27 September 2004
Introduction to Course
participation in the course
Start chapter 1
Yes, recitations this week; will complete chapter 1 in recitation
Why study genetics?
relationship to other fields of study
current events
possible explanation for human behavior
helpful for AMCAT, DAT, etc. studies
possible career
Introduction to the course
Course structure .... WorkbookLogo.gif
Why lecture?
direct and personal communication
learning by oral presentation
new items in literature (items from my mailbox)
some interaction
My problems with answering questions - no time for detailed discussions- problem with stress, need to discuss topics.
Why recitation?
direct and personal communication
quizzes (problem with Wednesday quizzes)
lots of interaction
ask questions
time for answers
may be that we have most learning during recitation
What is on the web?
Bi341Home Page
Lecture outlines (posted after lectures)
tentative lecture outlines to be updated..use caution
all non copyrighted graphics to date
other items of course information
The web in this course is a supplement, a way of distributing materials.
Printing; it is not necessary to print all of the web materials; outline may be printed at 70% or less.
Caution!: There is a lot of information on the web; it can be a waste of time. Learn genetics first.
Problem with using all computer materials
Workbook
Simplistic exercises to help you learn genetics.
two copies on reserve in library
SmartCopy (1915 SW 6th Ave)
Review Syllabus
Exams
Problem with first exam
Start working on the course early, get a good grade on the first exam!
you are in trouble if you fall behind
Communication with me
Before and after class
During recitation
the Basket - usually answered next lecture session
e-mail - usually answered same day M-F, sometimes Saturday
Office hours: Monday 1-2, Thursday 1-2; Room 416 Science-2
You may set up study groups after lecture today; people interested may gather in the front of the lecture hall.
Yes, recitations meet this week; Wednesday and Thursday.
Of great importance for the course: We have a population with a lot of variation regarding interest in genetics, speed of learning, amount of time which may be devoted to this course, university majors, jobs, etc.
Some of the majors which have been represented are: Biology, chemistry, woman's studies, anthropology, accounting, environmental sciences, engineering, administration of justice, theater arts, computer science, english, and health education.
Some of the goals students have: medicine and related fields, botany, zoology, academics, business, arts, citizens
Questions about the course?
Meet after class to establish study groups
Some graphics used in lecture are not on the web; they are copyrighted.
Best to use plain text when e-mailing, due to problem of viruses/etc.
Some other introductory materials
transmission / molecular / population genetics (text: pages 1; 6-7)
eukaryotes / prokaryotes (text: pages 1; 9-12)
genetics in society / medicine / biology
PKU: 1/13,000 births; "In 1961, Oregon developed the world's first system to screen all newborns for PKU" "For every dollar spent testing for PKU and hypothyroidism, $4 of costs are saved....."
Eugenics - (Galton 1883; "..the study of agencies under social control that may improve or impair the hereditary qualities of future generations of man..." Rieger, Michaelis and Green 1976. Glossary of Genetics and Cytogenetics Springer-Verlag)
influence of WW-2
influence of Francis Galton (Darwin's cousin) and the eugenics movement.
Eugenics site from Cold Spring Harbor Laboratory
http://www.eugenicsarchive.org/eugenics/
New book: The Unfit: A History of a Bad Idea ....By Elof Axel Carlson
Some introductory ideas (not in text or scattered in text)
variation, gene / environmental interactions
variation, continuous / discontinuous
genotype / phenotype; use of term partial
phenotype - the appearance of the organism, as purple flower color
genotype - the gene symbols used to represent the individual
will give an A for turning in your complete genotype
norm of reaction
norm of reaction range of phenotypic variation for a single genotype in different environments .. (see pages 92; 491-492)
Example: Achillea millefolium work of Clausen, Keck and Hiesey, 1958
Developmental Plasticity - review of book in American Scientist Jan-Feb 2004 not on web
../../Other%20Graphics/DevPlasticity.gif
Major topic of chapter 1 is cellular reproduction in eukaryotes: Mitosis and meiosis
Chromosome complement of eukaryotes
Generally see chromosomes during stages of mitosis and meiosis
mitosis - chromosome number remains constant
meiosis - chromosome number reduced by one half
expansion and contraction of chromosome from nucleosome structure to mitotic metaphase chromosome: pop bead example
This relates to Figure 8.19 and figures 8.17 - 8.22; we will discuss this in detail later in the course.
Figure 8.22 (not on web) ....../../Other%20Graphics/8x22.gif
29 September 2004
We will complete most of chapter 1 in recitation this week
Some basic observations
a lot of genetics is developed from model organisms like yeast, E. coli, Drosophila, humans.....
We deal a lot with models - cartoons -; we must realize the difference between models and reality.
Most items studied are super complicated and they may differ between model organisms.
Some conclusions turn out to be wrong
Again, we observe chromosomes generally during stages of mitosis and meiosis
Kinds of chromosomes
"ordinary" chromosomes (mitotic, most meiotic)
giant chromosomes
polytene example 1; example 2; in somatic cells, many stranded chromosomes, somatically paired, banded
lampbrush (meiotic)- mostly seen in oocytes, largest about 1 mm long in amphibians
For the present discussions we will consider "ordinary chromosomes"
Chromosome anatomy series ..... ../ChromAtanomy.html
../CentromereLocation.GIF
../chromosomeTid.GIF
../ChromosomeAnatomy.GIF
../chromosomeTid3.gif
Mitosis
cell cycle (Text figure 1.14).... 1.14.gif (in text, not web)
brief article about Howard and Pelc,1953 .... Nature 426: 759 18/25 Dec 03
replicated and unreplicated chromosomes
stages of mitosis
../mitosis.gif
Examples from the plant Vicia faba (broad bean, fava bean):
Photomicrographs of mitosis in Vicia ...../MitosisSequence2.html
metaphase, anaphase, telophase; metaphase; anaphase; metaphase (colchicine); metaphase (colchicine)
blood lily phase contrast movie not on our web server... mitosislily.mov
But, you may get it at: http://www.unc.edu/depts/salmlab/mitosis/Bloodlily.mov
Home made animation of mitosis .... mitosis animation
Concept of check points for control of mitosis - page 194 in text
Concept of the karyotype ....Karyotype ("The entire chromosome complement of an individual or cell, as seen during mitotic metaphase" from Griffith (6 ed) text p. 869) And added to the definition: chromosomes cut out and arranged in a standard format)
some of the important items in the technique:
phytohemagglutinin stimulates mitosis of some white blood cells
colcemid (colchicine) inhibits spindle formation
fixative kills cells, Giemsa stain colors chromosome
1 October 2004
recitations crowed; space in Wednesday evening, Thursday morning
complete chapter 1 quickly (we did most of this in recitation) and on to chapter 2
Examples of karyotypes
MitoticSpread from the web.. MitoticSpread.gif
Rob's karyotype reduced.... rob1reduced.JPG
Rob's karyotype large ....rob1.JPG
Newman's chromosomes... NewmanChroms.GIF
Part of the report on my chromosomes (not on the web.....).. KaryoReport.GIF
From the karyotype we may learn concepts of:
term: set of chromosomes
haploid/diploid
homologous chromosomes
sex chromosomes/autosomes
Meiosis
overview
Why study meiosis?
basis of Mendelian genetics
we are the products of meiosis
how does the reduction in chromosome number occur?
Premeiotic interphase; G1, S, G2
details of meiosis
Outline of stages....... MeiosisStages.GIF
Diagrams of meiosis...DiagramsMeiosis.html
meiosis sequence.... ../MeiosisSequence.html
Stage descriptions; each stage defined by a few words
A simple animation of meiosis (in need of repair).
Idea of difference between reality (that seen under microscope) and models. Example... pachytene1.GIF
Chiasma, chiasmata
Metaphase-I bivalent
Interesting question: Why the bivalent? In some organisms we even have bivalents if there is no crossing over and therefore no chiasmata (example males in Drosophila melanogaster)
word: bivalent given as tetrad in text
Importance of the bivalent
Models and reality, again......models and reality
Special Features of meiosis
1) crossing-over
2) Synaptonemal complex (mentioned page 19 in text)
Electron micrograph on
the web:
http://www.utexas.edu/courses/zoo325/syncomp.htm
not on the web.... synaptonemal complex 3.gif
model: ...synaptonemalComplex5.gif
3) Question of pairing of X and Y chromosomes in humans
X and Y chromosomes were once identical
Now only small portions are homologous - the pseudoautosomal regions (PAR)]
Pseudoautosomal X-Y.gif
4) Random alignment of bivalents at metaphase-I plate
Figure 1.23
over 4 million combinations
Chromosomes assorted independently into the gametes
5) Segregation and Independent Assortment of chromosomes
demonstrated by use of heteromorphic pairs of chromosomes
X and Y chromosomes
addition of heterochromatin to one homologue
6) Pairing and synapsis
bouquet arrangement at interface between leptotene and zygotene
example: Salemander meiosis not on web .... ../boquet.gif
Zickler, D. and N. Kleckner (1998). "The leptotene-zygotene transition of meiosis." Annu Rev Genet 32: 619-97.
difference between pairing and synapsis
recent paper on phs1 gene; poor homologous synapsis
"the phs1 gene is required for pairing
to occur between homologous chromosomes. In the phs1 mutant, homologous
chromosome synapsis is completely replaced by synapsis between nonhomologous
partners." "Thus, in the phs1 mutant, synapsis is uncoupled from
recombination and pairing. The protein encoded by the phs1 gene
likely acts in a multistep process to coordinate pairing, recombination,
and synapsis." Pawlowski, W. P., I. N. Golubovskaya, et al. (2004).
"Coordination of meiotic recombination, pairing, and synapsis by PHS1."
Science 303(5654): 89-92
Gene leads to non-homologous pairing, lack of chiasmata
and non-disjunction
Other mutations cause telomere-misplacement. Bass, H. W., S. J. Bordoli, et al. (2003). "The desynaptic (dy) and desynaptic1 (dsy1) mutations in maize (Zea mays L) cause distinct telomere-misplacement phenotypes during meiotic prophase." J Exp Bot 54(380): 39-46.
Differences between text and my materials (lecture and web)
Crossing over begins in leptotene or earlier but is complete at pachytene. Some references say that crossing over occurs during pachytene.
We see chiasmata for the first time at diplotene with the light microscope.
Text has pairing at leptotene. This is a loose pairing which differs from the tight pairing of zygotene (synapsis). In our discussion we use the term pairing to be of the tight variety; that which we can see with the light microscope.
The bivalents continue to shorten from pachytene through diakinesis.
Figure 1.21 showing chiasmata is terrible; looks like mitotic chromosomes - http://www.irn.pdx.edu/~newmanl/diplotene.GIF
Figure 1.21 (not on the web):
../../Other%20Graphics/BadDiplotene.gif
Relative to differences between the text and lectures regarding meiosis. Please follow the lecture and our web materials. There is a lot of confusion these days regarding terminology and specific events.
Excellent, long, detailed account of early prophase in: ..Zickler, D. and N. Kleckner. 1999 Meiotic chromosomes: integrating structure and function. Ann Rev Genet 33(6678): 603-754. Article available via PSU connection, URL follows--
Annual Review of Genetics available via PSU computers
Concept of cohesion of sister chromatids in mitosis and meiosis.
proteins: Cohesin, condensin, separase
General model for cohesion....../cohesinsequence.html
cohesin - Amon model ... ../cohesionAmonModel.gif
Amon, A. (2001). "Together until separin do us part." Nat Cell Biol 3(1): E12-4.
cohesion meiosis Allshire model ... ../CohesionAllshireModel.gif
Allshire, R. (2004). "Cell division: guardian spirit blesses meiosis." Nature 427(6974): 495-7.
References:
Bernard, P., et al. 2001 Requirement of heterochromatin for cohesion at centromeres. Science 294(5551): 2539-42.