1. Genetics Lab Dr. Jeff Young young@biol.wwu.edu Office Hours: BI 412 MWT 10 - 11 am or by appointment Lecture: T 11 – 11:50 pm in ES410 Lab: WF 1:30 - 4:30 pm in BI454

2. Course Goals Content goals : Content goals : i.You should understand and be able to apply classical genetic and molecular genetic principles in a laboratory setting. Specifically, you should obtain a reasonably sophisticated understanding of several major aspects of genetics, including Mendelian Genetics, prokaryotic genetics, and molecular genetics. ii.You should acquire skills in handling model organisms, keeping detailed research records, analyzing data and writing scientific reports. Process goals : Process goals : i.You should improve your critical thinking skills through the analysis of experimental data. ii.You should improve your quantitative reasoning skills. iii.You should improve your written communication skills.

3. Lab Notebook Will be used to record your activities and observations during each laboratory period… Will be used to record your activities and observations during each laboratory period… with numbered pages, with numbered pages, with table of contents, with table of contents, organize your notebook by experiment and not by class period. organize your notebook by experiment and not by class period. Prepare and hand in an abstract of the day’s work. Prepare and hand in an abstract of the day’s work. Work up and analyze your data as soon as you've completed the experiment and while it is still fresh in your mind. Work up and analyze your data as soon as you've completed the experiment and while it is still fresh in your mind.

4. Texts/Lab Manual/etc. None. Hand outs (also posted). Genetics texts on reserve. Attendance is mandatory.

5. Evaluation Notebooks 40 points total Notebooks 40 points total Lab Behavior 30 points Lab Behavior 30 points Formal Lab Write-ups 100 pts. Formal Lab Write-ups 100 pts. Mid Term and Final 50 pts. (each) Mid Term and Final 50 pts. (each) Pop quizzes and other assignments 30 pts. Pop quizzes and other assignments 30 pts. Approximate Grading Scale Approximate Grading Scale 270-300 points A 240-269 points B 210-239 points C 180-209 points D Below 180 points F

6. Schedule

7. Mendel Revisited C. elegans is a nematode, phyllum Nematoda. Nematodes can be free-living or parasitic and can be found in terrestrial or aquatic habitats. C. elegans is a nematode, phyllum Nematoda. Nematodes can be free-living or parasitic and can be found in terrestrial or aquatic habitats. Bacteriovorous : in the lab, C. elegans is fed on E. coli. Bacteriovorous : in the lab, C. elegans is fed on E. coli. Self-fertilizing : adult C. elegans are usually self- fertilizing protandrous hermaphrodites. Thus it is easy to generate homozygous mutant stocks. Self-fertilizing : adult C. elegans are usually self- fertilizing protandrous hermaphrodites. Thus it is easy to generate homozygous mutant stocks. The lifecycle takes about 2.5 days at 25 0 C The lifecycle takes about 2.5 days at 25 0 C C. elegans is diploid and has five pairs of chromosomes (named I, II, III, IV and V) and sex chromosome(s) (X). C. elegans is diploid and has five pairs of chromosomes (named I, II, III, IV and V) and sex chromosome(s) (X). Gender is determined by an XX (hermaphrodite) - XO (male) chromosomal system. Gender is determined by an XX (hermaphrodite) - XO (male) chromosomal system. Males are found rarely (about 0.05% of normal lab populations). Males are found rarely (about 0.05% of normal lab populations). The commonest lab strain, and the designated "wild type" strain, is called N2. The commonest lab strain, and the designated "wild type" strain, is called N2. Hermaphrodites have exactly 959 cells, each cell derived in an exact and invariable manner. Hermaphrodites have exactly 959 cells, each cell derived in an exact and invariable manner. Males have 1031 cells. Males have 1031 cells. Caenorhabditis elegans A small, free-living bacteriovorous soil nematode. Parts

8. C. elegans Genome The C. elegans genome is spread across six approximately equally sized chromosomes (5 autosomes, one X). The C. elegans genome is spread across six approximately equally sized chromosomes (5 autosomes, one X). The genome size is 97 Megabases (Mb) The genome size is 97 Megabases (Mb) The genomes of other nematodes are in the same range. Brugia malayi, a filarial parasite of humans, has a genome of 100 Mb. The genomes of other nematodes are in the same range. Brugia malayi, a filarial parasite of humans, has a genome of 100 Mb. The AT content is 60%. The AT content is 60%. The genome is sequenced. The genome is sequenced.

9. C. elegans Nomenclature Tower of Babel

10. Making Crosses C. elegans is usually a self-fertilizing hermaphrodite. However, it is possible to set up genetic crosses… C. elegans is usually a self-fertilizing hermaphrodite. However, it is possible to set up genetic crosses… C. elegans (0.05%) males are found in natural, or wildtype populations C. elegans (0.05%) males are found in natural, or wildtype populations they develop after accidental non- disjunction of the X chromosomes in gametogenesis (males are XO they develop after accidental non- disjunction of the X chromosomes in gametogenesis (males are XO the rate of non-disjunction can be increased by exposing a population of hermaphrodites to heat shock (30 deg. C for >6 hrs) the rate of non-disjunction can be increased by exposing a population of hermaphrodites to heat shock (30 deg. C for >6 hrs) Male sperm out-competes hermaphrodite sperm, Male sperm out-competes hermaphrodite sperm, ”male lines" can be propagated indefinitely by picking individual males and hermaphrodites ”male lines" can be propagated indefinitely by picking individual males and hermaphrodites him strains, mutant lines that yield high frequencies of males. him strains, mutant lines that yield high frequencies of males.

11. Wt (N2) X unc-32; dpy-11 Wtuncdpy

12. Lab Life Cycles

13. Diagram Cross due Friday, in Notebook… P: N2 X unc-32; dpy-11 F1: Genotype(s), Ratio F2: Genotype(s), Ratio Save Room for the next assignment: F3 generation, from wt phenotype F2s. Tails Movements ~Size

14. Bioinformatics Wednesday, Introduction to Bioinformatics