Genetics LabGenetics LabDr. Jeff Young [email protected] Dr. Jeff Young [email protected] Office Hours: BI 412 MWT 10 - 11 am or by appointmentOffice Hours: BI 412 MWT 10 - 11 am or by appointmentLecture: T 11 – 11:50 pm in ES410Lecture: T 11 – 11:50 pm in ES410Lab: WF 1:30 - 4:30 pm in BI454Lab: WF 1:30 - 4:30 pm in BI454
Course GoalsCourse Goals
Content goalsContent goals: : i.i. You should understand and be able to apply classical You should understand and be able to apply classical
genetic and molecular genetic principles in a laboratory genetic and molecular genetic principles in a laboratory setting. Specifically, you should obtain a reasonably setting. Specifically, you should obtain a reasonably sophisticated understanding of several major aspects of sophisticated understanding of several major aspects of genetics, including Mendelian Genetics, prokaryotic genetics, including Mendelian Genetics, prokaryotic genetics, and molecular genetics. genetics, and molecular genetics.
ii.ii. You should acquire skills in handling model organisms, You should acquire skills in handling model organisms, keeping detailed research records, analyzing data and keeping detailed research records, analyzing data and writing scientific reports.writing scientific 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.
EvaluationEvaluation
Notebooks Notebooks 40 points total40 points total
Lab Behavior Lab Behavior 30 points 30 points
Formal Lab Write-upsFormal Lab Write-ups 100 100 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
270-300 points A270-300 points A
240-269 points B240-269 points B
210-239 points C210-239 points C
180-209 points D180-209 points D
Below 180 points FBelow 180 points F
ScheduleSchedule
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 chromosomes (named I, II, III, IV and V) and sex chromosomes (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
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 X).autosomes, one 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 they develop after accidental
non-disjunction of the X non-disjunction of the X chromosomes in gametogenesis chromosomes in gametogenesis (males are XO (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
Diagram CrossDiagram Crossdue Friday, in Notebook…due Friday, 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 wt F3 generation, from wt phenotype F2s. phenotype F2s.
Tails
Movements~Size
BioinformaticsBioinformaticsWednesday, Introduction to BioinformaticsWednesday, Introduction to Bioinformatics
