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CILIATEMOLBIO-L  August 2010

CILIATEMOLBIO-L August 2010

Subject:

Re: input for a new edition of the Tetrahymena Methods in Cell Biology volume

From:

"Asai PhD, David J" <[log in to unmask]>

Date:

Tue, 3 Aug 2010 14:28:12 -0400

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text/plain

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text/plain (91 lines)

Several folks have successfully used Tetrahymena as a system for undergraduates, including people who are at small colleges.  These include using Tetrahymena in formal courses as well as for independent research projects.  Perhaps a section on Tetrahymena as a vehicle for education would inspire future users.

David J. Asai
Director
Precollege and Undergraduate Science Education
Howard Hughes Medical Institute
4000 Jones Bridge Road
Chevy Chase, MD  20815
voice:  301-215-8874
em:  [log in to unmask]

-----Original Message-----
From: Ciliate Molecular Biology [mailto:[log in to unmask]] On Behalf Of Kathy Collins
Sent: Tuesday, August 03, 2010 12:37 PM
To: [log in to unmask]
Subject: input for a new edition of the Tetrahymena Methods in Cell Biology volume

Hi everyone,

Ed Orias and I are planning the 2011 edition of the Tetrahymena Methods in
Cell Biology volume.  We would like your input on a tentative chapter
outline below, including your interest in writing a section (you can borrow
from the previous edition or other sources, and April 1 would be the deadline).

Our goal is to not have to do this again anytime soon - in other words, to
put together a volume that is more at a level of operational principles than
reviews of the current state of a field or detailed methods. Nothing that
could be downloaded for free from PubMed or accessed through TGD should be
in the book. The idea would be to have something that one would want to read
most of, or could read all of, as an education on what has been done with
Tetrahymena, what could be done, and why the system is (or is not)
particularly interesting or enabling for a topic or method. It does seem a
challenge to be comprehensive and yet concise, but the book can't be too
long if we want to encourage people (including ourselves and our lab
members) to read most of it as an inspiration for what to use Tetrahymena to
discover.

Send comments (this week would be best, later also OK) to us at
[log in to unmask]
[log in to unmask]

Thanks in advance for your thoughts!
Kathy and Ed

Overview of the model system
A. Ciliates: evolution, population diversity, ecology; AMIC condition;
karyorelicts
B. Nuclear dualism: MAC and MIC genomes, chromosome structures, relation of
MAC to MIC physical linkage; chromatin differences; gene content, codon use
C. Cytoskeleton and membranes, including membrane compartments, ciliary
organization, cell motors; ciliary transport, basal bodies; cell division;
cortical manipulation?
D. Nuclear events of veg growth: MAC and MIC replication, segregation,
assortment and copy number control, checkpoints
E. Nuclear events of conjugation

Cell culture, visualization, and fractionation
1. cell culture: veg growth (different media), stationary phase, starvation
(+/- conjugation competence), conjugation; short term and long term working
cultures
2. assays of cellular ultrastructure by microscopy
3. assays/isolation of chromatin including specific nuclei, nucleoli, ChIP
4. assays/isolation of membrane and secretory compartments
5. assays/isolation of cytoskeletal structures; cell motors

Strain construction and functional studies
6. Strains: From T. pyriformis to T. thermophila; thermophila inbred strains
and their origin; how inbred is inbred, how different are inbred strains,
star and AMIC strains
7. Crossing: Genetic mapping; genetic construction of strains with multiple
mutations; genome-wide forward genetic strategies: rescue by
complementation? artificial chromosomes?
8. Genetic engineering in veg growth (MAC): selectable markers; somatic gene
knockout, endogenous locus tagging, transgene strategies with promoter
choices; protein and nucleic acid tags for affinity purification;
operational definition of an essential gene
9. Germline genetic engineering (MIC): DNA-based germline gene knockout
strategies (including effect of gene copies in the MAC), RNA-based gene
knockout; MAC genetic engineering using developmentally-processed vectors
10. Strain engineering for heterologous protein overexpression?

Resources
11. Strain freezing and the stock center
12. Databases: TGD and TGED; cross compare to Paramecium databases?

Pioneering insights - may have to skip these if not enough space
F. Self-splicing RNA: RNA as a catalyst and an enzyme
G. Chromosome ends: telomeric repeats and telomerase
H. Histone variants and modifications: the histone code

I. Opportunities for the future

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