Genetics LabGenetics LabDr. Jeff Young young@biol.wwu.edu Dr. Jeff Young young@biol.wwu.edu Office Hours: BI 412 MR 10 - 11 am or by appointmentOffice Hours: BI 412 MR 10 - 11 am or by appointmentLecture: T 11 – 11:50 pm in AW410Lecture: T 11 – 11:50 pm in AW410Lab: WF 1:30 – 3:30 pm in BI454Lab: WF 1:30 – 3:30 pm in BI454

Course GoalsCourse Goals

Content goalsContent goals: :

i.i. You should understand and be able to apply classical genetic and You should understand and be able to apply classical genetic and molecular genetic principles in a laboratory setting. Specifically, molecular genetic principles in a laboratory setting. Specifically, you should obtain a reasonably sophisticated understanding of you should obtain a reasonably sophisticated understanding of several major aspects of genetics, including Mendelian Genetics, several major aspects of genetics, including Mendelian Genetics, prokaryotic genetics, and select approaches in molecular prokaryotic genetics, and select approaches in molecular genetics. genetics.

ii.ii. You should acquire skills in handling model organisms, keeping You should acquire skills in handling model organisms, keeping detailed research records, analyzing data and writing scientific detailed research records, analyzing data and writing scientific reports.reports.

  Process goalsProcess goals: :

i.i. You should improve your critical thinking skills through the You should improve your critical thinking skills through the analysis of experimental data. analysis of experimental data.

ii.ii. You should improve your quantitative reasoning skills. You should improve your quantitative reasoning skills.

iii.iii. You should improve your written communication skills.You should improve your written communication skills.

Lab NotebookLab Notebook

Texts/Lab Manual/etc.Texts/Lab Manual/etc.None.None.Hand outs…also posted, Hand outs…also posted, http://www.biol.wwu.edu/young/322/http://www.biol.wwu.edu/young/322/Genetics texts on reserve.Genetics texts on reserve.

Attendance is mandatory. Attendance is mandatory.

EvaluationEvaluation

Notebooks Notebooks 40 points total,40 points total, 1 pt/lab, pre-lab hand in 1 pt/lab, pre-lab hand in 

Lab Behavior Lab Behavior 30 points 30 points

Formal Lab Write-upsFormal Lab Write-ups 50 50 pts. pts. 

Mid Term and FinalMid Term and Final 50 pts. 50 pts. (each) (each) 

Pop quizzes and other Pop quizzes and other assignmentsassignments 30 pts.  30 pts. 

Approximate Grading Approximate Grading ScaleScale

225-250 points A225-250 points A 200-224 points B200-224 points B 175-199 points C175-199 points C 150-174 points D150-174 points D Below 150 points FBelow 150 points F

Schedule*Schedule*

*Subject to Change*Subject to Change

Mendel Mendel RevisitedRevisited

C. elegansC. elegans is a nematode, phyllum Nematoda. is a nematode, phyllum Nematoda. Nematodes can be free-living or parasitic and Nematodes can be free-living or parasitic and can be found in terrestrial or aquatic habitats. can be found in terrestrial or aquatic habitats.   

BacteriovorousBacteriovorous: in the lab, : in the lab, C. elegans C. elegans is fed on is fed on E. coliE. coli. . 

Self-fertilizingSelf-fertilizing: adult : adult C. elegans C. elegans are usually are usually self-fertilizing protandrous hermaphrodites. Thus self-fertilizing protandrous hermaphrodites. Thus it is easy to generate homozygous mutant it is easy to generate homozygous mutant stocks.  stocks.  

The lifecycle takes about 2.5 days at 25The lifecycle takes about 2.5 days at 2500 C C  

C. elegans C. elegans is diploid and has five pairs of is diploid and has five pairs of autosomes (named I, II, III, IV and V) and sex autosomes (named I, II, III, IV and V) and sex chromosome(s) (X). chromosome(s) (X). 

Gender is determined by an XX (hermaphrodite) - Gender is determined by an XX (hermaphrodite) - XO (male) chromosomal system .XO (male) chromosomal system .

Males are found rarely (about 0.05% of normal Males are found rarely (about 0.05% of normal lab populations).  lab populations).  

The commonest lab strain, and the designated The commonest lab strain, and the designated "wild type" strain, is called N2. "wild type" strain, is called N2. 

Hermaphrodites have exactly 959 cells, each cell Hermaphrodites have exactly 959 cells, each cell derived in an exact and invariable manner. derived in an exact and invariable manner. 

Males have 1031 cells.Males have 1031 cells.

Caenorhabditis elegansCaenorhabditis elegans

A small, free-living A small, free-living bacteriovorous soil bacteriovorous soil

nematode.nematode.

Parts

Cell FateCell Fate

C. elegans C. elegans GenomeGenome

The The C. elegansC. elegans genome is genome is spread across six spread across six approximately equally approximately equally sized chromosomes (5 sized chromosomes (5 autosomes, one (or two) autosomes, one (or two) X).X).  

The genome size is 97 The genome size is 97 Megabases (Mb) Megabases (Mb) 

The genomes of other The genomes of other nematodes are in the same nematodes are in the same range. range. Brugia malayiBrugia malayi, a , a filarial parasite of humans, filarial parasite of humans, has a genome of 100 Mb. has a genome of 100 Mb.   

The AT content is 60%. The AT content is 60%. 

The genome is The genome is sequenced. sequenced.

C. elegans C. elegans NomenclatureNomenclature

Tower of Babel

MakingMaking CrossesCrosses

C. elegansC. elegans is usually a is usually a self-self-fertilizingfertilizing hermaphrodite. hermaphrodite. However,However, it is possible to set up it is possible to set up genetic crosses…genetic crosses…

C. elegansC. elegans (0.05%) males are (0.05%) males are found in natural, or wildtype found in natural, or wildtype populations populations  they develop after accidental non-they develop after accidental non-

disjunction of the X chromosomes disjunction of the X chromosomes in gametogenesis (males are XO), in gametogenesis (males are XO), 

the rate of non-disjunction can be the rate of non-disjunction can be increased by exposing a increased by exposing a population of hermaphrodites to population of hermaphrodites to heat shock (30 deg. C for >6 hrs), heat shock (30 deg. C for >6 hrs), 

Male sperm out-competes Male sperm out-competes hermaphrodite sperm,hermaphrodite sperm, ””male lines" can be propagated male lines" can be propagated

indefinitely by picking individual indefinitely by picking individual males and hermaphrodites males and hermaphrodites 

himhim strains, mutant lines that strains, mutant lines that yield high frequencies of males.yield high frequencies of males.

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

WtWt uncunc dpydpy

LabLab Life CyclesLife Cycles

~25 oC

Following Following ProtocolsProtocols

Keep track of steps, Keep track of steps, regardless of who is doing regardless of who is doing

the work.the work.

If something needs done, If something needs done, make sure someone does make sure someone does

it;it;

-might be JY,might be JY,-might be lab mate, might be lab mate,

-might be you.might be you.

Friday

Wednesday

Friday

Diagram CrossDiagram Crossdue Thursday, in Notebook…due Thursday, in Notebook…

P:P: N2 X N2 X unc-32; dpy-unc-32; dpy-1111

F1: Genotype(s), RatioF1: Genotype(s), Ratio

F2: Genotype(s), RatioF2: Genotype(s), Ratio

Save Room for the next Save Room for the next assignment:assignment:

F3 generation, from F3 generation, from wt wt phenotype F2sphenotype F2s. .

Tails

Movements~Size

BioinformaticsBioinformaticsWeds., Introduction to BioinformaticsWeds., Introduction to BioinformaticsRoom CF 26, 1:30 – 3:20 pmRoom CF 26, 1:30 – 3:20 pm