Nabble - Bio.net - Chlamy

BAC

2009-10-23T09:43:11Z

Do you know how to search BAC of Chlamy genome on the web please?

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growing and mating Chlamy in 96-well plates

2009-10-13T09:05:47Z

Dear Chlamy community
I'm trying to grow and mate Chlamy in 96-well plates. I'd be curious to
hear from other people who have experience in this area.

My personnal experience with flat bottom plates is that the cells tend
to form a ring at the bottom, and I don't think it's good if you want to
reach decent cell densities or see your cells survive for a decent
period of time. Has anyone compared round-bottom or V-shaped plates ?
Any feelings about plastic ? Polystyrene, vs. polyethylene, vs. special
plastics (e.g. Nunc Microwell low-binding) ? I'd be tempted to go for a
low-binding plastic, because Chlamy likes to swim around, but do the
cheaper plates work ?
Is agitation possible at all in these small wells ? How do you control
evaporation, especially of the outermost wells ?
What about large-volume wells ? I tried 1.3 ml and 2 ml Deepwell plates,
but the cell density remained low so I never gained much in terms of
yield. The surface/volume ratio becomes terrible, and the opaque plastic
reduces light access. The cells tends to fall to the bottom. Has anyone
had more success ?
And mating ? There are quite a few labs out there who do matings in
96-well format, but I'm not sure what type of plate they use, and how
they place the cells in gametogenesis conditions. Does diluting from TAP
into water or N-free medium works ? Has anyone succeeded in storing the
zygotes in the wells ? I myself have used cat litter, but its handling
becomes quite messy in a microtiter plate format. Do glass beads work ?

Thanks for your answers, and other thoughts on this not-so-trivial subject

Olivier Vallon

--
Olivier VALLON
CNRS, UMR 7141
CNRS/Université Pierre et Marie Curie
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75005 Paris
FRANCE

ovallon@...
tel: (33) (0)1 5841 5058
fax: (33) (0)1 5841 5022
http://www.ibpc.fr/UMR7141/

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Chlamy Meeting June 6-June 10, 2010: SAVE THE DATE

2009-10-06T05:34:41Z

Dear Colleague:
We hope you will be interested in attending the 2010 Chlamy meeting, which
will be held in the greater Boston area next June. Watch for more
announcements as we develop the final CHLAMY2010 program.

Please add the dates to your calendar!

14th International Conference on the Cell and Molecular Biology of
Chlamydomonas
Wheaton College, Norton, Massachusetts
Sunday June 6 - Thursday June 10, 2010

Keynote Speaker: Ritsu Kamiya

Topics to be included:
Gene Expression and microRNAs
Chloroplasts and Mitochondria
Flagellar Structure, Motility and Signaling
Biofuels and Metabolism
The Intraflagellar Transport system and Flagellar Assembly
Photosynthesis
Light Perception and Photoresponses
Circadian Rhythms and the Cell Cycle
Adaptation and Stress Responses
Basal Bodies and Centrioles
Development and the Sexual Cycle
Evolution

Organizers:
David Mitchell (Upstate Medical University, Syracuse, NY, USA)
Stephen Miller (University of Maryland Baltimore County, Baltimore, MD,
USA)

Contact:
David R. Mitchell, Ph.D.
Department of Cell and Developmental Biology,
SUNY Upstate Medical University
750 E. Adams St.
Syracuse, NY 13214, USA
T-315-464-8575
FAX-315-464-8535
Email:mitcheld@...

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gametes

2009-09-23T16:43:35Z

I am wondering if anyone knows a simple way to detect the presence of
gametes in a population of chlamydomonas reinhardtii _without_ running
a mating reaction. are there any cytometric methods known for this?

also, i am wondering if anyone has any experience studying populations
of gametes that are not permitted to mate. in the literature it is
clear that gametes can survive nutrient deficiency for long periods.
has anyone studied this process systematically?

thank you very much,
Seppe Kuehn
The Rockefeller University
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Re: Chlamy Digest, Vol 46, Issue 1

2009-09-02T10:25:06Z

Frej-
It also depends on the purpose for replica plating. I have used 96 well plates for stock plates for years. I use a multichannel pipettor to fill the wells with whatever media you choose and a 96 pin applicator or an 8channel pipettor to transfer samples from an 'old' plate to a fresh one.

If you just need to transfer a small amount (dot blot/ lysing for enzymatic assay etc) this may also work, but Whatman paper is probably better. I know for certain that it cuts down stock maintenance time
******
Karen K. Bernd, Ph.D.
Co-director Merck/AAAS Undergraduate Science Research Program
Associate Professor of Biology at Davidson College
http://www.bio.davidson.edu/bernd

No trees were harmed in the typing of this email,
but thousands of electrons were terribly inconvenienced.
Please don't print this e-mail unless you really need to.

________________________________
From: <chlamy-request@...>
Reply-To: <chlamy@...>
Date: Wed, 2 Sep 2009 13:05:12 -0400
To: <chlamy@...>
Subject: Chlamy Digest, Vol 46, Issue 1

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Today's Topics:

1. replica plating (Frej Tulin)
2. Re: replica plating (Elizabeth Harris)

----------------------------------------------------------------------

Message: 1
Date: Tue, 1 Sep 2009 18:02:12 -0400
From: Frej Tulin <frej.tulin@...>
Subject: [Chlamydomonas] replica plating
To: chlamy@...
Message-ID:
<c8dd4ce40909011502u867b1a6hf6e6e9146b20077a@...>
Content-Type: text/plain; charset=ISO-8859-1

Dear all
Does anyone have a good method for replica plating Chlamydomonas plates? I
am currently using the standard budding yeast method with a velveteen. I
find that the colonies tend to 'smear out', which makes it difficult to
distinguish individual colonies, especially when the plate has a lot of
colonies.

Is there a filter paper or another material that gives better result?
Many thanks!
/frej

------------------------------

Message: 2
Date: Wed, 2 Sep 2009 07:30:27 -0400
From: Elizabeth Harris <chlamy@...>
Subject: Re: [Chlamydomonas] replica plating
To: chlamy@...
Message-ID: <p06200700c6c40722d5ed@[192.168.1.47]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

>Does anyone have a good method for replica plating Chlamydomonas plates?

Whatman #1 filter paper works much better for Chlamy than velveteen.
There's a detailed description of how to go about it, including
photographs, in the first edition (1989) of The Chlamydomonas
Sourcebook, pages 42-47. A shorter version of the same text appears
in the second edition, volume 1, pages 255-256.

--

Elizabeth H. Harris

Chlamydomonas Center
http://www.chlamy.org/

------------------------------

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End of Chlamy Digest, Vol 46, Issue 1
*************************************

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Re: replica plating

2009-09-02T04:30:27Z

>Does anyone have a good method for replica plating Chlamydomonas plates?

Whatman #1 filter paper works much better for Chlamy than velveteen.
There's a detailed description of how to go about it, including
photographs, in the first edition (1989) of The Chlamydomonas
Sourcebook, pages 42-47. A shorter version of the same text appears
in the second edition, volume 1, pages 255-256.

--

Elizabeth H. Harris

Chlamydomonas Center
http://www.chlamy.org/

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replica plating

2009-09-01T15:02:12Z

Dear all
Does anyone have a good method for replica plating Chlamydomonas plates? I
am currently using the standard budding yeast method with a velveteen. I
find that the colonies tend to 'smear out', which makes it difficult to
distinguish individual colonies, especially when the plate has a lot of
colonies.

Is there a filter paper or another material that gives better result?
Many thanks!
/frej
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ethanol

2009-08-09T13:00:03Z

Hi All,
We want to measure ethanol production (and release in the medium) by
Chlamydomonas strains undergoing anaerobic metabolism. What is a
convenient way to do it (that a new graduate student could handle)?
Or if not, what is the non-convenient way to do it?

I see a company (SA Biosciences) sells an assay kit based on ADH, but
do you have to treat the culture medium before using it in the assay?
I am concerned about inhibitors, etc. in the medium.

Thanks for your help.
David Herrin

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Teaching site

2009-08-03T10:57:45Z

The Chlamy Teaching site is back up, now at

http://nutmeg.easternct.edu/~adams/ChlamyTeach/

Mike Adams
Biology Dept
Eastern Connecticut State University
Willimantic, CT 06226
860-465-5305

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is autolysin comercially available?

2009-06-30T06:20:11Z

Dear all,

could anyone please tell me if there is a possibility to buy g-autolysin?
With many thanks,

Pavla Prikrylova

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Re: about the fosmid

2009-06-01T16:31:57Z

Hi, Xiaobo:
Once you get the BAC, if you are interested in a learning about a BAC
Retrieval method that we learned about from a colleague in the fly
community, please let us know. The method uses recombineering in a
cell that harbors a BAC to retrieve any fragment of DNA up to 12-20kb
independently of location of restriction sites.
~Bill Snell

On Jun 1, 2009, at 2:17 PM, Xiaobo Li wrote:

> Hi All,
>
> I am a new person to the Chlamy community. Recently I want to clone a
> genomic fragment of about 7kb. Considering the size, PCR maybe a
> challenge.
> So I want to order the fosmid covering it and hopefully can obtain the
> fragment by digestion. Anyone knows where to order the fosmid? Thank
> you
> very much.
>
> Xiaobo
>
> --
> *************************************
> Xiaobo Li
> Graduate Assistant
> DOE Plant Research Laboratory
> Department of Plant Biology
> Michigan State University
> East Lansing, MI 48824
> *************************************
> _______________________________________________
> Chlamy mailing list
> Chlamy@...
> http://www.bio.net/biomail/listinfo/chlamy

William J. Snell, Ph.D.
Department of Cell Biology,
University of Texas Southwestern Medical School
Rm. K2-226
5323 Harry Hines Blvd.
Dallas, TX 75390-9039
T-214-648-2332
FAX-214-648-8694
Email:william.snell@...

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about the fosmid

2009-06-01T12:17:21Z

Hi All,

I am a new person to the Chlamy community. Recently I want to clone a
genomic fragment of about 7kb. Considering the size, PCR maybe a challenge.
So I want to order the fosmid covering it and hopefully can obtain the
fragment by digestion. Anyone knows where to order the fosmid? Thank you
very much.

Xiaobo

--
*************************************
Xiaobo Li
Graduate Assistant
DOE Plant Research Laboratory
Department of Plant Biology
Michigan State University
East Lansing, MI 48824
*************************************
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phenotypic heterogeneity

2009-05-11T09:20:54Z

I am wondering if anyone has any experience assaying chlamy for
phenotypic heterogeneity. I'm looking for a broad screen to be
applied to a single strain and mating type (UTEX 2244, mt+). Does
anyone have any experience using phenotype microarrays like those
made by biolog with chlamy?

thanks!
seppe

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v3 annotations mapped to v4 genome assembly and Augustus models (again)

2009-04-09T05:06:16Z

Dear Chlamy Community,

I was told that the links in my previous email did not show up! My
apologies; I've spelled them out below in case your email viewer can't
handle the hyper-linked text. In general, you can go to http://erik.freshboom.com/chlamy/
and navigate from there (it's a minimalist's website at the moment).

Sincerely,
erik

---
Dear Chlamy Community,

This is to announce that JGIv3 Chlamy genome annotations have been
mapped to the current AUGUSTUS gene models for the v4 Chlamy genome
assembly (a.k.a. the AUGUSTUS "update 5/UTR5" gene models).

For those who attended the Chlamy '08 meeting, you may recall mention
of (an earlier set of) these gene models, which were generated in
collaboration with Mario Stanke (the author of AUGUSTUS) and Chun
Liang: http://augustus.gobics.de/predictions/chlamydomonas/

Although the recently release JGIv4.0 gene models incorporated the
AUGUSTUS gene predictions as a source of input, the resulting models
can differ significantly in the details and the two sets should be
viewed as distinct if not complementary. The advantages of the
AUGUSTUS model set include simultaneously-consistent alternative
transcript and UTR predictions; a possible disadvantage (anecdotally)
is that some of the current AUGUSTUS models may fuse two or more
genes. Regardless, improving the AUGUSTUS Chlamy gene models remains
an active and ongoing project.

If you'd like to use the AUGUSTUS models, you now have some functional
annotations to work with, courtesy of the community's efforts on v3 of
the Chlamy genome. You may download an Excel file for these mappings
here (http://erik.freshboom.com/chlamy/CRv4_AnnotationMappings/JGIv3_to_CRv4AugustusU5.map20090407.xls
) A tab-delimited version of this file and other related files are
available within the same directory (http://erik.freshboom.com/chlamy/CRv4_AnnotationMappings/
).

For more details about these results, please refer to the README page.

These mapping results along with additional functional annotation data
will be available from the AUGUSTUS Chlamy website within the next few
days. Regular updates to these annotations will be posted over the
next couple of weeks: for download at the freshboom.com site and for
more user-friendly interactive use at the AUGUSTUS website.
Importantly, Elizabeth Harris and I are working hard to make sure all
the available genetic linkage markers/data/references are incorporated
with these mapped annotations; when we're done, we will post them
(along with any editorial corrections/additions).

These mapped annotations will also be available soon in association
with the AUGUSTUS models at the JGI Chlamy v4 genome browser (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html
) (and possibly at the budding ChlamyBase.org website (http://www.chlamybase.org/)
).

Those of you who have been waiting awhile for these, thanks for your
patience!

If you have any questions or comments, feel free to contact me. In
particular, if you notice any errors or have any corrections/additions
to Your Favorite Gene(s), please kindly let me know; I will make sure
it gets fixed and reflected in future updates, for the benefit of the
Chlamy community.

Sincerely,
erik

---
Erik F. Y. Hom
Postdoctoral Fellow, Murray Lab
MCB, Harvard University
52 Oxford St., NWLabs 458.40-8D
Cambridge, MA 02138, USA

Lab: +1-617-496-1384 | -1489
Fax: +1-617-496-1541

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v3 annotations mapped to v4 genome assembly and Augustus models

2009-04-09T04:24:53Z

Dear Chlamy Community,

This is to announce that JGIv3 Chlamy genome annotations have been
mapped to the current AUGUSTUS gene models for the v4 Chlamy genome
assembly (a.k.a. the AUGUSTUS "update 5/UTR5" gene models).

For those who attended the Chlamy '08 meeting, you may recall mention
of (an earlier set of) these gene models, which were generated in
collaboration with Mario Stanke (the author of AUGUSTUS) and Chun
Liang: http://augustus.gobics.de/predictions/chlamydomonas/

Although the recently release JGIv4.0 gene models incorporated the
AUGUSTUS gene predictions as a source of input, the resulting models
can differ significantly in the details and the two sets should be
viewed as distinct if not complementary. The advantages of the
AUGUSTUS model set include simultaneously-consistent alternative
transcript and UTR predictions; a possible disadvantage (anecdotally)
is that some of the current AUGUSTUS models may fuse two or more
genes. Regardless, improving the AUGUSTUS Chlamy gene models remains
an active and ongoing project.

If you'd like to use the AUGUSTUS models, you now have some functional
annotations to work with, courtesy of the community's efforts on v3 of
the Chlamy genome. You may download an Excel file for these mappings
here. A tab-delimited version of this file and other related files
are available within the same directory.

For more details about these results, please refer to the README page.

These mapping results along with additional functional annotation data
will be available from the AUGUSTUS Chlamy website within the next few
days. Regular updates to these annotations will be posted over the
next couple of weeks: for download at the freshboom.com site and for
more user-friendly interactive use at the AUGUSTUS website.
Importantly, Elizabeth Harris and I are working hard to make sure all
the available genetic linkage markers/data/references are incorporated
with these mapped annotations; when we're done, we will post them
(along with any editorial corrections/additions).

These mapped annotations will also be available soon in association
with the AUGUSTUS models at the JGI Chlamy v4 genome browser (and
possibly at the budding ChlamyBase.org website).

Those of you who have been waiting awhile for these, thanks for your
patience!

If you have any questions or comments, feel free to contact me. In
particular, if you notice any errors or have any corrections/additions
to Your Favorite Gene(s), please kindly let me know; I will make sure
it gets fixed and reflected in future updates, for the benefit of the
Chlamy community.

Sincerely,
erik

---
Erik F. Y. Hom
Postdoctoral Fellow, Murray Lab
MCB, Harvard University
52 Oxford St., NWLabs 458.40-8D
Cambridge, MA 02138, USA

Lab: +1-617-496-1384 | -1489
Fax: +1-617-496-1541

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companion web site for Chlamydomonas Sourcebook

2009-02-13T07:44:15Z

Those of you who have the new Chlamydomonas Sourcebook, second
edition, are probably aware that the "companion web site" for this
volume at Elsevier
(http://www.elsevierdirect.com/companion.jsp?ISBN=9780123708731) is a
garbled mess. We've been trying since early December to get this
fixed, so far without success. George Witman and I have therefore
created an alternative index page at
http://www.chlamy.org/companion.html that provides descriptions and
links for the two methods files for volume 2 and the many terrific
videos that accompany volume 3.

Most of the links on our page lead to the Elsevier site but these
URLs may change if they ever respond to our requests for revision.
If you discover one that isn't working, please let me know.

--

Elizabeth H. Harris

Chlamydomonas Center
http://www.chlamy.org/

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Available antibodies

2009-02-05T07:50:38Z

I would like to show students some double(triple?) labeling in Chlamy
and would specifically be interested in a combination of any flagellar
protein and hsp70. I am having problems finding commercial Ab that are
likely to recognize Chlamy and which are raise in different host
organisms. If anyone has catalog numbers for a good combination, I
would be very grateful

thanks

Mike Adams
Chairman
Biology Dept
Eastern Connecticut State University
Willimantic, CT 06226
adams@...
(860) 465-5305

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Chlamydomonas electroporation with Bio-Rad GenePulser Xcell

2009-01-12T02:27:55Z

Hi,
does anybody know a good setting on the Bio-Rad GenePulser Xcell
apparatus to electroporate Chlamy?
We were used to electroporate the algae with the Eppendorf Multiporator
in prokaryotic mode at 750V and 5ms but our numerous attempts to
reproduce that on the new apparatus failed.
We are using the sucrose/starch protocol established to electroporate a
cw15 strain.
Thank you

David

--

David Dauvillée

*"Biochemical Genetics and Functional Biology"*

Unité de Glycobiologie Structurale et Fonctionnelle

UMR 8576 CNRS

USTL / Bât C9

59650 Villeneuve d'Ascq

FRANCE

Tel: +33 3 20 43 65 43

Fax: +33 3 20 43 65 55

David.Dauvillee@...

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Re: Transformation

2009-01-08T09:28:23Z

On Jan 6, 2:28 pm, "Boettcher, Tara" <dac...@...> wrote:
> I am using CC-125 and CC-124 and trying to transform them with pSP124S with Bleo resistance marker, using both Karen Kindle method with glass beads and the Purton variation of the Karen Kindle method, and not having any luck.
> I've done an agar kill curve with zeocin, I have linearized the plasmid, and have tried autolysin treatments.
>
> Does anybody have insight on 'crucial steps', a new method to try, or a new plasmid with a different resistance marker I could try?
> Any help is greatly appreciated!

Dear Tara,

I have been transforming Chlamydomonas D66 with the sSP124S plasmid
because my background mutant already has the Streptomyces rimosus
aphVII (pSI103 plasmid with a aminoglycoside phosphotransferase
conferring paromomycin resistance) marker (Sizova et al. 2001). You
can readily get this plasmid from the Chlamy Center (http://
www.chlamy.org/plasmids.html) and it seems to be a marker that is much
easier to use.

As I understand, the BleR marker has fallen out of favor because of
some of the difficulties that can occur. For one, there seems to be
different strengths of Bleocin/Zeocin from batch to batch and each
order should be titrated separately. Further, the Sizova paper
mentions that the BLE protein dimer can only inactivate two antibiotic
molecules through drug sequestration. So it is as if the BLE
resistance is quenching the drug. Thus, variable expression levels in
your mutants should confer a pool of variable resistance in the
population of mutants you plate. If your concentration of Ble is too
high, you will select for mutants with mulitiple resistance gene
insertions. I have also noticed variable susceptibility to the zeocin
antibiotic in the wild-type cells based on factors like culture growth
stage and, of course, the density of cells plated. When working with
Ble-resistance it is important to have a good negative control that
goes through the entire transformation process, but without the
introduction of the plasmid. This is important, because the current
electroporation method I am employing makes even the wild-type cells
more susceptible to bleocin. I suspect, but have not tested, that
this is due to a combination of diluted cell number during transfers
and cell mortality during electroporation. Zeocin is also a mutagen,
which can result in point mutations unrelated to your site of
insertion, making tracking down the cause of a mutant phenotype nearly
impossible.

Microscopy confirms that the bead transformation methods lyses many
cells. As with your experience, I have had poor transformation
efficiency with the bead method, but it does work. It is important to
try lots of variations and keep records of everything (including cell
density at start of experiment ect.). I have also had good luck with
increasing the the plasmid concentration to make the bead beating
method work, but this has been reported to also increase the number of
transformants with multiple insertions. You can also try plating the
cells with starch.

Overall, you will likely have the best luck with the pSI103 plasmid
and electroporation. The APH protein inactivates paromomycin by
transferring a phosphate from ATP to the paromomycin antibiotic, and
can keep catalyzing this reaction. Thus, the effective range of
paromomycin, paromomycin:cell ratio, and variability due to
variability in gene expression/gene copy number reasoned to be much
better. In my hands, this seems to be the case.

Hope this helps!

-Jonathan Meuser

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how to limit growth

2009-01-07T01:38:15Z

A turbidostat will be the right culturing method for you, this would be
a technical way to limit the cell density. A change of the culture media
or rather the nutrient supply to limit cell density would always effect
the motility and the health status of the cells. The cells could loose
their motility and would reduce their metabolic turnover.

chlamy-request@... wrote:

> Send Chlamy mailing list submissions to
> chlamy@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bio.net/biomail/listinfo/chlamy
> or, via email, send a message with subject or body 'help' to
> chlamy-request@...
>
> You can reach the person managing the list at
> chlamy-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chlamy digest..."
>
>
> Today's Topics:
>
> 1. how to limit growth? (Seppe Kuehn)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Jan 2009 15:03:55 -0500
> From: Seppe Kuehn <skuehn@...>
> Subject: [Chlamydomonas] how to limit growth?
> To: chlamy@...
> Message-ID:
> <A1E67872-9870-4C35-A860-86E90990862D@...>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> We are looking for a protocol for growing Chlamydomonas Reinhardtii
> under phototrophic conditions where the final cell density is limited
> to ~10^5 cells/mL. We would like to do this without adversely
> effecting motility, metabolism, or overall health of the culture.
> We are currently working with the UTEX 2244 (mt+) strain (also known
> as CC-125) but are open to using other strains if necessary. Thus
> far Sager's medium has worked best for our application so a simple
> modification to this medium that limits final cell density would be
> ideal. Thank you!
>
> ------------------------------
>
> _______________________________________________
> Chlamy mailing list
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>
> End of Chlamy Digest, Vol 40, Issue 1
> *************************************
>

--
Christian Jebsen (Dipl.-Biol.)
University of Leipzig
Department of Plant Physiology
Johannisallee 21, 04103 Leipzig
Phone: #49-341-9736876 Fax:#49-341-9736899
jebsen@..., http://www.uni-leipzig.de/~pflaphys

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Transformation

2009-01-06T13:28:48Z

I am using CC-125 and CC-124 and trying to transform them with pSP124S with Bleo resistance marker, using both Karen Kindle method with glass beads and the Purton variation of the Karen Kindle method, and not having any luck.
I've done an agar kill curve with zeocin, I have linearized the plasmid, and have tried autolysin treatments.

Does anybody have insight on 'crucial steps', a new method to try, or a new plasmid with a different resistance marker I could try?
Any help is greatly appreciated!

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how to limit growth?

2009-01-05T12:03:55Z

We are looking for a protocol for growing Chlamydomonas Reinhardtii
under phototrophic conditions where the final cell density is limited
to ~10^5 cells/mL. We would like to do this without adversely
effecting motility, metabolism, or overall health of the culture.
We are currently working with the UTEX 2244 (mt+) strain (also known
as CC-125) but are open to using other strains if necessary. Thus
far Sager's medium has worked best for our application so a simple
modification to this medium that limits final cell density would be
ideal. Thank you!
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digesting gDNA in chlamys

2008-11-14T12:39:48Z

Hi all,

I am going to do southern blot hybridization with chlamy's gDNA and was
wondering about (a) the size of the gel, and (b) the required time to run
the gel to completely digest the gDNA. I appreciate any help.

Thanks
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Flagella antibodies

2008-11-05T13:47:01Z

Which commercially available antibodies show good reactivity with
Chlamy flagella proteins, other than tubulin?

Mike Adams
Chairman
Biology Dept
Eastern Connecticut State University
Willimantic, CT 06226
adams@...
(860) 465-5305

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O.D. and cell count

2008-10-08T09:39:29Z

Hi all.......does anybody have a reference table/standard curve for
correlating cell count in chlamys to OD?..........thanks...........Bio
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silencing Chlamy gene

2008-09-24T12:38:00Z

Chlamy folks,

I would like to silence a Chlamy nuclear gene.

Does anyone have any recommendations? Is there
a good method out there? I have not seen much
except for higher plants.

thanks in advance,sandy

Sandra Berry-Lowe
Associate Professor, Biology
University of Colorado at Colorado Springs
719-339-5276

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BLAST gainst AUGUSTUS proteins

2008-09-02T03:29:11Z

Dear all,

as Erik Hom mentioned that there were some requests for a BLAST service we set
up a BLAST server that allows to search protein and DNA sequences in the
AUGUSTUS protein set of Chlamydomonas.

http://gbrowse.gobics.de/blast/blast.php

The BLAST result list contains links to our genome browser (
http://gbrowse.gobics.de/cgi-bin/gbrowse/chlamydomonas/ ), which now also
contains the JGI gene sets (JGI2, JGI3, JGI3_1) mapped to a fourth version of
the genome assembly. Please, be aware that these JGI tracks are gene
structures from mapping back amino acid sequences that were derived on a
different assembly and are only close to the original JGI proteins and are
not always at unique locations.

Suggestions are always welcome, although I might not have time to realize any
request ;-)

Peace, Mario

--
----------------------------------------
Dr. Mario Stanke
Institut für Mikrobiologie und Genetik
Abteilung für Bioinformatik
Goldschmidtstr. 1, 37077 Göttingen, Germany
phone: +49 551 39 14926
http://gobics.de/mario
----------------------------------------

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research position

2008-08-03T16:20:50Z

A salaried research position is available at the Ohio State University in
the Department of Plant Cellular and Molecular Biology in Dr Patrice Hamel's
lab
(http://www.biosci.ohio-state.edu/pcmb/osu_pcmb/faculty_sites/patrice_hamel/
hamel_lab.htm). The position is for one year and starts on September 1 (date
is flexible). We wish to recruit a student with some laboratory experience
(BS or MS or eq. for instance) to study mitochondrial complex I assembly in
the green alga Chlamydomonas (see below for a scientific summary of the
project). Future hire will be exposed to molecular genetic and biochemistry
techniques and will work in close interaction with a graduate student.
Applicants can email Dr Hamel (hamel.16@...).

Many human pathologies such as myopathies and neurodegenerative disorders
like Parkinson's disease are associated with dysfunction of the
mitochondria. Among the most prevalent forms of mitochondrial dysfunction
(with an estimated incidence of 1 in 10,000 live births) are human
deficiencies in complex I, a multimeric enzyme of the respiratory chain.
With over 40 nucleus- and mitochondria-encoded subunits, one FMN molecule
and 8 Fe-S clusters, mitochondrial complex I or NADH-ubiquinone
oxido-reductase is the largest respiratory complex in the mitochondrial
inner membrane. The fact that, in 60% of cases, patients with complex I
defects carry no mutations in the structural genes suggests that mutations
in yet-to-be discovered assembly factors of complex I are important causes
of disease. We propose to study complex I assembly in the single-celled
green alga Chlamydomonas reinhardtii. Chlamydomonas mutants lacking complex
I are amenable to studies because they are viable and display a slow growth
in the dark. Our goals are: 1) clone the AMC1 and AMC2 genes from existing
amc1 and amc2 nuclear mutants (amc for assembly of mitochondrial complex I)
that display a complex I defect and carry out the functional analysis of
their gene products and 2) generate a collection of insertional mutants only
deficient for complex I assembly with the objective to discover novel
nuclear-encoded complex I assembly factors.

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Microalgal technician position

2008-07-14T14:03:39Z

Dear Colleagues,

An opening is available for a research technician working in
microalgal molecular biology at the Donald Danforth Plant Science
Center in St Louis. The position will focus on developing transgenic
algae for biofuels production. Salary is commensurate with
experience. Please send CV and names of references to; sayre.2@....

Regards,

Richard Sayre
**************************************************************************
Richard T. Sayre, Ph. D.
Department of Plant Cellular and Molecular Biology
318 W. 12th Avenue, 570 Aronoff Labs
Ohio State University
Columbus, OH 43210 USA
Phone: 614-292-9030; Fax: 614-292-6345
Sayre Lab: http://www.biosci.ohio-state.edu/~plantbio/osu_pcmb/people/sayre.htm
BioCassava Plus: http://biocassavaplus.org/

New address after September 1, 2008
Director, Enterprise Rent-A-Car Institute for Renewable Fuels
Donald Danforth Plant Science Center
975 N. Warson Rd.
St. Louis, MO 63132
http://www.danforthcenter.org/

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GreenGenie2

2008-05-20T05:40:00Z

GreenGenie2 is an updated and retrained version of Genie for
predicting genes in Chlamydomonas. It is trained on 2600 EST
assemblies. The link for submitting your DNA sequence is below.
http://bifrost.wustl.edu/cgi-bin/greengenie2/greenGenie2

Susan K. Dutcher
Professor and Interim Chair
Department of Genetics
Department of Cell Biology and Physiology
Washington University School of Medicine
St. Louis, MO 63110

dutcher@...
314-362-2765

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arabidopsis orthologs

2008-05-11T17:07:05Z

I'm looking for where somebody has assigned the relationships
between an algae and Arabidopsis at the genome level. Something like what
the Homologene database is doing, but they don't seem to include any
algae.

Peter Palenchar

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Frameshift mutagens

2008-05-08T16:46:44Z

We are developing a reverse genetics strategy for finding mutations in
specific genes. Presently we are using uv mutagenesis but would like to
try other mutagens to get a broader spectrum of mutants. We have tried a
frameshift mutagen, ICR-191. Does anyone have any experience to maximize
the mutation rate using ICR-191? Is there other frameshift mutagens we
could try with chlamy?

Thanks,

Marilyn

--
<>-<>-<>-<>-<>-<>-<>-<>-<>-
Marilyn Kobayashi
Niyogi Lab
441 Koshland Hall
Plant and Microbial Biology
University of California
Berkeley, CA 94720
510-643-6604

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Need help to find a working mithramycin staining protocol for Chlamydomonas

2008-04-28T08:33:21Z

Dear Chlamydomonas community,

I am PhD student working on Chlamydomonas reinhardtii and tried to
stain cw15 (mt-) cells with mithramycin, a dye for the nucleus I found
in the Chlamydomonas Source Book. I referred Bridget & Whatley (1975)
to strain the cells by adding 20 µg/ml mithramycin and 5 mM MgCl2
(final concentration). I incubated the cells 20 min at room
temperature and in the absents of light before I watched them through
the microscope (Zeiss Axiophot, 450-490 nm excitation, 510 nm beam
splitter, 520 nm barrier filter).
Unfortunately I was not successful staining the cells. I only could
see strong red auto-fluorescent of chloroplasts but no yellow/green
fluorescent nucleus.

Is there anybody out there knowing a working mithramycin staining
protocol for Chlamydomonas who is willing inaugurate me into the
secret of staining cells with mithramycin?

Many thanks in advance!

Kind regards
Stefanie

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Information on culturing Chlorella

2008-04-17T17:52:52Z

Hello, this is a Chinese girl that need your help.
would you please provide me some information about the Chlorella?
the culture media, growing conditions, maintenance and protocols for
pigment analysis (e.g. Carotenoids, e.g. xanthophyls).
I see that on your web.I want to do some research about it, but could not
find enough information.

Thanks for you help.

Regards

Yours,
Jackie
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cover illustrations for the new Chlamydomonas Sourcebook

2008-04-04T11:25:16Z

As you're probably aware, a new edition of The Chlamydomonas
Sourcebook is currently in production. We are looking for
photographs or drawings suitable for the covers of each of the three
volumes. These illustrations can be in full color.

Our editors at Elsevier would like to have the final illustrations in
hand by April 18th, so we need to work quickly. If you have images
that you think might be suitable, please send low-resolution .jpg
files for review to Elizabeth Harris, chlamy@....

The three volumes, with their working subtitles, are as follows:

Volume 1. Introduction to Chlamydomonas and Its Laboratory Use (by
Elizabeth Harris)

Suitable illustrations might include light micrographs or EMs of
individual cells or gametes pairing; we're open to all possibilities
here

Volume 2. Organellar and Metabolic Processes (edited by David Stern)

For this one, perhaps something on the "green" side of Chlamy?
Roughly half of this volume is concerned with various aspects of
metabolism, and half with photosynthesis, respiration, and biogenesis
of chloroplast and mitochondria.

Volume 3. Cell Motility and Behavior (edited by George Witman)

Here we'd like to see an immunofluorescence image of the cell, an EM
of the flagellum/basal body, or perhaps a line drawing illustrating
IFT or some other process or structure.

Thanks in advance for your interest and help!

--

Elizabeth H. Harris

Chlamydomonas Center
http://www.chlamy.org/

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