Summer 2008 Course Descriptions

All courses below are approved to be taught in Summer 2008; however, some (or all) may not be offered.  The course numbers that are offered, in either Pre-Session, Summer I or Summer II, are linked to the Schedule of Classes. Classes with alternative delivery modes (Web based, cable TV, correspondence, etc) are noted in the Schedule at the section level.  The complete list below is a good indicator of what may be offered over the next few years (contact department about offerings).  For explanations of course elements see the Key to Course Descriptions.

Genetics (GENE)  Department Info

GENE 400 -- Computer Concepts and Perl Programming  (3 units)
Description:  This course is designed for biology students who have no experience in computer programming. It will cover basics of computers and perl programming. The student will be able to write simple programs, for example, parse files to extract information, reformat files, and summarize the content of a file. This will greatly save time of visually parsing pages of output from such programs as Blast and enable the student to better data mine the massive amounts of data in genomic and biological databases. The student will also learn concepts in computers so that they can easily collaborate with computational researchers and programmers.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  MCB 400; MCB is home department.
May be convened with:  GENE 500.
Usually offered:  Fall.

GENE 416 -- Bioinformatics and Genomic Analysis  (3 units)
Description:  Analysis of genome sequences for function using local and internet computer resources. Consult instructor for appropriate prerequisites before enrolling.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  programming experience.
Identical to:  MCB 416; MCB is home department.
May be convened with:  GENE 516.
Usually offered:  Fall.

GENE 426 -- Population Genetics  (3 units)
Description:  General introductory course on empirical and theoretical population genetics. It will involve two weekly lectures, weekly problem sets, and regular readings from the primary literature. A major goal of this course is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. As much as any field of biology, population genetics has been divided into a theoretical and an empirical branch. However, these two bodies of knowledge are intimately related and this course will cover both in roughly equal amounts. We will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision), methods of measuring genetic variation in nature, and experimental tests of important ideas in population genetics. The course will also cover a few more specialized topics such as transposable elements, the evolution of multigene families, and molecular clocks.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  ECOL 182R, ECOL 182L, ECOL 335; ECOL 320 or PL S 312.
Identical to:  ECOL 426; ECOL is home department.
May be convened with:  GENE 526.
Usually offered:  Spring.

GENE 449A -- Plant Genetics and Genomics  (3 units)
Description:  A 3 unit lecture/discussion course that provides an advanced treatment of the current knowledge and experimental approaches used in genetic and genomic analysis, with emphasis on plants. Basic understanding of Mendelian genetics, gene and genome structure and function is required.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  PL S 312.
Identical to:  PL S 449A; PL S is home department.
May be convened with:  GENE 549A.
Usually offered:  Spring.

GENE 473 -- Recombinant DNA Methods and Applications  (4 units)
Description:  Relevant techniques for the isolation, purification, and cloning of genes in E. Coli hosts. Eukaryotic lambda genomic DNA clones will be characterized by restriction mapping, hybridization analysis, and sequence analysis. Writing emphasis course.  This is a Writing Emphasis Course.
Grading:  Regular grades are awarded for this course: A B C D E.
Special course fee required:  $150.
Prerequisite(s):  satisfaction of the Mid-Career Writing Assessment (MCWA) or the former upper-division writing proficiency requirement (UDWPE); BIOC 460 or BIOC 462A. Concurrent registration, MCB 411.
Typical structure:  6 hours laboratory, 2 hours lecture.
Identical to:  MCB 473; MCB is home department.
May be convened with:  GENE 573.
Usually offered:  Fall, Spring.

GENE 498 -- Senior Capstone  (1-3 units)
Description:  A culminating experience for majors involving a substantive project that demonstrates a synthesis of learning accumulated in the major, including broadly comprehensive knowledge of the discipline and its methodologies. Senior standing required.
Grading:  Regular or alternative grades can be awarded for this course: A B C D E or S P C D E.
Usually offered:  Fall, Spring.

GENE 499 -- Independent Study  (1-6 units)
Description:  Qualified students working on an individual basis with professors who have agreed to supervise such work.
Grading:  Alternative grades are awarded for this course: S P C D E.
Usually offered:  Fall, Spring.

GENE 500 -- Computer Concepts and Perl Programming  (3 units)
Description:  This course is designed for biology students who have no experience in computer programming. It will cover basics of computers and perl programming. The student will be able to write simple programs, for example, parse files to extract information, reformat files, and summarize the content of a file. This will greatly save time of visually parsing pages of output from such programs as Blast and enable the student to better data mine the massive amounts of data in genomic and biological databases. The student will also learn concepts in computers so that they can easily collaborate with computational researchers and programmers. Graduate-level requirements include writing a functional specification that is due at mid-term and at the end of the semester. A functional specification will describe a computational problem that the student wants solved to aid in their biological research.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  MCB 500; MCB is home department.
May be convened with:  GENE 400.
Usually offered:  Fall.

GENE 501 -- Molecular and Medical Genetics  (3 units)
Description:  Acquire a basic understanding of human molecular genetics and learn how to apply that understanding in the pathophysiology of disease.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  PED 501; PED is home department.
Usually offered:  Fall.

GENE 509C -- Statistics for Research  (3 units)
Description:  Statistical concepts and methods applied to research in other scientific disciplines. Principles of estimation and hypothesis testing for standard one-and two-sample procedures. Correlation, linear regression. Contingency tables and analysis of variance.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  MATH 110 or 112.
Identical to:  MATH 509C; MATH is home department.
Usually offered:  Fall, Spring.

GENE 513 -- Statistical Genetics for Quantitative Measures  (3 units)
Description:  This course provide the student with the statistical tools to describe variation in quantitative traits, particularly the decomposition of variation into genetic, environmental, and gene by environment interaction components. Convariance (resemblance) between relatives and heritability will be discussed, along with the topics of epistasis, oligogenic and polygenic traits, complex segregation analysis, methods of mapping quantitative trait loci (QTL), and estimation procedures. Microarrays have multiple uses, each of which will be discussed and the corresponding statistical analyses described.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  A course on basic genetic principles such as AN S 213, GENE 433, GENE 533, or GENE 545 and a current course on basic statistical principles such as GENE 509C or MATH 509C. A course in linear models MATH 561 and a course in statistical inference Math
Identical to:  AN S 513; AN S is home department.
Usually offered:  Fall.

GENE 516 -- Bioinformatics and Genomic Analysis  (3 units)
Description:  Analysis of genome sequences for function using local and internet computer resources. Consult instructor for appropriate prerequisites before enrolling. Graduate-level requirement include a research project, written report, and a class presentation.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  MCB 500.
Identical to:  MCB 516; MCB is home department.
May be convened with:  GENE 416.
Usually offered:  Fall.

GENE 522 -- History of Genetics  (2 units)
Description:  Discoveries which have led to the present state of knowledge in the various areas of genetics and related disciplines, with particular attention to the context of the time periods in which they were made.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  Undergraduate biology or genetics course, or consent of instructor.
Identical to:  ANTH 522, ECOL 522.
Usually offered:  Fall.

GENE 525 -- Speciation  (2 units)
Description:  [Taught alternate years 1999 - 2000] Mechanisms of evolution in the formation of races and species of animals and plants.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  ECOL 320.
May be repeated:  for credit 1 time (maximum 2 enrollments).
Identical to:  ECOL 525; ECOL is home department.
Usually offered:  Spring.

GENE 526 -- Population Genetics  (3 units)
Description:  General introductory course on empirical and theoretical population genetics. It will involve two weekly lectures, weekly problem sets, and regular readings from the primary literature. A major goal of this course is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. As much as any field of biology, population genetics has been divided into a theoretical and an empirical branch. However, these two bodies of knowledge are intimately related and this course will cover both in roughly equal amounts. We will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision), methods of measuring genetic variation in nature, and experimental tests of important ideas in population genetics. The course will also cover a few more specialized topics such as transposable elements, the evolution of multigene families, and molecular clocks. Graduate-level requirements include additional exam questions, additional readings from the literature, and presentation of a 15 minute overview and synthesis of a specialized topic in population genetics.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  ECOL 526; ECOL is home department.
May be convened with:  GENE 426.
Usually offered:  Spring.

GENE 530 -- Conservation Genetics  (3 units)
Description:  Basic methods and theories of genetic analyses, application of these principles to promote conservation and long term survival of free-ranging species, and exploration of current conservation genetic literature.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  ECOL 320, PL S 312, basic genetics class, or consent of instructor.
Identical to:  RNR 530; RNR is home department.
Usually offered:  Fall.

GENE 533 -- Human Genetics  (3 units)
Description:  Basic genetic theory and techniques, as applied to the human species; methods of analysis of genetic and environmental variation among individuals and populations.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  ANTH 533, ECOL 533, MCB 533.
Usually offered:  Fall.

GENE 549A -- Plant Genetics and Genomics  (3 units)
Description:  A 3 unit lecture/discussion course that provides an advanced treatment of the current knowledge and experimental approaches used in genetic and genomic analysis, with emphasis on plants. Basic understanding of Mendelian genetics, gene and genome structure and function is required. Graduate-level requirements include leading 3 course discussions on review articles and problem sets and write a paper based on each of the three research discussions that they lead.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  PL S 549A; PL S is home department.
May be convened with:  GENE 449A.
Usually offered:  Spring.

GENE 568 -- Nucleic Acids  (4 units)
Description:  Chemistry, structure, and function of nucleic acids; replication, transcription translation, gene organization, regulation of gene expression and organelle nucleic acids. Both procaryotic and eucaryotic systems will be considered.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  BIOC 411 or consent of instructor.
Identical to:  BIOC 568; BIOC is home department.
Usually offered:  Fall.

GENE 570 -- Molecular Genetics  (3 units)
Description:  Molecular genetics and biology of microorganisms, and the application of principles derived from microorganisms to major unsolved problems in medicine, such as the primary causes of aging and cancer. Specific topics include the molecular biology of bacterial viruses, the mechanisms of DNA replication, DNA repair, mutation and genetic recombination. Other topics are the evolution of sexual reproduction, the role of DNA damage and repair in aging, and the role of DNA damage, mutation and apoptosis in progression to cancer.
Grading:  Regular grades are awarded for this course: A B C D E.
Identical to:  CBA 570; CBA is home department.
Usually offered:  Fall.

GENE 573 -- Recombinant DNA Methods and Applications  (4 units)
Description:  Relevant techniques for the isolation, purification, and cloning of genes in E. Coli hosts. Eukaryotic lambda genomic DNA clones will be characterized by restriction mapping, hybridization analysis, and sequence analysis. Writing emphasis course. Graduate-level requirements include a one hour discussion section of classic and recent papers featuring major advances in molecular biology or their application to current issues or problems.
Grading:  Regular grades are awarded for this course: A B C D E.
Special course fee required:  $150.
Typical structure:  6 hours laboratory, 2 hours lecture.
Identical to:  MCB 573; MCB is home department.
May be convened with:  GENE 473.
Usually offered:  Fall, Spring.

GENE 589 -- Cancer Genetics  (3 units)
Description:  Understanding of correlations of molecular biology/chromosomal change in human cancer and the role of genetic change in progression and metastasis of cancer.
Grading:  Regular grades are awarded for this course: A B C D E.
Prerequisite(s):  ECOL 320, MCB 320.
May be repeated:  for credit 1 time (maximum 2 enrollments).
Identical to:  CBIO 589; CBIO is home department.
Usually offered:  Fall.

GENE 594 -- Practicum  (1-3 units)
Description:  The practical application, on an individual basis, of previously studied theory and the collection of data for future theoretical interpretation.
Grading:  Alternative grades are awarded for this course: S P C D E.
Usually offered:  Fall, Spring, Summer.

GENE 595H -- Problems in the Biology of Complex Diseases  (2 units)
Description:  Complex diseases (CDs: e.g., asthma, allergy, COPD, obesity, inflammatory bowel disease, hypertension, coronary artery disease, diabetes, rheumatoid arthritis, multiple sclerosis, schizophrenia) are the next major challenge in human biology because they are at the same time unique, common and difficult to decipher. The complexity of CDs lies in their pathogenesis, in which a constellation of environmental and genetic factors interact in intricate ways to alter biological thresholds and response patterns, modifying disease susceptibility. Since both genes and environmental exposures contribute to CDs, the biological pathways involved in CD pathogenesis depend on the genetic background of a given population and the specific environment to which that population is exposed. Hence, asthma, obesity and hypertension in Arizona may not be the same as asthma, obesity and hypertension in Iceland.
Grading:  Regular or alternative grades can be awarded for this course: A B C D E or S P C D E.
Identical to:  CBA 595H; CBA is home department.
Usually offered:  Spring.

GENE 599 -- Independent Study  (1-6 units)
Description:  Qualified students working on an individual basis with professors who have agreed to supervise such work. Graduate students doing independent work which cannot be classified as actual research will register for credit under course number 599, 699, or 799.
Grading:  Alternative grades are awarded for this course: S P C D E.
Usually offered:  Fall, Spring.

GENE 670 -- Recent Advances in Genetics  (2 units)
Description:  Recent advances in the field of genetics.
Grading:  Regular grades are awarded for this course: A B C D E.
May be repeated:  for credit 4 times (maximum 5 enrollments).
Identical to:  ECOL 670.
Usually offered:  Fall.

GENE 695D -- Human Genetic Disease Colloquium  (3 units)
Description:  The course will cover a few medical genetic disorders in depth, with different topics each year. Clinical presentation, pathophysiology, genetic mechanisms and biochemical features will be considered. Readings will come mainly from the primary biomedical literature.
Grading:  Regular or alternative grades can be awarded for this course: A B C D E or S P C D E.
May be repeated:  for credit 3 times (maximum 4 enrollments).
Usually offered:  Fall.

GENE 695E -- Science, Society, and Ethics  (1 unit)
Description:  Practical colloquium focusing on ethical issues raised in the research laboratory setting.
Grading:  Regular or alternative grades can be awarded for this course: A B C D E or S P C D E.
Identical to:  MCB 695E; MCB is home department.
Usually offered:  Spring.

GENE 699 -- Independent Study  (1-4 units)
Description:  Qualified students working on an individual basis with professors who have agreed to supervise such work. Graduate students doing independent work which cannot be classified as actual research will register for credit under course number 599, 699, or 799.
Grading:  Alternative grades are awarded for this course: S P C D E.
May be repeated:  an unlimited number of times, consult your department for details and possible restrictions.
Usually offered:  Fall, Spring, Summer.

GENE 795A -- Laboratory Research Rotation  (1-3 units)
Description:  Students are exposed to research areas in Genetics and potential advisors. Brief report of rotation accomplishments must be submitted with faculty's signature at end of each rotation. Minimum 45 contact hours required for each credit unit.
Grading:  Regular or alternative grades can be awarded for this course: A B C D E or S P C D E.
Prerequisite(s):  Limited to Genetics major and minor graduate students.
May be repeated:  for a total of 12 units of credit.
Usually offered:  Fall, Spring.

GENE 900 -- Research  (1-8 units)
Description:  Individual research, not related to thesis or dissertation preparation, by graduate students.
Grading:  Alternative grades are awarded for this course: S P C D E K.
May be repeated:  an unlimited number of times, consult your department for details and possible restrictions.
Usually offered:  Fall, Spring, Summer.

GENE 910 -- Thesis  (1-8 units)
Description:  Research for the master's thesis (whether library research, laboratory or field observation or research, artistic creation, or thesis writing). Maximum total credit permitted varies with the major department.
Grading:  Alternative grades are awarded for this course: S P E K.
May be repeated:  an unlimited number of times, consult your department for details and possible restrictions.
Usually offered:  Fall, Spring, Summer.

GENE 920 -- Dissertation  (1-9 units)
Description:  Research for the doctoral dissertation (whether library research, laboratory or field observation or research, artistic creation, or dissertation writing).
Grading:  Alternative grades are awarded for this course: S P E K.
May be repeated:  an unlimited number of times, consult your department for details and possible restrictions.
Usually offered:  Fall, Spring, Summer.

GENE 930 -- Supplementary Registration  (1-9 units)
Description:  For students who have completed all course requirements for their advanced degree programs. May be used concurrently with other enrollments to bring to total number of units to the required minimum.
Grading:  Grade of K is awarded for this course except for the final term.
May be repeated:  an unlimited number of times, consult your department for details and possible restrictions.
Usually offered:  Fall, Spring, Summer.