Genome Biology [5.0 units] Introduction to the concepts behind genome biology and a detailed overview of the many tools used in comparative genomics. Specific topics include genome assembly, gene modeling and comparative genomics, transcriptomics, and proteomics of prokaryotic and eukaryotic organisms. Students carry out real scientific projects in collaboration with course faculty and produce new genomic data of publishable quality. Mandatory weekly three hour lab is part of this course. Prerequisite: BIO 141 . Normal Letter Grade only. Discussion, Laboratory included. View course scheduling information
	QSB 244: Phylogenetics: Speciation and Macroevolution [4.0 units] Provides the theory behind reconstruction of evolutionary relationships and introduces the comparative methods and tools of phylogenetics. Topics include use of morphological, molecular, and fossil data in distance, parsimony, likelihood, and Bayesian frameworks for investigating geographic patterns and rates of speciation, phenotypic evolution, diversification, extinction, and biogeography. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 244L: Phylogenetics Laboratory: Speciation and Macroevolution [1.0 unit] Practice in reconstruction of evolutionary relationships and introduces the comparative methods and tools of phylogenetics. Topics include morphological, molecular, and fossil data in distance, parsimony, likelihood, and Bayesian frameworks for investigating geographic patterns and rates of speciation, phenotypic evolution, diversification, extinction, and biogeography. Corequisite: QSB 244 . Normal Letter Grade only. Laboratory included. View course scheduling information
	QSB 245: Biogeography [3.0 units] Will explore a diversity of current topics in Biogeography, providing an overview of the field’s history, development, and a prospectus for its near future. We will consider relevant methods, advances in related fields, and application of biogeographic information in a changing world. Normal Letter Grade only. Course may be repeated 3 times for credit. View course scheduling information
	QSB 246: Community Ecology [3.0 units] Will cover major themes and current topics in community ecology, including patterns in the diversity, abundance, and composition of species in communities and the processes underlying these patterns such as environmental filtering, species interactions, evolutionary history, and neutral processes. Knowledge obtained in BIO 148 is strongly suggested. View course scheduling information
	QSB 248: Advanced Topics in Ecology [3.0 units] Course utilizes directed readings and discussion of classical and current literature in ecology, including physiological, population, community, ecosystem, landscape, and global ecology studies. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 249: Topics in the History, Philosophy, and Practice of Science [3.0 units] Explores special topics in the history, philosophy, and practice of science, such as the nature of interdisciplinary interactions, the concept of “paradigm shift”, relationships between politics and science, and the influence of new technologies. Does not fulfill the “third course requirement” of QSB degrees except by petition to QSB EPC. Normal Letter Grade only. Course may be repeated 3 times for credit. View course scheduling information
	QSB 250: Embryos, Genes and Development [3.0 units] Principles of developmental biology as revealed through analysis of invertebrate and vertebrate system. Animal models are used to examine the molecular and cellular mechanisms that influence cell fate. Cell signaling is studied in the context of embryonic pattern formation and the development of body plans and organ systems. Graduate level students read discuss and critique current research papers relevant for the field. Prerequisite: QSB 290 and BIO 110 or equivalent, or consent of instructor. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 251: Advanced Molecular Immunology [4.0 units] This is a comprehensive introduction to advanced principles of immunology. Topics include innate immune defense, immunoglobulin gene rearrangements, antigen presentation, lymphocyte trafficking, regulation of lymphocyte development, lymphocyte activation and effector functions, dendritic cell biology, immune response to infection and diseases of the immune system. Sessions will consist of lectures, student presentations and discussion of seminal and current research articles. Students will also attend a weekly immunology seminar of current research presentations by immunology scientists. View course scheduling information
	QSB 252: Cancer Genetics and Tumor Biology [3.0 units] Topics include viral and hormonal carcinogenesis, molecular aberrations in cancer, tumor development, epigenetic and cancer, tumor immunology, oncogenes. Prerequisite: Quantitative and Systems Biology majors only or consent of instructor. Normal Letter Grade only. View course scheduling information
	QSB 253: Evolution and Development [3.0 units] Compares and contrasts the developmental cues of a variety of animals and emphasizes how conserved developmental pathways have been manipulated through evolutionary processes to produce different physical features. The effects of regulatory region mutations, gene duplication, and genetic co-opting will be investigated. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 261: Human Physiology [3.0 units] Understanding the mechanisms underlying function of major human organs. Emphasis includes neural transmission and action potential, cardiovascular, renal and gastrointestinal physiology, metabolism, and endocrinology. Laboratory experiments demonstrating and reinforcing topics covered in lecture with an emphasis on scientific method. Discussion section critically reads and evaluates papers in physiology and provide an opportunity for the students to practice presenting scientific data to an audience. Normal Letter Grade only. Discussion, Laboratory included. View course scheduling information
	QSB 270: Academic Writing in Graduate Studies [2.0 units] Designed to increase the writing proficiency of graduate students, with a focus on strategies for reading critically, organizing and developing thoughts, choosing appropriate vocabulary, and generating and revising writing in a given scientific field. Topics address scientific disciplines. Projects may include writing abstracts, research reports, literature reviews, posters, and grant proposals. View course scheduling information
	QSB 271: Advanced Neurobiology: Brain Dysfunction and Neurodegenerative Diseases [3.0 units] Teaches in-depth cellular, molecular and genetic based mechanisms of brain dysfunctions by drug abuse, altered neuronal activities, and neurodegenerative diseases. Fundamental neurobiology of the central nervous system, pharmacology/toxicology, biochemistry, anatomy and genetics of the brain will be covered. View course scheduling information
	QSB 280: Advanced Mathematical Biology [3.0 units] Graduate level mathematical modeling and data analysis skills for life science researchers taught through hands-on computational laboratories. Topics include population models, predator-prey and competition systems, epidemic models with applications to sexually transmitted diseases, dynamic diseases, enzyme kinetics, biological oscillators, and switches. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 281: Molecular Dynamics and Biomolecular Simulation [4.0 units] Uses lectures and laboratory exercises to teach the practice of biomolecular modeling. Topics include classical molecular dynamics, molecular mechanics and visualization. The laboratories involve simulations of systems including water, DNA and proteins. The course includes two projects for the students to apply molecular simulation to their graduate research. Normal Letter Grade only. Discussion, Laboratory included. View course scheduling information
	QSB 282: Bioinformatics [5.0 units] Graduate level introduction to tools, algorithms, statistics, and databases used in bioinformatics, emphasizing an open-source, command-line toolbox approach. Topics covered as in BIO 182, plus critical assessment of bioinformatics literature, introduction to Perl, and an independent research project. Mandatory computer laboratory, for which prior programming experience helpful but not assumed. Discussion, Laboratory included. View course scheduling information
	QSB 283: Population Genetics [3.0 units] The various factors that affect gene flow and frequency within a population. Theories of selection, neutrality, drift, hitchhiking, recombination, mutation, isolation, in-breeding, and selfish genetic elements are taught along with statistical tests and experimental methods for detecting these forces. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 289: Research Forums in Quantitative and Systems Biology [3.0 units] Research forums involve cooperative discussions about literature and research led by at least two faculty preferably from different disciplines, giving graduate students practice in engaging in scientific communication, scholarship, interdisciplinary research exchange and identification of open research problems. In a typical week, about one half of contact hours would consist of faculty presentation of key literature around a certain scientific concept or technique, and one half of student presentations of additional literature applying that concept or technique, coverage and integration of diverse scientific literature, and group discussion. Course may be repeated for credit. Discussion included. View course scheduling information
	QSB 290: Current Topics in Quantitative and Systems Biology [3.0 units] Principles and applications of systems and synthetic biology to the investigation and engineering of biological systems of all kinds, from molecules to ecosystems. Coverage of core concepts and techniques with coverage of current literature and connections made to current research in QSB at UC Merced. Group and individual assessments include oral presentation and discussion of literature, interdisciplinary synthesis through written reviews and a final white paper research proposal applying systems and synthetic biology to individual research interests. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 291: Research Forums in Quantitative and Systems Biology [1.0 unit] Seminar series covering current topics in quantitative and system biology presented by visiting speakers chosen by QSB faculty and students with occasional presentations by UC Merced faculty and student members of QSB. Satisfactory/Unsatisfactory only. Course may be repeated for credit. View course scheduling information
	QSB 292: Quantitative and Systems Biology Group Meeting [1.0 unit] Meetings to describe current progress and research plans lead by individual QSBGG faculty. Normal Letter Grade only. Course may be repeated for credit. View course scheduling information
	QSB 293: Quantitative and Systems Biology Journal Club [1.0 unit] Student-led presentation, analysis, and discussion of reading assignments from the scientific literature. Normal Letter Grade only. Course may be repeated for credit. Discussion included. View course scheduling information
	QSB 294: Responsible Conduct of Research [1.0 unit] Seminar covering responsibilities and expectations for researchers as well as advice for success in graduate school and science careers, required for NIH-funded graduate students. Satisfactory/Unsatisfactory only. View course scheduling information
	QSB 295: Graduate Research [1.0-12.0 units] Supervised research. Course may be repeated for credit. Laboratory included. View course scheduling information
	QSB 296: Professional Skills Development [3.0 units] To introduce incoming and continuing graduate students to the art of grantsmanship and effective scientific communication. Will also emphasize manuscript preparation and critique, and oral presentation skill development. Prerequisite: Enrollment priority given to first year School of Natural Sciences graduate group. Priority given to QSB graduate students. Enrollment by students in other SNS graduate groups will be considered. Normal Letter Grade only. Discussion included. View course scheduling information
	QSB 297: Systems Biology: From Molecules to Metabolic Networks [3.0 units] Provides a rigorous introduction to the theories, tools, and applications of systems biology. The course is organized around the biological flow of information known as the central dogma of biology. In essence we translate DNA into RNA and extend this information into metabolic and cellular networks. The course introduces experimental and high throughput approaches for generating large datasets, theory, algorithms, and computational approaches for their analysis. Data for analysis will come from ongoing systems biology projects taking place in the Instructor’s lab (genomics, transcriptomics, proteomics, metabolomics, fluxomics) as well as those of collaborators at UC Merced and other nearby institutions (metagenomics, phosphoproteomics, chenomics). The course may take advantage of presentations by guest lecturers with expertise in one of the many aspects of systems biology, or one of the sciences upon which it crucially depends. Normal Letter Grade only. View course scheduling information
	QSB 298: Directed Group Study [1.0-12.0 units] Group project under faculty supervision. Course may be repeated for credit. Laboratory included. View course scheduling information
	QSB 299: Directed Independent Study [1.0-12.0 units] Independent project under faculty supervision. Course may be repeated for credit. View course scheduling information
	QSB 399: University Teaching [1.0 unit] Centered on a student’s classroom experiences as a Teaching Assistant in an undergraduate Biological Sciences course. Provides a faculty-directed opportunity to implement teaching practices presented in the course Teaching and Learning in the Sciences. Involves video-taping of teaching, peer review, and weekly meetings with faculty. Prerequisite: QSB 201 or MATH 201 are corequisites. Must hold at least a 25%-time appointment as a Teaching Assistant for an undergraduate course in BIO. Satisfactory/Unsatisfactory only. Course may be repeated 1 time for credit. Discussion, Laboratory included. View course scheduling information

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Course Descriptions

QSB 200: Molecular Cell Biology

QSB 200: Molecular Cell Biology

QSB 201: Teaching and Learning in the Sciences

QSB 202: Graduate Level Biochemistry

QSB 207: Physical Biochemistry

QSB 212: Advanced Signal Transduction and Growth Control

QSB 214: Tissue Engineering Design

QSB 215: Principles of Biological Technologies

QSB 217: Lab on a Chip: Developing 3rd World Diagnostics for Global Health

QSB 220: Cellular Microbiology

QSB 223: Human Parasitology

QSB 227: Virology

QSB 241: Advanced Genomic Biology

QSB 242: Genome Biology

QSB 244: Phylogenetics: Speciation and Macroevolution

QSB 244L: Phylogenetics Laboratory: Speciation and Macroevolution

QSB 245: Biogeography

QSB 246: Community Ecology

QSB 248: Advanced Topics in Ecology

QSB 249: Topics in the History, Philosophy, and Practice of Science

QSB 250: Embryos, Genes and Development

QSB 251: Advanced Molecular Immunology

QSB 252: Cancer Genetics and Tumor Biology

QSB 253: Evolution and Development

QSB 261: Human Physiology

QSB 270: Academic Writing in Graduate Studies

QSB 271: Advanced Neurobiology: Brain Dysfunction and Neurodegenerative Diseases

QSB 280: Advanced Mathematical Biology

QSB 281: Molecular Dynamics and Biomolecular Simulation

QSB 282: Bioinformatics

QSB 283: Population Genetics

QSB 289: Research Forums in Quantitative and Systems Biology

QSB 290: Current Topics in Quantitative and Systems Biology

QSB 291: Research Forums in Quantitative and Systems Biology

QSB 292: Quantitative and Systems Biology Group Meeting

QSB 293: Quantitative and Systems Biology Journal Club

QSB 294: Responsible Conduct of Research

QSB 295: Graduate Research

QSB 296: Professional Skills Development

QSB 297: Systems Biology: From Molecules to Metabolic Networks

QSB 298: Directed Group Study

QSB 299: Directed Independent Study

QSB 399: University Teaching