Nabble - Bio.net - Arab-gen

Re: Vector NTI Replacement

2009-11-25T22:07:53Z

On Nov 24, 9:19 am, "Holt, Ben F. III" <benh...@...> wrote:

> Hi All,
>
> I am curious to hear what others are using for managing and manipulating their DNA sequences on the computer. We have used VectorNTI for years, but now that they have switched to the annual fee, we would like to consider alternatives.
>
> Thoughts?
> Ben
>
> ========
> Ben Holt
> Assistant Professor
> University of Oklahoma
> Department of Botany and Microbiology
> GLCH Rm 219
> 770 Van Vleet Oval
> Norman, OK 73019
> Phone (405)325-9018
> FAX (405)325-7619http://www.ou.edu/cas/botany-micro/faculty/holt.html

Hi Ben,

ApE is a favorite of mine. I find it handy for designing constructs
and handling sequencing data.

http://www.biology.utah.edu/jorgensen/wayned/ape/

**I am not affiliated with the author in any way**

-Allan

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Postdoctoral Position

2009-11-25T18:06:12Z

POSTDOCTORAL POSITION
Plant-Microbe/Pest Interactions

A postdoctoral research associate position is available at the
University of California, Riverside. Our lab studies the resistance
signaling pathway mediated by the tomato gene Mi-1 against nematodes
and aphids. The project entails characterization of genes involved
during early pest recognition events. Research opportunities also
exist to participate in identification of aphid effectors. The
position is available February 1, 2010.

We are looking for a highly motivated individual with a PhD and a
strong background in molecular genetics. Experience in biochemistry
and functional genomics approaches are highly desirable. Oral and
written communication skills in English and ability to interact and
work with others are essential. Prior work with nematodes or insects
is not required.

To apply, please send a cover letter describing research interests, a
curriculum vitae and names and e-mail addresses of three references
to: isgouhi.kaloshian@...

--
****************************************************************
Isgouhi Kaloshian
Professor
University of California
Department of Nematology
Riverside, CA 92521
USA

email: isgouhi.kaloshian@...
telephone: (951) 827-3913
fax: (951) 827-4434

http://www.faculty.ucr.edu/~ikalosh
****************************************************************
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Vector NTI Replacement

2009-11-25T11:18:41Z

We are using ApE, an open-source software that is capable to do the
gateway reactions. You can download it from here:

http://www.biology.utah.edu/jorgensen/wayned/ape/

You can drag and drop VNTI files into it and work from there.

Good luck !

udi

*********************************

Ehud Katz

Postdoctoral fellow

Department of Plant Sciences,

Plant Reproductive Biology, Mail Stop 5

University of California

One Shields Ave,

Davis, CA 95616

Phone No.: 530-7547322

e-mail: ekatz@...

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Brachypodium arrays

2009-11-25T06:28:22Z

Dear All,

The NASC Affymetrix service is now able to offer the Affymetrix
Brachypodium GeneChip.

The array is being offered as part of our normal full Affymetrix
service, which includes RNA QC, labeling, hybridisation and data
delivery. Assistance can also be provided with experimental design and
data analysis. The cost is currently £420 (+VAT / local tax) per array.

The array could also be used with our Xspecies technique (http://affymetrix.arabidopsis.info/xspecies/
) to study related species.

For more information on the NASCArrays service please see: http://affymetrix.arabidopsis.info/
or email affy@...

Best Wishes

Neil Graham

-------------------------------------------------
Nottingham Arabidopsis Stock Centre
Plant and Crop Sciences Division
University of Nottingham
Sutton Bonington Campus
Loughrough
LE12 5RD

www.arabidopsis.info
-------------------------------------------------

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Vector NTI Replacement

2009-11-24T09:19:30Z

Hi All,

I am curious to hear what others are using for managing and manipulating their DNA sequences on the computer. We have used VectorNTI for years, but now that they have switched to the annual fee, we would like to consider alternatives.

Thoughts?
Ben

========
Ben Holt
Assistant Professor
University of Oklahoma
Department of Botany and Microbiology
GLCH Rm 219
770 Van Vleet Oval
Norman, OK 73019
Phone (405)325-9018
FAX (405)325-7619
http://www.ou.edu/cas/botany-micro/faculty/holt.html

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Nature News article on TAIR funding cuts

2009-11-23T11:45:03Z

Dear colleagues,

I'd like to draw your attention to the Nature News article on TAIR
funding cuts that appeared in last Thursday's issue. The news article
includes a comment box at the bottom where you can voice your opinion on
the cuts or add suggestions on what could be done to solve this problem:

http://www.nature.com/news/2009/091118/full/462258b.html

A substantial number of comments on this piece will help make the case
that the community cares about this issue.

Best,

Eva Huala
TAIR Director

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TurboYFP in plants/Arabidopsis?

2009-11-23T00:56:56Z

Hi.

I am wondering whether anyone has tried TurboYFP from Evrogen in
plants yet. We just tried the related PhiYFP and could not detect any
expression in Tobacco transients.

Best wishes,
Marcus.

Dr Marcus Heisler
Developmental Biology Unit
EMBL Heidelberg
Meyerhofstrasse 1
69117 Heidelberg
Germany

email: heisler@...
phone: +49 6221 3878603

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Postdoctoral position available

2009-11-22T10:38:10Z

I am writing to ask that the advertisement for a postdoctoral position in my
laboratory included below be posted on your site.

I would be happy to answer any questions. Thank you in advance for your
help.

Karen S. Schumaker
Departments of Plant Sciences and Molecular and Cellular Biology and The
BIO5 Institute
University of Arizona
Forbes 303
Tucson, AZ 85721
(520) 621-9635
http://www.ag.arizona.edu/research/schumaker/

__

A postdoctoral associate position is available at the University of Arizona
as part of a Department of Energy-funded project to study endogenous
programs that control plant growth and development and how those programs
are altered to enable the plant to grow in non-optimal conditions
(http://www.ag.arizona.edu/research/schumaker/). A major focus of our work
is to understand the roles of the Calcineurin B-Like calcium binding
proteins in the establishment of developmental specificity during
calcium-mediated signaling in Arabidopsis. We are looking for a highly
motivated individual with a Ph.D. degree and a demonstrated ability to carry
out outstanding research in the fields of plant development, genetics or
related disciplines. Proven experience with molecular biology techniques
and demonstrated written and oral communication skills are essential
qualifications. Ability to interact and work collaboratively with others is
also critical. The position is available February 1, 2010.

To apply, send a curriculum vitae and the names and contact information
(address, phone, fax and e-mail) for three references to Karen Schumaker,
Ph.D. (schumake@...), School of Plant Sciences, University of
Arizona, Tucson, Arizona 85721-0036, United States. FAX 520-621-7186. The
University of Arizona is an EEO/AA Employer-M/W/D.V.

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BAR News: new eFP Browser cell-type-specific data sets and views for other species, and protein structures in ePlant

2009-11-19T15:09:59Z

Hello Arabidopsis and other Plant Researchers,

The Bio-Array Resource is pleased to announce the inclusion of several new
cell-type-specific expression data sets in our Arabidopsis eFP Browser at
http://bar.utoronto.ca/efp.

These cell-type-specific data sets in the Tissue Specific view include:

-a floral meristem set from Venu Reddy's lab at UCR;
-pollen germination data from Mark Johnson (Brown) and Ravishankar
Palanivelu (Arizona);

and in a new Root view:

-salt and iron-deficiency root cell-type-response data from the Benfey Lab
(Duke);
-high-resolution root spatiotemporal expression data, again from the Benfey
Lab;
-nitrogen root cell-type-responses from the Birnbaum Lab (NYU);

Many thanks to Siobhan Brady, Benfey lab members, Venu Reddy, Mark Johnson
and others for input in the creation of these eFP views. The Root view alone
provides a snapshot of 196 different combinations of cell-types versus
environmental responses or developmental stages (xylem and phloem pole
pericycle, procambium, xylem, phloem, phloem companion cells and other cell
types in 13 different sections generated by Dustin Cartwright and Hardeep
Nahal using an EM algorithm from Cartwright et al. 2009: try it out with
PIN1, At1g73590, as a nice example!), from 268 data sets across 6.1 million
data points.

We're also premiering eFP Browsers for barley and rice in beta - find the
links to these on the BAR homepage at http://bar.utoronto.ca. In addition,
it is now possible to explore Poplar data from the Campbell Lab's
PopGenExpress data sets using our Expression Angler and Expression Browser
tools. The links are also on the BAR homepage.

Finally, our ePlant now contains predicted protein structures for
approximately 72% of the Arabidopsis proteome, based on work carried out in
collaboration with Lawrence Kelley at Imperial College London using his
Phyre algorithm. Check it out at http://bar.utoronto.ca/eplant.

Feedback as always is welcome!

Best regards,

Nick

.........................................
Nicholas Provart, PhD
Assistant Professor, Plant Cyberinfrastructure & Systems Biology
Director, Graduate Program in Genome Biology and Bioinformatics
Member, Centre for the Analysis of Genome Evolution and Function
Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto
25 Willcocks St., Toronto, ON. M5S 3B2. CANADA

Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878
URL. http://www.csb.utoronto.ca/faculty/provart-nicholas
The Bio-Array Resource. http://www.BAR.utoronto.ca
email. nicholas.provart@...
TTC. Spadina LRT, Willcocks St.

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Looking for a good GR-inducible vector with a GFP Tag

2009-11-18T07:31:28Z

Greetings all!

I am looking for a GR inducible vector that also has a tag. Preferably, the
tag would be GFP, but I could use something else if need be.

Does anyone have experience with a good vector?

Thanks in advance for suggestions!

Beth Rueschhoff, Ph.D.
Department of Genetics
NC State University
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Arabidopsis

2009-11-18T05:04:09Z

dear sir
i want to infect Arabidopsis thaliana using nematode
(M.incognita) .can please guide to know that which mixture(soiil,sand
vermiculite and cocopete) is best for plant growth as well as for
nematode holding capacity.

i am hopinbg your reply.

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4 Post-Doc + 3 Lab. Asst positions at INRA Versailles, France / Loudet' lab

2009-11-17T17:39:40Z

We are looking for 4 highly motivated post-doc candidates to work on
Arabidopsis natural variation for growth and the response to the abiotic
environment, as well as cis-acting regulation of gene expression. Also, 3
lab. assistant positions available.
More information and contacts available by following this link (pdf):
http://www.inra.fr/vast/Positions_2010_Loudet_INRAVersailles.pdf
These 2-3 years fellowships are available at INRA, Versailles (France), in
<http://www.inra.fr/vast/>the VAST lab.
Please forward this offer to your network and students.

O.
________________________________________________________

Olivier Loudet

INRA, National Institute for Agricultural Research
Versailles, France

V.A.S.T group -- Variation and Abiotic Stress Tolerance

Mail: loudet@...
Science: www.inra.fr/vast
MyWeb: <http://olivier.loudet.net/>olivier.loudet.net
MyOwnGenes:
<http://teva.loudet.net/>teva.loudet.net &
<http://laena.loudet.net/>laena.loudet.net

" Catch your Fire in your Turn and Let it Burn "
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Re: Arab-gen Digest, Vol 55, Issue 8

2009-11-16T01:07:49Z

Dear Jay Shah
you can grow the arabidopsis in an quartz sand if you are perticularly
interested to study the roots. while using quartzsand you autoclave and use
and every two or 3 days once you can add half MS or Hogland solution. the
quartz sand allow roots to grow with out any difficulty .
hope you may find it easy.
wish success.

On Sun, Nov 15, 2009 at 10:34 PM, <arab-gen-request@...>wrote:

> Send Arab-gen mailing list submissions to
> arab-gen@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bio.net/biomail/listinfo/arab-gen
> or, via email, send a message with subject or body 'help' to
> arab-gen-request@...
>
> You can reach the person managing the list at
> arab-gen-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Arab-gen digest..."
>
>
> Today's Topics:
>
> 1. Growing Arabidopsis in vermiculite (jay shah)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 13 Nov 2009 19:33:07 -0330
> From: jay shah <ecolik12@...>
> Subject: [Arabidopsis] Growing Arabidopsis in vermiculite
> To: arab-gen@...
> Message-ID:
> <11acc0af0911131503s39c1730dqa8d12494aaed8abd@...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello all,
>
> I would like to grow Arabidopsis in a way that i should not have any micro
> organisms in the substrate in which i am growing them.
>
> Can i use vermiculite instead of soil?
>
> is there any other means in which i can grow the plants so that i have no
> microbial contamination in the growing environment, specially roots? I
> would
> like to measure certain compounds, which in presence or micro organisms can
> create an error in the analysis.
>
> Regards,
>
> --
> Jay Shah.
>
> TOUGH TIMES NEVER LAST, TOUGH PEOPLE DO
>
>
> ------------------------------
>
> _______________________________________________
> Arab-gen mailing list
> Arab-gen@...
> http://www.bio.net/biomail/listinfo/arab-gen
>
> End of Arab-gen Digest, Vol 55, Issue 8
> ***************************************
>

--
Ramu.S.V
Research Associate
COE, DBT
Molecular plant physiology lab,
dept of crop physiology,
UAS, GKVK, Bangalore
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Growing Arabidopsis in vermiculite

2009-11-13T15:03:07Z

Hello all,

I would like to grow Arabidopsis in a way that i should not have any micro
organisms in the substrate in which i am growing them.

Can i use vermiculite instead of soil?

is there any other means in which i can grow the plants so that i have no
microbial contamination in the growing environment, specially roots? I would
like to measure certain compounds, which in presence or micro organisms can
create an error in the analysis.

Regards,

--
Jay Shah.

TOUGH TIMES NEVER LAST, TOUGH PEOPLE DO
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PhD position availible in plant physiology

2009-11-10T09:20:52Z

Uppsala University hereby declares the following position to be open
for application:

PhD student position in Physiological Botany
at the Evolutionary Biology Centre, the Department of Physiological
Botany (http://www.ebc.uu.se) announces a PhD student position in the
project The role of the Arabidopsis HETEROCHROMATIN PROTEIN1 in plant
development.

In plants as well as in animals the control of chromatin structure in
response to endogenous and exogenous cues determines gene expression
patterns that regulate cell differentiation and development. The
available project focuses on an Arabidopsis mutant, terminal flower2
(tfl2). The gene encodes the plant HETEROCHROMATIN PROTEIN1 (HP1), a
homologue to the Drosophila HP1 genes that are involved in basic
processes as DNA replication, recombination and repair but also in
epigenetics and gene activation/repression during differentiation. The
single copy gene in Arabidopsis encodes a protein most similar to HP1
proteins that regulate gene activation/ repression in other organisms
and it has been shown to localize to euchromatic regions of the
chromosomes. Mutations in tfl2 have a pleiotropic effect indicating a
global role, possibly regulating different developmental processes in
response to light. Our data points to the importance of TFL2 in two
phase-transitions during the plant life cycle: embryo postembryonic
development as well as vegetative reproductive development. Recent
results show that TFL2 physically interact with proteins in hormone
signal transduction pathways as well as chromatin of both hormone
biosynthesis and response genes. The successful candidate will
collaborate with another PhD student in this area of hormone
regulation of plant development.

The successful candidate should have a university degree in biology,
favourably with the combination of plant biology and molecular
biology. The application should include personal background including
a description of undergraduate training, a complete CV, copies of
university degree and degree thesis as well as the names and e-mail
addresses to two referees.

The PhD position is full time employment position for a tenure of four
years. However, the possibility for the tenure to be extendable to a
maximum of five years exists to allow the inclusion of university
level biology teaching and/or laboratory supervision into the PhD
education.

For more information please contact Dr Annika Sundås-Larsson, that
will function as the supervisor, by e-mail
annika.sundas-larsson@... or by phone +46-18-4712819. Union
representatives are Anders Grundström, SACO-rådet, tel: +46 18-471
5380, Carin Söderhäll, TCO/ST, tel: +46 18-471 1996 and Stefan
Djurström, SEKO, tel: +46 18-471 3315.

The application should be sent , preferrably by e-mail to:
registrator@..., or by fax + 46 18 471 2000, or by mail to:
Registrar´s Office, Uppsala University, Box 256, SE-751 05 UPPSALA,
Sweden. In any correspondence, please use the reference number UFV-PA
2009/2423. Application no later than 16 November, 2009

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Five posts at UEA and a Project Leader position at John Innes Centre

2009-11-09T03:23:22Z

Five new academic staff appointments at UEA and a Project Leader at the John Innes Centre have been created as a result of substantial new investments in the Earth and Life Systems Alliance (ELSA) and the Tyndall Centre for Climate Change Research. The posts offer excellent opportunities for continuing, or developing, internationally outstanding research careers.

The Tyndall Centre for Climatic Change Research
Three Lecturer Posts Ref: ATR842 (£37,651 to £43,622 per annum)

UEA is the Headquarters of the Tyndall Centre (www.tyndall.ac.uk), which includes the universities of Manchester, Southampton, Oxford, Newcastle, Sussex and Cambridge. At UEA, the Tyndall Centre's interdisciplinary activities span the Faculty of Science and the Faculty of Social Sciences. These new positions will be based alongside existing Tyndall colleagues within the School of Environmental Sciences.

You must have a PhD (or equivalent) in an appropriate discipline in physical, natural, or social science, ideally with research interests in one or more of: land use and climate change; food security and climate change; mitigation, adaptation and behavioural change; energy and climate security; climate change and prosperity, and you must also be able to satisfy all other essential elements of the person specification. Applications from candidates with research interests in other climate-related areas will also be considered.

The Earth and Life Systems Alliance (ELSA)
Two UEA Lecturer or Reader posts Ref: ATR841 (£37,651 to £43,622 per annum for lecturer, £44,930 to £52,086 for reader)

John Innes Centre Project Leader (Tenure-track) Ref: 1001841 (£33,780 - £37,534. A higher pay band (£42,769 to £47,521) may be offered to an exceptional candidate).

ELSA (www.elsa.ac.uk<http://www.elsa.ac.uk>) is a major strategic collaboration between UEA and the John Innes Centre (JIC). It brings together UEA's expertise in environmental science and climate change, with JIC's expertise in plant and microbial biology to understand, predict and mitigate the impact of environmental change on biodiversity, biogeochemical cycles and agricultural systems. We seek applicants with outstanding research and publication records in this area. The successful candidates will either have or be expected to establish an internationally high-profile independent research programme that includes substantial collaboration between JIC and UEA.

For all ELSA posts, you must have a PhD (or equivalent); a research background in ecology, molecular or evolutionary biology, biogeochemistry, microbiology, plant biology, social science or environmental modelling and be able to satisfy all other elements of the person specification. Successful candidates will have a developing international research reputation, which will already be established for appointment to the higher level.

Closing date: 12 noon on 30 November 2009.
http://www.uea.ac.uk/hr/jobs/acad/atr841.htm

Professor Alastair Grant
Deputy Head of School
School of Environmental Sciences
University of East Anglia, Norwich, NR4 7TJ, UK
Phone +44 1603 592537

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Re: Arab-gen Digest, Vol 55, Issue 4

2009-11-06T09:29:55Z

In reply to the question of Eric Brenner about teaching and Arabidopsis in
intro biology:

At Utrecht University we have a one week course (divided over 2 weeks) on
the experimental cycle. Students have to follow this cycle almost full
circle. We pregrow a number of Arabidopsis mutants (sex-1 of course, always
a favourite, pgm, but also a few hormone mutants) and their WT for them in
the growth chamber, in pots, at 2 light intensities. The measurements they
have to do are necessarily fixed already beforehand, but they have to find
information about their mutant on the web and in the literature, and then
they have to formulate the exact question and the hypothesis they have, both
about the effect of light and of the mutation.

Then they measure traits at 3 levels: gene expression of Rubisco and a CAB
gene by qPCR, Rubisco and chlorophyll content, and specific leaf area, along
with dry weight:fresh weight ratio's, leaf size and shape, leaf angle and
what they like to measure more.

They have to calculate a number of variables and enter them all on papers
with predesigned tables with the relevant traits. In this way we can see
whether relative differences in gene expression translate into a differences
in the Chlorophyll:Rubisco ratio, and how these changes relate to
differences in SLA, or concentration per unit fresh or dry weight. They have
to draw their conclusions, make a poster and present these for other
students of their year.

Great fun! Success,

Hendrik Poorter

On Fri, Nov 6, 2009 at 6:03 PM, <arab-gen-request@...>wrote:

> Send Arab-gen mailing list submissions to
> arab-gen@...
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> http://www.bio.net/biomail/listinfo/arab-gen
> or, via email, send a message with subject or body 'help' to
> arab-gen-request@...
>
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> arab-gen-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Arab-gen digest..."
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>
> Today's Topics:
>
> 1. Arabidopsis in teaching intro. biology (Eric D Brenner)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 05 Nov 2009 10:09:55 -0500
> From: Eric D Brenner <eb50@...>
> Subject: [Arabidopsis] Arabidopsis in teaching intro. biology
> To: arab-gen@...
> Message-ID: <5f00e3b437e5de.4af2a473@...>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Colleagues,
>
> I would like to know if any of you use Arabidopsis in introductory biology
> teaching courses? If so, would you be so kind as to share with me the
> experiment that you perform, the strains/mutants used, and a general idea in
> how long the experiment takes, and the source and cost of materials?
>
> Thank you ever so kindly,
>
> Eric D. Brenner, PhD.
> Clinical Assistant Professor
> Department of Biology
> New York University
> 609 Silver Building
> 100 Washington Square East
> New York, NY 10003
> wk: 212-992-8693
> fx: 212-995-4204
>
>
>
>
> ------------------------------
>
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> End of Arab-gen Digest, Vol 55, Issue 4
> ***************************************
>

--
Dr. Hendrik Poorter
ICG-3; Research Institute Jülich
D-52428 Jülich; Germany

tel: +49-(0)2461-61-6833
www.science.poorter.eu
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Re: Arab-gen Digest, Vol 55, Issue 3

2009-11-06T06:40:11Z

Dear Jean-Luc GALLOIS
are you asking for pBI121. if so yes we have that but how do i send to you.
let me know the details
ramu

On Thu, Nov 5, 2009 at 10:34 PM, <arab-gen-request@...>wrote:

> Send Arab-gen mailing list submissions to
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> than "Re: Contents of Arab-gen digest..."
>
>
> Today's Topics:
>
> 1. looking for pBI221 (Gallois)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 04 Nov 2009 08:14:38 +0100
> From: Gallois <Jean-Luc.Gallois@...>
> Subject: [Arabidopsis] looking for pBI221
> To: arab-gen@...
> Message-ID: <4AF129DE.4000101@...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear colleagues,
> I am looking for an old plasmid, pBI221 (if I recall well, a pUC-based
> plasmid with a 35Spromoter-GUS-Nosterm construct in it). It used to be
> sold by Clontech, in the old days.If anyone has some left and could
> spare me an aliquot, I would be grateful.
> Regards
> Jean-luc
>
> --
> Jean-Luc GALLOIS
> INRA-UR 1052
> Génétique et Amélioration des Fruits et Légumes
> Domaine St Maurice, BP94
> 84143 Montfavet cedex, France
> tel : +00 33 (0)4 32 72 27 96
> e-mail : jlgallois@...
>
>
>
>
> ------------------------------
>
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> End of Arab-gen Digest, Vol 55, Issue 3
> ***************************************
>

Affymetrix tobacco array

2009-11-06T01:05:29Z

Dear All

The NASC Affymetrix service is now able to offer the tobacco GeneChip.

This has been developed by Adavnced Technologies Cambridge (ATC) and
contains probe-sets for > 43,000 tobacco sequences (http://www.bat-science.com/groupms/sites/BAT_7AWFH3.nsf/vwPagesWebLive/DO7LTLWC?opendocument&SKN=2
).

The array is being offered as part of our normal full Affymetrix
service, which includes RNA QC, labeling, hybridisation and data
delivery. Assistance can also be provided with experimental design and
data analysis. All the data generated from this array will be made
publicly available through the NASCArrays database. The cost is
currently £450 (+VAT) per array.

The array could also be used with our Xspecies technique (http://affymetrix.arabidopsis.info/xspecies/
) to study related species.

For more information on the NASCArrays service please see: http://affymetrix.arabidopsis.info/
or email affy@...

Best Wishes

Neil Graham

--------------------------------------------------
NASC
Plant and Crop Sciences Division
University of Nottingham
Sutton Bonington Campus
Loughrough
LE12 5RD

www.arabidopsis.info
-------------------------------------------------

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Arabidopsis in teaching intro. biology

2009-11-05T07:09:55Z

Dear Colleagues,

I would like to know if any of you use Arabidopsis in introductory biology teaching courses? If so, would you be so kind as to share with me the experiment that you perform, the strains/mutants used, and a general idea in how long the experiment takes, and the source and cost of materials?

Thank you ever so kindly,

Eric D. Brenner, PhD.
Clinical Assistant Professor
Department of Biology
New York University
609 Silver Building
100 Washington Square East
New York, NY 10003
wk: 212-992-8693
fx: 212-995-4204

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looking for pBI221

2009-11-03T23:14:38Z

Dear colleagues,
I am looking for an old plasmid, pBI221 (if I recall well, a pUC-based
plasmid with a 35Spromoter-GUS-Nosterm construct in it). It used to be
sold by Clontech, in the old days.If anyone has some left and could
spare me an aliquot, I would be grateful.
Regards
Jean-luc

--
Jean-Luc GALLOIS
INRA-UR 1052
Génétique et Amélioration des Fruits et Légumes
Domaine St Maurice, BP94
84143 Montfavet cedex, France
tel : +00 33 (0)4 32 72 27 96
e-mail : jlgallois@...

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Assistant Professor Position Available; University of Missouri

2009-11-03T16:09:14Z

UNIVERSITY of MISSOURI
Position Description: The Division of Plant Sciences, University
of Missouri, invites applications for a tenure-track position in
plant cell wall biology. The 12-month, assistant professor position
is 60% research and 40% teaching.
Responsibilities: The successful candidate will be expected to
establish an innovative, extramurally funded research program
on the biology, development, and degradation of plant cell walls
and associated ligno-cellulosic structures. Research should focus
on utilization of cellulosic compounds by the emerging biofuels
industries and by economically important food-animal
(livestock) species. The University of Missouri has a long
history of collaboration within the Division of Plant Sciences
and with other teams of scientists across campus. The candidate
will be expected to explore collaborative opportunities with the
Interdisciplinary Plant Group, the University of Missouri Center
for Sustainable Energy, and teams of scientists working on
thermo-chemical conversion of biomass, pasture-based dairies,
and the forage-based beef industry. Accessible to the candidate
are excellent laboratory and field research facilities (both on and
off-campus research centers) within the Missouri Agricultural
Experiment station network. The successful candidate is
expected to participate in the undergraduate and graduate
teaching and service missions of the Division of Plant Science.
Teaching responsibilities include an undergraduate forage crops
class, as well as a new course in bio-energy crops. Future
teaching opportunities could include self or team-taught
graduate courses in the candidate's area of expertise.
Qualifications: The applicant must have a Ph.D. degree in Crop
Science, Agronomy, Plant Sciences or related field. Effective oral
and written communications skills are required. Training in the
development, degradation, biochemistry, or physiology of cell
walls as it relates to the biofuels and/or food-animal industries is
desirable. Post-doctoral experience is also desirable.
Applications: Applicants should electronically submit to
PlantSci@... the following items in MSWord or
PDF format: a letter of application, a curriculum vitae,
transcripts, a list of four references and their contact
information, and reprints of major publications. Hard copies of
required materials can be sent to
Christa Smith, ESA
Division of Plant Sciences
1-41 Agriculture Bldg.
University of Missouri
Columbia, MO 65211.
Questions regarding this position should be directed to
Dr. Rob Kallenbach, Chair, Search Committee, at
kallenbachr@... or 573-884-2213.
Job Description #: 1506453; OARS file # 090218
Salary and Benefits: Benefits available include health, dental, life
and disability insurance and a retirement plan. Salary will be
commensurate with qualifications and experience.
Application Deadline: Review of applications will begin February
1, 2010 and will continue until a qualified candidate is identified.
The University of Missouri-Columbia is an Equal Opportunity/Affirmative
Action employer. To request ADA accommodations, please contact our ADA
coordinator. (V/TTY).
Visit the University of Missouri-Columbia's web site a

Gary Stacey, Ph.D.
Director, Center for Sustainable Energy
Assoc. Director, National Center for Soybean Biotechnology
Divisions of Plant Sciences and Biochemistry
Department of Molecular Microbiology and Immunology
271E Christopher S. Bond Life Sciences Center
University of Missouri
Columbia, MO 65211
Office phone: 573-884-4752
Lab Phone: 573-884-4799
FAX: 573-884-9676
email: staceyg@...<mailto:staceyg@...>
NEW LAB WEBSITE: http://www.staceylab.missouri.edu/
MU CSE site: http://www.energy.missouri.edu/
NCSB site: http://www.soybiotechcenter.org<http://www.soybiotechcenter.org/>
NSF Project site: http://www.soybeangenome.org<http://www.soybeangenome.org/>

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Regarding your question on Agrobacterium transformation

2009-11-03T08:31:52Z

Hi Ben,

I am writing regarding your question about Agrobacterium mediated transformation. As I have experienced after 48 hours of co-cultivation, the gene expression starts. As soon as the gene enters in the nucleus its transcription starts. Moreover its further expression depends upon the integration position of gene in the chromosome. I have observed that in gene gun transformation, next day expression was observed.
This is my understanding on the topic.

Regards

Muhammad Shahzad Anjam
Lecturer Biotechnology, Institute of Biotechonology ,
Bahauddin Zakariya University , Multan (www.bzu.edu.pk)
Pakistan .

Contact Details:
Office (Phone) +92(0)61 9210071-4, Ext: 1924, 3900
Cell Phone: +92-333-8174001
E-mail: shahzadanjam@...
E-mail: shahzadbio@...

Get your preferred Email name!
Now you can @ymail.com and @rocketmail.com.
http://mail.promotions.yahoo.com/newdomains/aa/
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The timespan between Agrobacterium infection and active exgenous gene expression

2009-11-01T17:07:56Z

I am wondering, after infected by Agrobacterium tumefaciens, how soon will
the gene in the T-DNA fragment will start to be actively expressed in
Arabidopsis. Are there any studies on this topic? Thanks.

Ben
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Job posting

2009-10-27T04:31:24Z

To whom it corresponds,

Find below the description of our job offer with kindly request to post it in the Arabidopsis Bionet:

International PhD Program Tuebingen, Spring 2010

The Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory in Tuebingen, Germany, invite applications for PhD positions in: Evolutionary Biology, Ecological Genomics, Developmental Genetics, Animal Development , Plant Development, Quantitative Genetics, Molecular & Cell Biology, Biochemistry, Structural Biology and Bioinformatics

Highly qualified applicants from all countries are invited to apply. All applicants must hold or anticipate receiving a Diploma or Masters degree by the time of their start as a PhD student at our institutes. Candidates have to be fluent in written and spoken English. The positions are funded by Max Planck Fellowships.

Application form, evaluation forms (2 needed) and all details about our online registration are available at <http://www.eb.mpg.de/phd-program> www.eb.mpg.de/phd-program

Application deadline is November 25, 2009. After the review of completed applications selected candidates will be invited for personal interviews in Tuebingen during February 10-12, 2010.

Thanking you for the posting in advance!

With kind regards,

Carolina Müller

Dr. Carolina Müller, PhD Program Coordinator

Tel: +49 7071 601 1354

Fax: +49 7071 601 1353

E-mail: <mailto:carolina.mueller@...> carolina.mueller@...

PhD Program Office

Max Planck Institute for Developmental Biology

Spemannstr. 35; 72076 Tübingen

http://www.eb.tuebingen.mpg.de/phd-program

Dr. Carolina Müller, PhD Program Coordinator

Tel: +49 7071 601 1354

Fax: +49 7071 601 1353

E-mail: <mailto:carolina.mueller@...> carolina.mueller@...

PhD Program Office

Max Planck Institute for Developmental Biology

Spemannstr. 35; 72076 Tübingen

http://www.eb.tuebingen.mpg.de/phd-program

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postdoc position: Arabidopsis-aphid interactions

2009-10-26T22:05:00Z

A postdoctoral position is available to study interactions between
Arabidopsis and Myzus persicae (green peach aphid) in Georg Janders lab
at the Boyce Thompson Institute. The focus of this research is the
functional analysis of aphid saliva, with particular emphasis placed on
identifying salivary effectors that either facilitate insect feeding or
elicit plant defense responses. Other research will include analysis of
mutants and natural variation in Arabidopsis aphid resistance. Development
of additional areas of interest within the scope of the project is
encouraged. The position will be filled as early as January, 2010, and
funding is available for two years. Candidates with backgrounds in
molecular biology, insect behavior assays, or small molecule analysis are
particularly encouraged to apply. The Boyce Thompson Institute is a
private not for profit research organization located on the campus of
Cornell University in the scenic Finger Lakes region of upstate New York.
Information about the institute and its facilities can be found at
http://bti.cornell.edu. BTI is an equal opportunity employer. Please send
a description of prior research experience, career goals, curriculum
vitae, and contact information for three references to: Georg Jander,
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; email:
gj32@...; phone: (607) 254-1365.

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LR Gateway reaction pENTR223.1-Sfi-ORF in to pK7WGF2- problem

2009-10-26T02:44:06Z

My question is did any of you had a problem doing the LR reaction (gateway
recombination) with the* *pENTR223.1 Sfi-ORF (from ABRC) and the* *pK7WGF2
(or any other Gateway Destination vector). If you had this problem how did
you solve it?
Thanks
--
Yuval Kaye
Department of Plant & environmental Sciences
Institute of Life Sciences
The Hebrew University of Jerusalem
Givat Ram, Jerusalem, 91904, Israel
E-Mail:yuval.kaye@... <E-Mail%3Ayuval.kaye@...>
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Postdoc position: plant-insect interactions

2009-10-24T19:08:50Z

A postdoctoral position is available to study plant-insect
interactions in Georg Jander's lab at the Boyce Thompson Institute.
Genetic, biochemical, and insect behavior research approaches will be
used to study natural variation in maize resistance to aphids and
rootworms. Responsibilities of the successful applicant will include
the design and implementation of laboratory and field experiments
related to maize-insect interactions. Development of additional areas
of interest within the scope of the project is encouraged. The
research will also involve close interactions with engineers at
Cornell University who are developing automated insect detection
systems for laboratory and agricultural applications. The position
will be filled as early as January, 2010, and funding is available
for three years. Candidates with backgrounds in genetic mapping and
quantitative genetics are particularly encouraged to apply. The Boyce
Thompson Institute is a private not for profit research organization
located on the campus of Cornell University in the scenic Finger
Lakes region of upstate New York. Information about the institute and
its facilities can be found at
<http://bti.cornell.edu/>http://bti.cornell.edu. BTI is an equal
opportunity employer. If interested, please send a description of
prior research experience, career goals, curriculum vitae, and
contact information for three references to: Georg Jander, Boyce
Thompson Institute for Plant Research, Ithaca, NY 14853, USA; email:
<mailto:gj32@...>gj32@...; phone: (607) 254-1365.

*********************************************************
Georg Jander
Boyce Thompson Institute for Plant Research
Tower Road
Ithaca, NY 14853

gj32@...
Phone: 607-254-1365
FAX: 607-254-1502
http://bti.cornell.edu/jander/

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fluorescent protein vectors

2009-10-24T09:01:35Z

Hi,
I'm looking for a pDONR P2R-P3 vector or a binary vector without
promoter containing a C-terminal fluorescent tag other than YFP or GFP.
Thanks

Nuria

--
**************************

Nuria Sanchez Coll, PhD.
Dangl Lab
Dept. of Biology, CB#3280
Coker Hall Rm. 108
Univ of North Carolina
Chapel Hill, NC 27599-3280

Phone 919-962-5838
Fax 919-962-1625

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Arabidopsis cDNA expression library for yeast needed

2009-10-23T20:30:02Z

Hi all,

We are looking for Arabidopsis cDNA expression library for yeast driven
by GAL promoter (or any other inducible promoter), preferably one
enriched with low abundant cDNAs . If anyone knows where I can find it
or if you have one, please drop me a line.

Any help will be appreciated. Thank you, udi

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

Ehud Katz

Postdoctoral fellow

Department of Plant Sciences,

Plant Reproductive Biology, Mail Stop 5

University of California

One Shields Ave,

Davis, CA 95616

e-mail: ekatz@...

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IPMB Gramene and Plant Ontology workshop

2009-10-22T12:10:34Z

Dear IPMB Congress participants,

We would like to invite the attendees of the 9th International Plant
Molecular Biology (IPMB) Congress (http://www.ipmb2009.org/) to be held
from October 25-30, 2009 in St. Louis, MO, USA to the Gramene Database
and Plant Ontology Workshop.

The workshop is free and open to everyone.

Time: Monday October 26, 6-9pm

Location: Room # 104/105 @ the meeting venue

Workshop Title: Comparative Plant Genomics with the Gramene database and
Plant Ontology project

Schedule:
6-7pm: GRAMENE (www.gramene.org)
-Get familiar with Gramene Database
-How Gramene can help in your research
-Questions and Answers

7-8pm: PLANT ONTOLOGY (www.plantontology.org)
-Get familiar with Plant Ontology (PO) resource
-How can PO resource help you
-Questions and Answers
8-9pm:
Discussion with the community of interested researchers and
their participation in building community based curation
network.
- Plant Gene Wiki
- Metabolic and regulatory Networks
- Your feedback and interests.

--
Pankaj Jaiswal
Web: www.gramene.org
www.plantontology.org

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Post Doctoral Positions

2009-10-22T08:42:27Z

POST-DOCTORAL POSITIONS
Multiple positions in the areas of:
· Plant Cell Biology

· Protein Stability

· Signal Transduction

· Synthetic Biology

· Protein Structure and Function

Join a dynamic group working on cutting-edge approaches in Plant Molecular Biology and Synthetic Biology. Synthetic Biology is an exciting and broad approach using rational and computational design of genes, proteins and genetic systems for a specific purpose (Basu et al., 2005; Bio et al., 2006; Bowen et al., 2008; Das and Baker, 2008). Synthetic Biology brings the accuracy of electrical and computer engineering to plant molecular biology and design of new plant traits. One example, it is possible to control what is sensed in plants with computer designed receptors. Synthetic Biology work has produced programmable three- dimensional pattern formation and spatiotemporal control of cell signaling.
We have been using synthetic biology to re-design plants with useful traits and understand fundamental question about natural processes. We are expanding plant synthetic biology to broader areas such as those described for yeast and bacteria. For example, we provide input with computer designed receptors that activates a plant synthetic signal transduction pathway. Normal signal transduction is not a linear process but instead involves interactions with numerous components and pathways allowing fine-tuning of a response to a specific cell, tissue, developmental stage or environment. To begin to dissect complex signal transduction processes we built a synthetic system (Antunes et al., 2009b; Antunes et al., 2009a) and are using the tools of synthetic biology to further the approach. Because our system is constructed of modular and standardized parts we can re-assemble the system to ask how native molecules work. For details please see: http://rydberg.biology.colostate.edu/sites/medfordlab/ . The synthetic signal transduction system or biological input-output pathway is directed to producing a specific output. The output could accumulation of biofuels, flowering or a visual response. Our system is modular and by making chimeric molecules (e.g., synthetic::natural) we are able dissect fundamental processes normally used by plants.
These are competitive positions for Post-doctoral Associates and Research Associates and offer generous salaries. Applicants must be U.S. citizens. The successful candidate will join a dynamic group applying synthetic biology to plants. In addition to the above, because we believe any new technology should have a positive impact on the environment we collaborated with PrecisionBiosciences (http://www.precisionbiosciences.com<http://www.precisionbiosciences.com/>/) , and computationally re-designed proteins to produce a means to target T-DNAs and remove unwanted DNA (e.g., herbicide and antibiotic resistant genes).
For post-doctoral positions, a Ph.D. in molecular biology, cell biology plant molecular biology or a related field is required. Ideal applicants will have experience in molecular biology, plant cell biology or gene cloning. Experience with transgenic plants is helpful but not essential. Well developed skills in written and verbal communication are desirable. The incumbents are expected to interact with other post-docs, graduate students, and undergraduate students. Duties include a variety, molecular biology techniques, cell biology studies, synthetic gene construction, bacterial expression, production and analysis of transgenic plants, planning experimental approaches based on research literature, and interpreting results. The successful individuals will be self-motivated and capable of independent thought and research.
The Medford lab is located in the Biology Department at Colorado State University in Fort Collins, Colorado. Fort Collins is a city of 130,000 located at the base of the Rocky Mountains about an hour north of Denver. Colorado boasts 300+ sunny days a year and numerous recreational activities exist from the nearby mountains such as world class skiing and hiking.
Please apply at: http://www.biology.colostate.edu/employment.html Click on the link for Post-Doctoral Associate or Research Associate Open pool. Indicate attention to Dr. June Medford.

Antunes, M.S., Morey, K.J., Tewari-Singh, N., Bowen, T.A., Smith, J.J., Webb, C.T., Hellinga, H.W., and Medford, J.I. (2009a). Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5, 270.
Antunes, M.S., Morey, K.J., Smith, J.J., Albrecht, K.D., Bowen, T.A., Zdunek, J.K., Troupe, J.F., Cuneo, M.J., Webb, C.T., Hellinga, H.W., and Medford, J.I. (2009b). Computationally-designed receptors and synthetic signal transduction allow plants to serve as detectors for human and environmental use. (in review).
Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H., and Weiss, R. (2005). A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134.
Bio, F.A.B.G., Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R. (2006). Engineering life: building a fab for biology. Sci Am 294, 44-51.
Bowen, T.A., Zdunek, J.K., and Medford, J.I. (2008). Cultivating plant synthetic biology from systems biology. New Phytol 178, 583-587.
Das, R., and Baker, D. (2008). Macromolecular modeling with rosetta. Annu Rev Biochem 77, 363-382.

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Plant culture vessels for arabidopsis

2009-10-22T06:12:57Z

I am looking for Plant cell culture vessels with specific dimensions to grow
Arabidopsis plants. They were available with SIGMA as Phytacon Vessel with
lid (product number P5557), clear polypropylene, Autoclavable with
dimensions
as Rim approx. 116 mm diam. (approx. 4-1/2 in.)
Base 86 mm diam. (3-3/8
Size: H 140 mm.
However, Sigma has discontinued this particular product. Please suggest me
an equally good product (which stands repeated autoclaving) from
other companies
in US.

Thank you.

Surekha

Dear Surekha

I refer back to your above stated requirements.Please advise if you got the
products are not.If still interested..I can provide you further details.

Abdul Aziz M.Yousuf

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Removal of the lower epidermal layer from mature rosette leaves?

2009-10-21T17:53:09Z

Dear Arabidopsis community,

We are looking for a method to conveniently remove the lower epidermal layer (and preferably mesophyll) from mature rosette leaves. This is for a high throughput screen so the procedure needs to be relatively simple. We have tried floating leaves o/n on pectinase or physically peel away the epidermis, but the latter is way too tedious for the numbers of leaves we need to process. Scraping on fine sandpaper has not worked for us either. If anyone has ideas or proven methods we would be glad to hear.

Thanks, Antony

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Faculty Position in Plant Biology at Penn State University

2009-10-21T13:30:55Z

The Department of Biology at The Pennsylvania State University invites
applications for tenure-track faculty positions at the Assistant,
Associate, or Full Professor level in Plant Biology, with research
programs in molecular, cellular, and/or developmental aspects of plant
biology. We particularly encourage applications from individuals whose
work is related to energy storage in plants (including carbon
partitioning; synthesis of cell walls, starch and lipids; and genetic
control of these metabolic pathways) as well as other areas related to
the physiology and development of land plants. Penn State is an
international center for plant biology research, with particular
emphases in cell biology, development, genomics, ecology, and
evolution. Penn State has an outstanding interdisciplinary plant
biology graduate program (http://www.huck.psu.edu/education/plant-biology
), excellent plant growth facilities, and a number of core resources
that provide research support (http://www.huck.psu.edu/facilities),
including bioimaging, molecular biology, genomics, and proteomics.
Interaction with existing research programs is particularly
encouraged. Prospective candidates should have a strong record of
research accomplishments, ability to secure extramural grants, and a
commitment to teaching undergraduates. Candidates should email a
letter of application, curriculum vitae, research prospectus,
statement of teaching interests, and names and contact information of
at least three references, all as a single PDF document, to plantenergy4@...
. Publications and manuscripts (not more than three) may also be
submitted as separate PDF documents along with the application. Review
of completed applications will begin November 23, 2009.

Penn State is committed to affirmative action, equal opportunity and
the diversity of its workforce.

Michael J. Axtell, Ph.D.
Assistant Professor of Biology
410 Life Sciences Bldg.
Pennsylvania State University
University Park, PA 16802 USA
PH: 814-867-0241
http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/

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