bionet.genome.arabidopsis Google Group

Deadline Approaching - CFP - APBC2010

phoebe.c...@deakin.edu.au (Phoebe Chen) — Fri, 03 Jul 2009 02:33:40 UT

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Deadline Approaching 20 July ! - Call for Papers - APBC2010
The Eighth Asia-Pacific Bioinformatics Conference (APBC2010)
Bangalore, India, 18-21 January 2010
[link]
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Job Opening: Plant Ontology Project Coordinator

jaisw...@science.oregonstate.edu (Pankaj Jaiswal (OSU)) — Thu, 02 Jul 2009 20:02:11 UT

Deadline extended until July 31st.
Also, if you are attending the following meetings please feel free to
contact us to learn more about this position and the project:
ASPB-Plant Biology 2009 : Contact Pankaj Jaiswal
BSA Botany & Mycology 2009: Contact Aaron Liston
Position Title:
Research Associate (Senior Postdoc) / Research Associate (Postdoc)

Reply to "Could anyone help me on Arabidopsis genomic DNA" (Arab-gen Digest, Vol 50, Issue 15)

cmmcmich...@wisc.edu (COLLEEN M MCMICHAEL) — Wed, 01 Jul 2009 15:10:30 UT

Hi Chunmei,
I have often had problems with PCR using genomic DNA as a template. For the most part, using the CTAB DNA preparation versus other faster, yet dirtier, preparations has helped tremendously. Since you are already using this preparation method, you might now want to try using additives that will help melt your DNA/primers, stabilize the polymerase, etc (for example add DMSO, glycerol, glycine betaine or BSA). BSA has helped more than any other additive for me. Also, increasing the buffer (complete with Mg2+) concentration can also help (up to 1.6 X final). Finally, have you tried varying the annealing temperature for your primer set? I suggest using a gradient machine to test a rangeof tmperatures. Please keep in mind that all PCR products are unique in their needs, and that the best conditions for your reaction must be determined empirically. Here is a link to a website that helped guide me toward possible PCR variations to try: [link].

Re: Could anyone help me on Arabidopsis genomic DNA cloning?

amo...@gmail.com (Adrian) — Wed, 01 Jul 2009 15:59:45 UT

First at all, I would recommend to use 35 or 40 PCR cycles instead 20.
Second, I will use a hot start Taq an use 10 min. of initial
denaturation at 95 ºC, then the following denaturation steps should be
1 min. at 95 ºC. As tip I recommend to pipette several times the DNA
before add it to the PCR reaction.

Re: Arab-gen Digest, Vol 50, Issue 15

ramu.tiger...@gmail.com (Ramu gowda) — Wed, 01 Jul 2009 03:33:55 UT

Dear Chuanmei Zhu
DBBS(plant biology),
Washington University, St.Louis, MO,USA. 63130
the genomic DNA of arabidopsis has the introns,UTRS,etc thats why you may
not be able to amplify the expected amplicon, so its better to amplify from
CDNA, if you have plant tissue prepare RNA , from that prepare CDNA using

Twp postdoctoral positions at the University of North Texas

s...@unt.edu (Shah, Jyoti) — Tue, 30 Jun 2009 19:47:45 UT

Two postdoctoral positions are available in the Department of Biological Sciences at the University of North Texas, which is located in Denton near Dallas (Texas).
Position 1 (Requisition #090681): Postdoctoral position in Plant –Insect Interaction
University of North Texas is seeking a full time postdoctoral research associate to study plant defense response. The research emphasis will be on studying Arabidopsis defense responses to the green peach aphid. We seek candidates with a Ph.D. in molecular biology, entomology or a related field. Applicants should have expertise in plant molecular biology. Candidates with expertise working with aphids are preferred. The successful candidate must be able to design and conduct independent experiments. Excellent oral and written communication skills and the ability to work well in a team-based/collaborative research atmosphere are essential. The Postdoctoral Research Associate will work under the direction of Dr. Jyoti Shah in the Department of Biological Sciences.

Re: Embryogenic culture

anbuarun12...@gmail.com (Anbu) — Tue, 30 Jun 2009 12:43:51 UT

Dear Puna,
I am suggesting you the following,
1. Remove infected seeds before starting sterilization procedure.
2. Use autoclaved filter paper
3. Use minimal amount of seeds
I hope this will be very helpful to you.
looking forward to hear from you

Could anyone help me on Arabidopsis genomic DNA cloning?

zhuchuanme...@gmail.com (竺传美) — Tue, 30 Jun 2009 00:21:15 UT

Hi,
I am a graduate student in Washington University. I have trouble in cloning
a ~1.9 kb DNA fragment from Arabidopsis genomic DNA recently. The genomic
DNA was prepared by CTAB method and was dissolved in H2O. For 25ul PCR
reaction, I use DNA ~500ng, MgCl2 1.5mM, dNTP 160uM, Taq 2.5U, primer each

Re: [Arabidopsis] Embryogenic culture

evewurt...@gmail.com (Eve Wurtele) — Mon, 29 Jun 2009 18:00:27 UT

it might help to reduce the number of seeds you are using in each flask.
one bad seed contaminates the whole flask.
also, have you tried controls in which you do the same protocol, but do not
add ANY seeds- and then put on shaker.
this will help you rule out something to do with flasks, media, etc.

M.Sc. Position available: ABC transporters in plant secondary metabolism

db...@mtroyal.ca (David Bird) — Mon, 29 Jun 2009 17:31:11 UT

M.Sc. Position available: ABC transporters in plant secondary metabolism.
A graduate student is sought for a(n) MSc/PhD project under the joint
supervision of David Bird and Peter Facchini in the Department of
Biological Sciences at the University of Calgary. The goal of this
research program is to identify and characterize ABC transporters involved

Embryogenic culture

puna...@hotmail.com (punamaya Maharjan) — Mon, 29 Jun 2009 11:28:20 UT

Dear Sir/ madam
I would like to post my query in this page .
Thank you .
Puna
"Query"
Dear
arab-gen users,
I am posting a query related to
the problem of contamination in embryogenic cultures. If anybody has idea to overcome it, I highly appreciate any kind of your comments.
I
followed the method described in the paper by Mordhorst et al., 1998. As mentioned in the Mordhorst et al., 1998, seeds were

dexamethasone and microarrays

b.g.fo...@lancaster.ac.uk (Forde, Brian) — Fri, 26 Jun 2009 13:51:43 UT

Hi there

Can anyone point me to Arabidopsis microarray experiments where the
effect of dexamethasone on gene expression in *control* lines
(preferably in roots) has been reported? This would have been done for
comparison with transgenic lines expressing a Dex-inducible gene.

Many thanks

Brian

protein extraction from cambium

hcalla...@barnard.edu (Hilary S. Callahan) — Thu, 25 Jun 2009 14:12:09 UT

Hello,
Here is a question from one of my students. It's not about Arabidopsis,
but I would imagine that some readers of thi list have ideas about
extracting from very low protein concentration?
QUOTE:
I am in Finland right now working as a trainee for 4 months (well 2
months left to go). My project is looking at telomerase activity in

postdoctoral and PhD positions

vgr...@uwo.ca (Vojislava Grbic) — Wed, 24 Jun 2009 20:49:13 UT

FOUR POSTDOCTORAL POSITIONS AND TWO PhD POSITIONS
for work on PLANT-SPIDER MITE INTERACTION are
available beginning September 1, 2009, in the
labs of Miodrag and Vojislava Grbic at the Dept.
of Biology, The University of Western Ontario,
Canada ([link]).
A joint multidisciplinary effort funded by Genome

measuring flowering time?

horvat...@gmail.com (Dave Horvath) — Tue, 23 Jun 2009 16:15:50 UT

Hi, I am in the novel position of having to look for altered flowering
time in a transgenic arabidopsis carrying a gene from leafy spurge.
There seems to be multiple ways this has been done in the literature,
and I am wondering if any particular method has been more accepted
than others. Any advice on the best way to do this, as well as any