LISTSERV 16.0

Help for CILIATEMOLBIO-L Archives

UGA Help Desk

Request a List


CILIATEMOLBIO-L Archives

CILIATEMOLBIO-L Archives


CILIATEMOLBIO-L@LISTSERV.UGA.EDU


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Monospaced Font

LISTSERV Archives

LISTSERV Archives

CILIATEMOLBIO-L Home

CILIATEMOLBIO-L Home

CILIATEMOLBIO-L  August 2010

CILIATEMOLBIO-L August 2010

Subject:

round 2: more suggestions on a revised table of contents for the next methods volume?

From:

Kathy Collins <[log in to unmask]>

Date:

Thu, 12 Aug 2010 16:50:17 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (105 lines)

Based on everyone's very helpful input on the last draft, here is a revised
draft outline for the next methods volume. Suggestions for improvement are
welcome to [log in to unmask] and [log in to unmask]
Suggestions for authors are also welcome, although thankfully some people
have already volunteered for specific chapters.

Tentative table of contents 8/12/10 *VERY tentative thoughts about the
content of the chapters, for judging the scope overall*

Methods in Cell Biology: Tetrahymena thermophila

Introduction

1. Tetrahymena as a model organism

Systems perspectives (What has been/can be learned using Tetrahymena and how?)

2. Natural world context: what we need to know for evolutionary/phylogenetic
context, ecology, population diversity and isolation, estimates of sexual
versus asexual reproduction in the wild, seasonal behavior in native
environments? karyorelicts?

3. Nuclear dualism: MAC and MIC genomes, chromosome structures, relation of
MAC to MIC, phenotypic assortment and MAC copy number control in asexual
reproduction, nuclear differentiation in sexual reproduction, classes of IES

4. Ultrastructure: the cell overall; cortical patterning, the oral cavity,
cell pairing during conjugation

5. Membranes: cell membranes and membrane compartments; lipid profiles;
pathways for nutrient ingestion, excretion, secretion, phagocytosis,
autophagy?; preparations/purifications including rafts? Will explore models
for the evolution of mechanisms involved in membrane traffic.

6. Microtubules: overall types of structures; cilia including de/reciliation
and ciliary beating; cytoskeleton preparations/purifications including
tubulin prep

7. Chromatin: biochemical and functional characterization of histone
variants and modifications; chromatin compositions; DNA elimination;
epigenetics?; methods for ChIP

8. Genome-wide analyses: details of what genome sequencing revealed about
gene content and gene families; codon use; EST sequencing and expression
arrays; sRNA sequencing; proteomics including inventories from
organelles/secretion; resources including TGD and TGED and how they will
help to interrogate pathways

Operating principles (What approaches, tools, methods are available?)

9. Cell culture: nutrient requirements, media, temperature ranges for growth
and viability, density dependence, short term and long term working cultures
and why length of culture matters, strain storage, the stock center; growth,
stationary phase, starvation (+/- conjugation competence), conjugation;
growth without phagocytosis and/or ciliary motility

10. Strains: from T. pyriformis to T. thermophila {inbred strains and their
origin; how different are inbred strains here or below in genetics?},
collecting natural populations and their classification, the amicronucleate
condition

11. Genetics: crosses including to star (note the difference in genetic
versus physical amicronucleate condition; ie some star strains have MIC
content); genetic versus physical maps; {details of mating assays here or
below in behavior?} {strain inbreeding here or above?}

12. Transformation methods. DNA and RNA based transformation and
microinjection for the MAC and MIC; operational definitions of an essential
gene including somatic gene knockout versus knockdown; endogenous locus
tagging, transgene strategies with promoter choices; selectable markers;
antisense ribosomes, RNA silencing

13. Biochemical methods. whole cell DNA and RNA and protein; subcellular
fractionation including differential nuclei (alternatives to gum arabic),
nucleoli; principles for extracts cytoplasmic vs. nuclear vs. whole cell for
native/denaturing affinity purification; buffers, detergents, protease
inhibitors; protein/RNA/DNA tags for mass spec; MTT driven transgenes how
much Cd/Cu when, how long, how repeatedly

14. Cytological analysis: Assays of cellular ultrastructure by microscopy
(phase, IF, EM, FISH, etc., for tagged and untagged components); cell cycle
timings of replication/partition for MIC, MAC, organelles, and cell
membrane; phenotypes of perturbed cell cycle (define monsters), assays for
DNA content versus nuclear size; cell cycle mutants and what they tell us;
conjugation mutant phenotypes

15. Behavioral assays: motility (I antigens?); electrophysiology; social
interactions {mating assays here? include costimulation, tip
transformation, homotypic vs heterotypic pairing}; mucus discharge

16. Tetrahymena in the classroom

Concluding remarks

17. Opportunities for the future

**********************************
The 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, which would be
available elsewhere perhaps at TGD or the stock center websites. 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 could be) particularly interesting
or enabling.

Top of Message | Previous Page | Permalink

Advanced Options


Options

Log In

Log In

Get Password

Get Password


Search Archives

Search Archives


Subscribe or Unsubscribe

Subscribe or Unsubscribe


Archives

June 2019
May 2019
April 2019
March 2019
February 2019
December 2018
November 2018
October 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
December 2017
November 2017
October 2017
September 2017
August 2017
May 2017
April 2017
March 2017
January 2017
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
September 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
September 2014
August 2014
July 2014
May 2014
April 2014
March 2014
January 2014
December 2013
November 2013
October 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
September 2012
July 2012
June 2012
May 2012
April 2012
March 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
March 2011
February 2011
January 2011
December 2010
November 2010
September 2010
August 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
December 2006
November 2006
October 2006
September 2006
August 2006
June 2006
May 2006
March 2006
February 2006
January 2006
December 2005
November 2005
October 2005
August 2005
July 2005
June 2005
May 2005
April 2005
March 2005
February 2005
January 2005

ATOM RSS1 RSS2



LISTSERV.UGA.EDU

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager