Nabble - Bio.net - Dros

GFP on the cheap & LED fluorescence

2009-11-27T18:26:59Z

Hello all in flyland and happy thanksgiving!

TWO QUESTIONS:

Question the first:

I have a question about selecting GFP + and - embryos/larvae etc.

I have access to a stereofluorescence scope, but wondered if there was
a cheaper quicker way of finding GFP embryos without fighting for a
few moments on the scope, using up the expensive Hg lamp etc.

So i am in the midst of purchasing a gel documentation system, and
note that some systems have the capacity to select GFP as well. Either
through a filter on the camera or through a transluscent plate that
you put on top of the transilluminator (that I guess has to be pretty
broad spectrum - 302-560ish? to catch both uv for DNA work AND GFP
variants?)

My fantasy (OK I have no life) is to take my little egg collection
plates with emrbyos on them and put them in the gel doc system and
take a pic in bright field (i mean white light) and then GFP, then
take the plate out and look at the pictures and pick off the relevant
embryos. No waiting around while lamps heat up/explode, no fighting
with other people for the one fluorescent scope etc.

I use CyO-GFP Knirps, (don't know the stock#) and TM3-GFP BL6663.
Don't have an X-linked one but if you know one that's good, be
grateful for the info.

Question the seconde.

I heard a rumour that light sources for fluorescence microscopy are
going LED soon. I mean there is that yucky bluish thing but if it
works, it seems to me a major breakthrough (cheap, lasts forever etc).
Any info? Any recs for scopes that use this? Companies etc? Please
correct me if this is just something i made up and doesn't exist.

Cheers,

Sandra

Dept. Biology
Western Washington University
Bellingham WA

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cleaning glass vials - help!

2009-11-24T06:51:44Z

Hi Robin--

We use a high pH cleaning solution. It's mostly Potassium hydroxide.
Our local manufacturer is Madison Chemical and the cleaner is called
Challenge. There is a lot of info on their website
(http://www.madchem.com). A lot of companies make similar cleaners,
because they're used extensively for "Clean In Place" (CIP)
applications, such as cleaning dairy equipment without disassembly. You
shouldn't have too much trouble identifying something similar if you
want to buy locally. With most dishwashers, I think you'll need a fairly
long wash time to get vials clean.

Good luck,
Kevin

--
Kevin Cook, Ph.D.
Bloomington Drosophila Stock Center
Department of Biology
Indiana University
1001 E. Third St.
Bloomington, IN 47405-7005

kercook@...
812-856-1213 (office), 812-855-2577 (fax)
http://flystocks.bio.indiana.edu

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cleaning glass vials - help!

2009-11-23T07:18:27Z

Hello,

I am having quite a bit of trouble cleaning glass fly vials. My current procedure is as follows: autoclave, pull plugs, rinse, wash. The trouble is that our washer does not remove the pupal cases. I have tried changing the cycle numerous times and am going to try using a different soap. Nothing seems to work though. If anyone could please let me know how they wash glass vials at their facility and what kind of washer they use, I would really appreciate it. THANKS!

Best regards,
Robin

Robin L. Brese
Research Assistant
Department of Molecular Biology, Cell Biology, and Biochemistry
Brown University
Box G-L3
Providence, RI 02912
(401) 863-7365
Robin_Brese@...

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Tech position: UC-Berkeley

2009-11-20T08:24:47Z

A research technician position is available in the Bilder lab (http://mcb.berkeley.edu/labs/bilder/) at the University of California-Berkeley, studying epithelial morphogenesis and tumor suppression. The successful applicant will carry out genetic, molecular biological and microscopy-based experiments in research studying fundamental questions of cell biology and development.

The following qualifications are absolutely required:

-Bachelor's Degree in Molecular Biology, Genetics, Biochemistry or related discipline.

-One or more years of laboratory experience involving techniques listed above.

-Previous experience with Drosophila or other genetic organism.

-Demonstrated attention to detail; strong organizational and problem-solving skills; the ability to communicate effectively.

The position has a two-year term, and is ideal for applicants interested in gaining research experience prior to entering a graduate degree program.

To apply, send a cover letter describing previous experience, CV, and the names of three references to jschoenfeld@...
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yeast two-hybrid

2009-11-17T08:25:52Z

Hi all,

Does anybody know how to get a library of drosophila testis or male
drosophila for yeast two-hybrid? Thanks a lot!
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Re: finding BACs from other Drosophila species

2009-11-16T12:23:44Z

Matt Booker at the Drosophila RNAi Screening Center (DRSC) wrote a
tool for looking up genomic information for non-mel species, including
pseudoobscura. I think this can help you to identify the BACs of
interest.

http://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl

Please feel free to contact Matt if you have any questions about the
on-line tool or suggestions for improvement.

- Stephanie Mohr.

On Nov 16, 2009, at 5:42 AM, Rob Maeda wrote:

> I am trying obtain BACs from Drosophila pseudoobscura. I know we can
> order them from the BAC center (CHORI), but what I can't figure out is
> how one translates a genomic region to a BAC number. For
> melanogaster, one can just look at the gene region and the BACs
> covering it are listed or shown on screen. This does not seem to be
> the case for the other species. Can anyone tell me if there is an
> easy way to do this for the other sequenced species?
>
> Thanks a lot,
>
> Rob Maeda
> University of Geneva
> Dept of Zoology and Animal Biology
> robert.maeda@...
>
> _______________________________________________
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finding BACs from other Drosophila species

2009-11-16T02:42:53Z

I am trying obtain BACs from Drosophila pseudoobscura. I know we can
order them from the BAC center (CHORI), but what I can't figure out is
how one translates a genomic region to a BAC number. For
melanogaster, one can just look at the gene region and the BACs
covering it are listed or shown on screen. This does not seem to be
the case for the other species. Can anyone tell me if there is an
easy way to do this for the other sequenced species?

Thanks a lot,

Rob Maeda
University of Geneva
Dept of Zoology and Animal Biology
robert.maeda@...

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Can anyone know how to prove my shibire[ts] by behavioral test

2009-11-13T23:46:23Z

Dear all,

can anyone know how to test if my shibire-ts works or not by by obserbing behavior of flies on heatshock?

Thanks in advance.

Chao

___________________________________________________________
好玩贺卡等你发，邮箱贺卡全新上线！
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Visualizing Biological Data, 3-5 March 2010: Travel fellowships avaliable

2009-11-13T07:49:22Z

Dear colleagues,

We would like to remind you that November 16 is the deadline for registration and abstract submission for the first EMBO
Workshop on Visualizing Biological Data (VizBi, http://www.vizbi.org), 3-5 March 2010, at EMBL Heidelberg, Germany.

The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all
areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including
microscopy and magnetic resonance imaging). The workshop program includes high-profile speakers from each of these areas, as
well as keynote talks by Ben Fry (Seed Visualization), Bang Wong (Broad Institute) and Chris North (Virginia Tech) - for details,
see http://tinyurl.com/vizbi10Speakers.

We are pleased to announce that we have a limited number of student travel fellowships provided by the European Science
Foundation - see http://www.vizbi.org for details on how to apply. Furthermore, a 15% discount on the registration fee is available
to members of the International Society for Computational Biology (ISCB).

To apply to join the workshop, please go to http://www.vizbi.org and submit an abstract and image related to your work. In
addition to the program of speakers, participants are normally required to present a poster and to give a 'fast-forward'
presentation (limited to 30 seconds and 1 slide). If several people are working on the same project they may use the same
abstract to apply. However, we encourage registrants to submit work that reflects their own interests - and not necessarily new or
unpublished work. But, since places are limited, we will use submissions to select participants whose work is most relevant to the
goals of the workshop. Notifications of acceptance will be sent within three weeks after the close of submissions.

You may also submit your image for consideration for the VizBi Scientific Art prize. This prize will be awarded to the submitted
image that best conveys a strong scientific message in a visually compelling manner.

Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring!

SeÃ¡n O'Donoghue, EMBL
Jim Procter, University of Dundee
Nils Gehlenborg, European Bioinformatics Institute
Reinhard Schneider, EMBL

If you have any questions about the registration process please contact:

Adela Valceanu

Conference Officer
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8625
Fax: +49-6221-387 8158
Email: valceanu@...

For full event listings please visit our website: www.embl.org/events or sign up for our newsletterwww.embl.de/events/newsletter

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FlyBase Genome Database Curator/Annotator Position at Harvard University

2009-11-05T13:16:04Z

Genome Database Curator/Annotator, Biological Laboratories, Harvard
University

FlyBase seeks a full-time Ph.D.-level scientific curator/annotator to
join the FlyBase team in the Dept. of Molecular & Cellular Biology at
Harvard University, Cambridge, under the direction of Prof. William
Gelbart. This is a full-time staff position.

Job description:
Curational responsibilities at the Harvard site include the scanning and
abstracting of analysis of current literature on the molecular biology
of Drosophila, annotation and analysis of the Drosophila melanogaster
genome, coordination of the inclusion of high- throughput molecular
datasets into FlyBase, and design of improved interfaces for providing
molecular data to the user scientific research community. Curators work
as a part of a team, interacting with biologists at other FlyBase sites,
and coordinating with software engineers to develop and improve
software. Curators also interface with the scientific community,
assisting users on-line and at research conference workshops.

FlyBase is constantly evolving, seeking both to improve and to expand
its role within the Drosophila and wider scientific communities. The
ideal applicant will be enthusiastic about participating in this
process, bringing to the FlyBase group expertise and ideas concerning
emerging directions in Drosophila biology and genomic/proteomic analysis.

Required Education, Experience, Skills:
Ph.D. in molecular biology or genetics. Experience with molecular
genetics and Drosophila biology are essential.

To apply:
Please contact William Gelbart (gelbart@...), and include
a CV, a description of research experience and names of three
references. Please cc your communication to the senior curator, Dr.
Beverley Matthews (bmatthew@...).

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searching for EP stock

2009-10-26T13:04:36Z

Check with the Kyoto Stock Center. They were taking a bunch of the EP
insertions.

Kevin

--
Kevin Cook, Ph.D.
Bloomington Drosophila Stock Center
Department of Biology
Indiana University
1001 E. Third St.
Bloomington, IN 47405-7005

kercook@...
812-856-1213 (office), 812-855-2577 (fax)
http://flystocks.bio.indiana.edu

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searching for EP stock

2009-10-26T10:44:47Z

Now that the Szeged Centre has closed, does anyone know whether the Rorth EP
collection is intact anywhere else? I am looking for EP(3)0809, does anyone
happen to have this stock?

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problems with paper lids for stock bottles

2009-10-22T16:50:06Z

Hi!

We've been using paper lids from Genesee Scientific for our stock bottles (6
oz. square bottles). But now

Genesee has changed these paper lids (or their supplier) and those are not
great at all (they do not sit tight, bend easily and

the little lever to lift the lid tears is easily tearing). Does anyone know
of other suppliers for paper lids (42.75mm

in diameter) that are reliable?

Any help or suggestion on this topic would be greatly appreciated!

Best,

Geo

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Re: Dros Digest, Vol 54, Issue 7

2009-10-20T10:58:04Z

why it is not avialable from bloomington centre ?

On Tue, Oct 20, 2009 at 1:03 PM, <dros-request@...> wrote:

> Send Dros mailing list submissions to
> dros@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.bio.net/biomail/listinfo/dros
> or, via email, send a message with subject or body 'help' to
> dros-request@...
>
> You can reach the person managing the list at
> dros-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Dros digest..."
>
>
> Today's Topics:
>
> 1. location of GAL4 CD8GFP third chromosome insertion (ko)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Oct 2009 02:43:48 -0700 (PDT)
> From: ko <kafeikatie@...>
> Subject: [Drosophila] location of GAL4 CD8GFP third chromosome
> insertion
> To: dros@...
> Message-ID: <25972373.post@...>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi. Does anyone know the insertion site of the P{UAS-mCD8::GFP.L}LL6
> p-element found in Bloomington stock # 5130 (y[1] w[*]; Pin[Yt]/CyO;
> P{w[+mC]=UAS-mCD8::GFP.L}LL6). It was generated by Liqun Luo's lab and
> found in : Lee, T., Luo, L. (1999). Mosaic analysis with a repressible
> neurotechnique cell marker for studies of gene function in neuronal
> morphogenesis. Neuron 22(3): 451--461. Any mapping data would be most
> welcome. Thanks. Kate.
> --
> View this message in context:
> http://www.nabble.com/location-of-GAL4-CD8GFP-third-chromosome-insertion-tp25972373p25972373.html
> Sent from the Bio.net - Dros mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> _______________________________________________
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>
> End of Dros Digest, Vol 54, Issue 7
> ***********************************
>

--
Dr Gurudatta B.V., Ph.D.
Post Doctoral Fellow,
1071B, Rollins Research Centre
Biology Department,
MS:1940-001-1AC
Emory university, Atlanta, GA, USA 30322

phone Lab:+1 404-727-4250
Cell Phone:+1 678-643-6243
jaiganesha@...
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location of GAL4 CD8GFP third chromosome insertion

2009-10-20T02:43:48Z

Hi. Does anyone know the insertion site of the P{UAS-mCD8::GFP.L}LL6 p-element found in Bloomington stock # 5130 (y[1] w[*]; Pin[Yt]/CyO; P{w[+mC]=UAS-mCD8::GFP.L}LL6). It was generated by Liqun Luo's lab and found in : Lee, T., Luo, L. (1999). Mosaic analysis with a repressible neurotechnique cell marker for studies of gene function in neuronal morphogenesis. Neuron 22(3): 451--461. Any mapping data would be most welcome. Thanks. Kate.

SL2 or Kc transfection

2009-10-13T12:01:56Z

Dear All,
I am trying to test some putative fly promoter regions using luciferase assays. My transcription factors are in pcDNA3.1.
I saw some regulation of the promoters by the factors initially but when I tried to repeat them, its not working. The initial results were quite convincing.
Now there seems to be no or wacky effect of the factors on the same promoters. Is there any specific reason which might be the cause for this negative result.
Or its impossible to get expression from pCDNA3.1 vectors in fly cell lines.

Any input in this matter will be really appreciated.

Thank you very much
Arindam
--

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Stocks to be removed from the BDSC collection

2009-10-12T15:07:11Z

Selected obsolete, redundant, or low-use stocks are periodically removed
from the Bloomington Drosophila Stock Center collection to make room for
new additions. The "pruning page" at
http://flystocks.bio.indiana.edu/Cull/pruning.htm provides links to
lists of stocks that have been identified for discard and states the
last order date for a given set of stocks. Please review these lists for
stocks you might want to order before they are discarded. If you think a
listed stock warrants continued maintenance at the BDSC please contact us.

--
Kathy Matthews
Bloomington Drosophila Stock Center
Dept. of Biology, Indiana University
1001 E. 3rd St.
Bloomington, IN 47405-7005
email: matthewk@...
voice: 812-855-5782
fax: 812-855-2577

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Re: study of Drosophila behavior

2009-10-12T09:37:57Z

Samar Ezzat wrote:

> Dear all,
>
> I want to study the walking behavior of some trangenic lines of Drosophila . i will use videocamera , but from where can i get the photo optical data analyzer or the Frame -by -Frame film analysis software ?
>
>
> I will apperciate any suggestions given .
>
>
>
> with regards,
> behavior
>
>
>

ImageJ is very good, and will allow you to do frame/frame analysis, even
removing any constant background

chris

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Re: Seeking "Exploded view" diagram of Drosophila

2009-10-11T10:17:56Z

You can find several of these on FlyBase. From the home page go to
Image Browse and click on Adult. You will then see a list of
available images. If you use any of these we would appreciate your
citing their source and FlyBase.

--tk
kaufman@...

On Oct 9, 2009, at 5:33 PM, Chris Bazinet wrote:

>
> I'm looking for some nice diagrams of the Drosophila adult,ideally
> one that
> includes an exploded view showing some major internal organs (e.g.
> gonads,
> brain, gut, etc.) CAn anyone point me to a nice one?
>
> Thanks
>
> Chris Bazinet
>
> --
> View this message in context: http://www.nabble.com/Seeking-%22Exploded-view%22-diagram-of-Drosophila-tp25828219p25828219.html
> Sent from the Bio.net - Dros mailing list archive at Nabble.com.
>
> _______________________________________________
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Seeking "Exploded view" diagram of Drosophila

2009-10-09T14:33:47Z

I'm looking for some nice diagrams of the Drosophila adult,ideally one that includes an exploded view showing some major internal organs (e.g. gonads, brain, gut, etc.) CAn anyone point me to a nice one?

Thanks

Chris Bazinet

Postdoc: Mitochondrial genetics of aging at Brown University

2009-10-07T11:03:31Z

Postdoc at Brown University: Mitochondrial genetics of aging in
Drosophila

A postdoc position is available in the laboratory of David Rand and
Brown University to work on nuclear-mitochondrial genetic interactions
affecting longevity. The general theme of this NIH funded project is
to study the epistatic interactions among nuclear and mitochondrial
genotypes that diet-dependent alterations in longevity and related,
physiological and biochemical traits in Drosophila. Mitochondrial
genotypes from different strains and species of the melanogaster
subgroup are placed on various nuclear genetic backgrounds to dissect
the genetic basis of longevity and the extension of longevity by diet
restriction. The project involves demography experiments, molecular
and quantitative genetic assays of Drosophila strains, genetic mapping
experiments, gene expression and biochemical assays of specific
genotypes, and inferences from molecular population genetics and
evolution.

Applicants must have completed their PhD before starting the position,
and have a strong record of accomplishment from their dissertation
work. Applicants should have some combination of experience with
molecular genetic techniques, Drosophila genetics, longevity of life
history analyses, quantitative genetics, biochemical assays, molecular
evolution, computational analysis, and an interest in evolution or
genetics. The appointment is open for up to 3 years, and successful
candidates will receive guidance in the preparation of an NIH NRSA
Fellowship to pursue related projects.

The position is available now and applications will be reviewed until
the position is filled. To apply please send 1) a CV, 2) a short
statement of research interests and experience, including a paragraph
on how your previous experience makes you well qualified for this
position, and 3) contact information for three references to:

David Rand

email: David_Rand@...

Department of Ecology and Evolutionary Biology

Box G-W, 80 Waterman Street

Brown University

Providence, RI 02912

Voice: (401) 863-2890 (Office)

(401) 863-1063 (Lab)

Fax: (401) 863-2166

web pages:

http://research.brown.edu/research/profile.php?id=1100924991&r=1

http://www.brown.edu/Departments/EEB/rand/index.htm

The Department of Ecology and Evolutionary Biology at Brown is an
interactive group with strengths that span genomics, evolutionary
biology, functional morphology, ecology, and environmental science.
There are close ties to the Department of Molecular and Cellular
Biology, and the Center for Computational Molecular Biology, as well
as the Marine Biological Laboratory in Woods Hole

http://www.brown.edu/Departments/EEB/index.html

http://www.brown.edu/Departments/Molecular_Biology/

http://www.brown.edu/Research/CCMB/

http://www.mbl.edu

http://jbpc.mbl.edu/

http://ecosystems.mbl.edu/

Information on postdoctoral studies at Brown can be found here:

http://biomed.brown.edu/grad-postdoc/

Providence is widely recognized as the Venice of New England and is
wonderful place to live.

http://www.providenceri.com/

----------------------------------------------------------------------------------------------
David M. Rand
Professor of Biology
Department of Ecology and Evolutionary Biology
Box G-W, 80 Waterman Street
Brown University
Providence, RI 02912
Voice: (401) 863-2890 (Office - Walter Hall 202)
(401) 863-1063 (Lab - BioMed Center 516-518)
Fax: (401) 863-2166
email: David_Rand@...
web pages: http://www.brown.edu/Departments/EEB/rand/index.htm
http://research.brown.edu/research/profile.php?id=1100924991&r=1

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study of Drosophila behavior

2009-10-07T06:57:53Z

Dear all,

I want to study the walking behavior of some trangenic lines of Drosophila . i will use videocamera , but from where can i get the photo optical data analyzer or the Frame -by -Frame film analysis software ?

I will apperciate any suggestions given .

with regards,
behavior

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please help, problems with immunostaining Dros larva brain

2009-10-03T01:54:01Z

Dear all,

I am facing problems with homogenous immunostaining of the whole Dosophila larva (3rd instar) brain, as I found after confocal microscopy that the staining / antibody penetration into the interior of the brain was poor. May I know what are some of the solutions to overcome this problem and which holder device should I perform this immunostaining experiment in so as to obtain good mixing during the immunostaining process and do not have to worry about the loss of the very small-sized larvae brains?

I would greatly appreciate any suggestions given. Thank you very much for your kind help.

Best regards,
Joan Sim

Obesity In Drosophila

2009-09-29T02:53:12Z

Dear All,

I am new to these groups and somewhat stumbled across it if i'm
honest, currently I am a final year student at the University of Leeds
and for my research project I will be using drosophila.

The current idea is to take a group of obese drosophila and a group of
lean drosophila and identify how obesity may/or may not effect their
sleep patterns and identify possible reasons why. Hopefully I will
gain some interesting results that are meaningful as obesity and sleep
are big issues at the moment.

My question is how to make an obese drosophila? My intention was to
make a group of drosophila gorge on a high fat feed, but getting this
to occur maybe difficult and I was wondering if anybody knew a good
way on how to get obese flies?

I currently have a few ideas:
1. Starve the drosophila for a period then add a high fat food source
so hopefully they over eat
2. Try keeping the drosophila in a very small confined space with a
high fat food source
3. I am in the process of reading: 'A glucagon-like endocrine pathway
in Drosophila modulates both lipid and carbohydrate homeostasis
K. N. Bharucha,1* P. Tarr,2 and S. L. Zipursky2' here it mentions AKHR
mutants being obese, and so i was going to look into the possibility
of getting some of these mutants or creating them.

I must add that this is very much only an idea and work has not begun
properly yet, but any ideas on this plan or any helpful advice would
be appreciated immensely.

Thank-you

Joseph Kelly

contact emails: jokel_89@...
bs07j5k@...

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Drosophila Gal4 Gut Specific

2009-09-25T10:37:44Z

Hi -

I am interested in the microbiota in the gut of Drosophila. More specific,
I am interested in the effect of the enzyme paraoxonase 1 on the gut
microbiota. We already have transgenic paraoxonase flies, but I am
searching for the best GUT specific driver to express paraoxonase solely in
the gut. I guess my first choice right now is P{drm-GAL4.7.1}1.1 from the
Bloomington collection. Do you know of any others or better driver lines?
Thank you very much.

Mike R

--
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University of Iowa - Internal Medicine
EMRB 440 - Zabner Lab
m.v.rector@...
(319) 795-1691
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Postdoctoral Position in Drosophila Aging and Physiology

2009-09-25T05:32:52Z

Postdoctoral Position in Drosophila Aging and Physiology

A postdoctoral research position in the biology of Drosophila aging
and physiology is available in the group of Dr. Thomas Flatt at the
University of Veterinary Medicine (Department of Biomedical Research,
Institute of Population Genetics), Vienna, Austria (http://
i122server.vu-wien.ac.at/pop/Flatt_website/flatt_home.html). The
postdoc position is funded by a grant from the Austrian Science
Foundation (FWF) and will be for three years.

This research project will focus on the identification of the
molecular basis of the trade-off between reproduction and lifespan in
the fruit fly, Drosophila melanogaster, a powerful genetic model
system. In many organisms, from fruit flies to humans, reproduction
shortens lifespan, but the underlying mechanisms remain largely
unknown (see Flatt & Promislow 2007 in Science). Experiments in C.
elegans suggest that hormonal signals from the gonad affect longevity
(Hsin & Kenyon 1999 in Nature), and we have recently found that
germline ablation extends lifespan and affects insulin signaling in
Drosophila (Flatt et al. 2008 in PNAS). However, the details of this
systemic regulation of lifespan by the reproductive system remain
unclear. In our project we are interested in dissecting the endocrine
and physiological mechanisms that modulate the reproduction-longevity
trade-off. By employing mutant and transgene analysis, genetic
manipulation of the gonad, epistasis experiments, hormonal
manipulations, and physiological measurements we will examine the
mechanisms whereby signals from the reproductive system modulate
longevity.

We are seeking a highly talented, dynamic, independent, and self-
motivated young biologist with good social skills. The successful
candidate will have a Ph.D. and a strong background in genetics and
molecular biology using the Drosophila system. Some background in the
biology of aging, evolutionary biology, and/or physiology and
endocrinology would be ideal, but is not required. The working
language in the laboratory is English, so the candidate should be
proficient in spoken and written English. German skills, although
helpful, are not essential. The initial appointment will be made for
one year, with a possible extension to up to three years. The annual
salary is 54,180 Euro (before tax). The position is available as of
now, but the starting date is negotiable.

In a 2009 world-wide survey by the William M. Mercer Institute, Vienna
ranked first world-wide in terms of standards of living. Vienna is a
beautiful, historical yet modern city, located in the heart of Europe,
close to the Alps and to major cities like Munich, Zurich, Prague, and
Budapest. Being famous for its concert sites, opera houses, theathers,
museums, and coffee shops, Vienna also provides great outdoor
activities, such as sailing on the Neusiedler See, ice skating, biking
and hiking in the Viennese woods and the nearby Alps. Moreover, the
city has a wide range of great restaurants, bars, wineries, cinemas,
clubs, libraries, galleries, and art collections. The Vienna area is
also an exceptional and highly international research environment.
Four major life science universities and three world-class research
institutes (GMI, IMBA, IMP) provide a dynamic and interactive setting.
Vienna hosts an active Drosophila community, and the onsite
availability of the Drosophila RNAi center (VDRC) provides a great
opportunity for functional Drosophila work. In population genetics and
evolutionary biology, the Vienna research area also provides excellent
prospects, due to a growing number of evolutionary research groups.

To apply for this position, please send a single pdf file including:
(1) a cover letter explaining why you would like to join our group,
(2) your Curriculum Vitae (including a description of your skills),
(3) your publication list, (4) a statement of research interests, and
(5) contact details for 2-3 academic references who are willing to
write a reference letter on your behalf to the following email
address: thomas.flatt@...

Informal inquiries are welcome and should be sent to the same e-mail
address. For further information see (http://i122server.vu-wien.ac.at/
pop/Flatt_website/flatt_home.html).

The deadline for submission is 31 October 2009.

Dr. Thomas Flatt
University of Veterinary Medicine
Department of Biomedical Research
Institute of Population Genetics
Veterinärplatz 1 / Josef Baumann Gasse 1
A-1210 WIEN
Austria

VOX +43(0)1-25077-4334
FAX +43(0)1-25077-4390
E-mail: Thomas.Flatt@...

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Reactome Pathway Database User Survey

2009-09-24T08:57:15Z

Reactome is committed to providing access to high-quality pathway
information and helpful data analysis tools. With this in mind, we
are actively soliciting comments from the research community in order
to assess community needs. We are interested to hear about your
experience with Reactome, and would like to know a bit about your
background and research interests so that we can continue to improve
the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Thank you for taking part.

Robin Haw
Manager of Reactome Outreach
Outreach [at] reactome.org
http://www.reactome.org

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PhD fellowships in ageing biology

2009-09-22T03:54:08Z

Cologne International Graduate School

>From Embryo to old Age,

Development, Health and Disease

6 Fellowships

3-year Ph.D. programme starting spring 2010

The University of Cologne has a long-standing tradition and world-wide
reputation for top-level molecular biological research. Beginning in Spring
2010 the Research School in Biology From embryo to old age: the cell
biology and genetics of health and disease will be offering a high-level
Ph.D. programme for students with excellent qualifications. The
participating research groups use microbial, plant and animal model systems
to investigate cell biological and genetic mechanisms whose perturbation
during the life cycle of an organism results in disease.

The three-year programme starts with a six-month rotation and course period,
followed by a PhD project in one of the participating groups. Seminars and
training courses complement the research work. Comprehensive support is
provided throughout the programme. The programme language is English.
Accepted students will receive a laptop computer and 500 EUR to get started
in Cologne. No tuition fees are charged.

Six competitive three-year fellowships (initially 1000 EUR, then a minimum
of 1300 EUR per month) are available.

We invite you to apply to the IGSDHD in Cologne, the exciting city in the
heart of Europe.

To obtain further information please visit our website at:

<http://www.uni-koeln.de/bio-graduateschool/>
http://www.uni-koeln.de/bio-graduateschool/

Submission deadline for complete applications is October 31, 2009

Dr. Isabell Witt

Graduate School for Biological Sciences

Zülpicher Strasse 47

D-50674 Cologne

+49 (0) 221 4701683

fax: +49 (0) 221 4701632

isabell.witt@...

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ARTHROPOD GENOMICS SYMPOSIUM, June 10 to 13, 2010, in Kansas City

2009-09-21T10:29:51Z

Please SAVE THE DATES of.
June 10 to June 13
on your calendar and plan to attend the
4th ANNUAL ARTHROPOD GENOMICS SYMPOSIUM.

DATES: June 10 to 13, 2010
PLACE: Kansas City Marriott on the beautiful Country Club Plaza
SPONSOR: K-State Arthropod Genomics Center, Kansas State University
TENTATIVE SCHEDULE:
Thursday evening, June 10 - Keynote presentation and welcome reception
Friday & Saturday, June 11 and 12 - Platform and Poster sessions
Sunday morning, June 13 - Roundtable discussion with
the ArthropodBase Consortium
Noon, Sunday, June 13 - Activities will conclude

Speakers who are experts in arthropod genomics and bioinformatics with
applications in genomics will be announced soon! Additional speakers will
be selected from contributed posters.

Demonstrations: Database and bioinformatics tools developers will be
available at the meeting to provide hands-on demonstrations.

Visit our website, www.k-state.edu/agc, for updates as details are
finalized.

Please share this announcement with colleagues and students!

Doris Merrill, Program Coordinator
K-State Arthropod Genomics Center
Division of Biology, Kansas State University
104 Ackert Hall, Manhattan, KS 66506-4901
(785) 532-3482, dmerrill@...
www.k-state.edu/agc

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Bionet Arthropods news/discussion list request for comments

2009-09-21T09:49:52Z

There is interest among biologists who study various Arthropods
for a shared public news and discussion group. Please comment if
you would like to see a new Arthropod mailing list.

Values of sharing biology discussion and news among those who
study insects and crustaceans has been noted at recent venues,
including the Arthropod Genomics Symposia
(http://www.k-state.edu/agc/), Entomological Society meetings
(e.g. http://www.entsoc.org/), and recent arthropod genome projects.

BIOSCI/Bionet (www.bio.net) continues to serve such bioscience
community news needs, as it has since its inception 20
years ago by Michael Ashburner and others. Community group
lists at Bionet include DROSOPHILA, ARABIDOPSIS, MAIZE,
Medicago, CELEGANS, CHLAMYDOMONAS, Mycology, YEAST, and ZBRAFISH.
Bionet currently is maintained at Indiana University by Don
Gilbert, a genome informatician specializing in arthropods.

There are related mailing lists (see below). The uses and content of
this proposed list would presumably be similar. Please comment
whether you believe existing lists cover this need or prefer
a new one. Comment also on proposed charter and areas. Perhaps
this group should focus on one area such as genomics of arthropods.

Send your comments to bioforum@... for public discussion
or biosci-help@... (private to Don Gilbert).

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

Proposal for ARTHROPOD/bionet.arthropod (moderated)

One line Description: Arthropod Biology

Status: Moderated
Moderators: to be named

Proposed mailing list name: arthropod @ net.bio.net
bionet-arthropod @ net.bio.net (alias)
Proposed USENET name: bionet.arthropod

Charter:

The purpose of the ARTHROPOD newsgroup is to provide a public
forum for scientific discussion, communication and collaboration
of shared biology interests among scientists studying species of
Arthropoda, including insects and crustaceans. Topics may include
evolutionary biology, ecology and enviroment, genomics, molecular
and organismal biology, methods and biotechnology, informatics
and databases, and any other aspect touching on shared biology of
arthropods.

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

Related public mailing lists:

Arthropod Genomics Announcements
http://listserv.ksu.edu/archives/arthropodnews.html

Bionet Drosophila
http://www.bio.net/biomail/listinfo/dros

Vectorbase (mosquitoes, other human vectors)
http://www.vectorbase.org/Help/Mailing_lists

Aphid genomics
http://www.eco.princeton.edu/mailman/listinfo/aphidgenomics

Canadian Arthropods electronic mailing list
http://www.biology.ualberta.ca/bsc/english/mailinglist.html

List of various insect and arthropod mailing lists
http://www.ent.iastate.edu/List/directory/94/vid/4

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

Topics of Discussion:
-- please suggest areas of special interest

In addition this newsgroup will provide:
A forum for the exchange of information about future meetings
of interest to those studying insects, crustaceans and other
arthropods.

A venue for help and sharing of methods and techniques in areas
such as Biological resources; Evolutionary and phylogenetic
techniques; Genome analysis techniques; etc.

Proposed discussion leaders/moderators:
-- to be named

The suggested list name is ARTHROPOD or bionet.arthropod
Alternate spellings, ARTHROPODA or ARTHROPODS, can be considered
or other names.

Sincerely,

Don Gilbert
BIOSCI/bionet Manager
biosci-help at net.bio.net

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is there transposase repressor construct?

2009-09-16T09:09:33Z

Hi Olaf--

Using a repressor construct in crosses to make deletions from
trans-heterozygous P elements is a reasonable idea. I considered it when
we were using the method to make deletions for the Bloomington Stock
Center collection (described in Parks et al. (2004) Nature Genetics 36:
288-292), but decided it wasn’t worth it for our screens. Let me see if
I can explain my thinking.

First, it’s impossible to predict the exact positions of breakpoints of
deletions made by the Hybrid Element Insertion (HEI) mechanism in the
presence of trans-heterozygous P insertions. One breakpoint should
correspond to the insertion site of one of the starting insertions. The
other breakpoint will usually be in the vicinity of the insertion site
of the second P element, but you can’t predict exactly where it will
be--it could be proximal or distal to the second insertion or within the
transposon. No one knows why the hybrid element usually inserts near one
of the starting insertions. It’s probably a physical constraint on the
chromatids involved, but that’s just speculation. For an in-depth look
at the HEI mechanism, you should work your way through the following
three papers. It’s straightforward to see how their results apply to
trans-heterozygous P insertions.

Gray, Y.H., Tanaka, M.M., Sved, J.A. (1996). P-element-induced
recombination in Drosophila melanogaster: hybrid element insertion.
Genetics 144(4): 1601--1610.
Preston, C.R., Engels, W.R. (1996). P-element-induced male recombination
and gene conversion in Drosophila. Genetics 144(4): 1611--1622.
Preston, C.R., Sved, J.A., Engels, W.R. (1996). Flanking duplications
and deletions associated with P-induced male recombination in
Drosophila. Genetics 144(4): 1623--1638.

We were generating very large deletions. A local hop in the intermediate
generation preceding the Hybrid Element Insertion event giving rise to
the deletion wouldn’t change the predicted size of the deletion by very
much. Indeed, most of our deletions had the expected breakpoints at the
level of polytene cytology. A few kb of doubt about the positions of the
endpoints probably doesn’t matter too much for a deletion in the
megabase size range. I figured that anyone wanting to know the exact
genomic coordinates of the deletion breakpoints could characterize them
by sequencing off the ends of the P element retained on the chromosome
following the HEI deletion event.

I understand that it’s a different situation when you’re trying to
generate small deletions. A few kb difference between the size of the
deletion based on the insertion sites of the starting P elements and the
actual deletion size can make a big difference if you’re trying to
delete specific genes. Using a repressor construct MIGHT make sense, but
I think you still need to think about whether it’s worth the effort.
Basically, you’re playing a numbers game. Not every P element hops in
the presence of transposase in every generation. The probability of P
transposition in the intermediate generation of the screen is not that
high. It can happen, but the odds are in favor of it not transposing.
You may save yourself work by doing the screens as we described in Parks
et al. and then characterizing the breakpoints in the resulting
deletions. You can keep the ones with desirable breakpoints and discard
the others.

It would be interesting to know if the inclusion of a repressor
construct would prevent transposition in the intermediate generation of
the screen, so I’m not discouraging you from trying. I’m just saying
that it’s not absolutely necessary to get what you want.

If you want a single gene deletion, you may be able to get it more
easily from a conventional male recombination screen employing a single
P insertion as described in the Preston, Sved and Engels article cited
above. Those screens are easier and generate a lot of deletions of less
than ~10 kb. I don’t think screens using trans-heterozygous P insertions
would be my first choice for recovering small deletions. Of course, the
FLP-FRT system would be my first choice, but I’m guessing that
appropriate insertions aren’t available for the gene you’re interested
in if you’re thinking about HEI screens. You could also check to see if
appropriate insertions are available to use hobo transposition to make
deletions using P{wHy} insertions (see
http://flystocks.bio.indiana.edu/Browse/insertions/PwHy-top.htm).

I hope this helps a bit,
Kevin

--
Kevin Cook, Ph.D.
Bloomington Drosophila Stock Center
Department of Biology
Indiana University
1001 E. Third St.
Bloomington, IN 47405-7005

kercook@...
812-856-1213 (office), 812-855-2577 (fax)
http://flystocks.bio.indiana.edu

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is there transposase repressor construct?

2009-09-16T05:40:29Z

Dear Drosophilist’s

If you want to construct deletions using P-elements in trans (Adam C. Paré et al., Genetics, Vol. 181, 53-63, 2009), one have to combine one (first) p-element with the transposase source (Delta2-3). In this first step you can not avoid the mobilisation (or local hop) of this first p-element before you combine it with the second p-element.

My idea is to repress (inhibit respectively) P-element mobilization by the transposase repressor (product of the first three exons of the transposase gene).
Does anybody of you know if there is an existing transposase repressor element (containing only the first three exons of the transposase gene) inserted in genome of Drosophila? It shouldn’t be able to be mobilized by the wild type P-element transposase (like the Delta2-3 element or in a piggyBac element e.g.)?

Any suggestions or critics to the idea are welcomed!

hypothetic crossing scheme:

marked chromosome first p-element / CyO ; TMS (containing Delta2-3) Sb / Lyra or Drop (marked chromosome) p-(transposase-repressor)

crossing to

marked chromosome second p-element / CyO ; +/+

collect male offspring (Sb without Lyra or Drop)

marked chromosome first p-element / marked chromosome second p-element ; TMS (containing Delta2-3) Sb /+ (in the germ line of these males the transposase induced male recombination takes place)

crossing to
Plum-balancer / CyO

collect balanced male offspring (without Sb)

-------------------marker-------------first p-element---------------------------------------------------------------------------------------------------
--------------------------------------------------------------second p-element-----------marker------------------------------------------------------

male recombination results in

-------------------marker-------------first p-element ### second p-element-----------marker--------------------------------------------------
------------------------------------------------------balancer-------------------------------------------------------------------------------------------

(deleted segment = ###)
principle of method (Adam C. Paré et al., Genetics, Vol. 181, 53-63, 2009)

Best regards,
Olaf

Dr. Olaf Vef
Institute for Genetics
Johannes Gutenberg-University, Mainz
Johann-Joachim-Becher-Weg 32
D-55128 Mainz
GERMANY

email: ovef@...
Tel.: 049-(0)6131-3925347
Fax: 049-(0)6131-3925845

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RE: Food issues, please help

2009-09-16T01:55:46Z

Dear Helen

Dear Helen
Do you see something in your cultures? We had problems with the
development of a slimy layer of bacteria or fungi in the vails. Our
problem was solved by using more Nipagen/methyl paraben (1 gr/liter),
wich I think you should indeed ad late as it is heat sensitive. Our
protocol was not so clear about the amount and we were using much less
before, but I see also protocols using 2-3 gr/liter.
If not all stocks are affected, it might rather be something carried by
the flies than comming from the food.
Good luck, Hans

Dr. Hans Bakker
Hannover Medical School
Dept. Cellular Chemistry OE4330
Build. I3, Level 2, Room 3110
Carl-Neubergstrasse 1
30627 Hannover, Germany
bakker.hans@...
+49.511.5328245

-----Original Message-----
From: dros-bounces@...
[mailto:dros-bounces@...] On Behalf Of Helen
White-Cooper
Sent: Tuesday, September 15, 2009 3:39 PM
To: dros@...
Subject: [Drosophila] Food issues, please help

Dear all,

We have recently had serious problems with some of our fly stock
cultures, and would really like some input into what could be the
problem, and how to solve it.

We use a standard maize/dextrose/yeast/agar recipe. cooking is done in
a large food cooker, typically 40-50 litres per batch. We add propionic
acid and nipagen (dissolved in ethanol) just before dispensing. We cook
every 3-4 weeks. After dispensing we leave the vials/bottles overnight
before plugging. We store cooked food wrapped in autoclave bags at 4C.

We leave the food to come to room temperature before use. Fly stocks
are cultured in an 18C room, or at room temperature.

Last year (september) we bought a new batch of maize. Initially the
food was good and all the flies were happy. Over the next few months
the quality of the food declined, and stocks began to suffer. By March
this year we had big problems. In the most seriously affected stocks
the adults died after being put on the new food. In other stocks the
flies were alive, laid eggs, but no eggs hatched. In many stocks eggs
hatched (at least some did), but it would be 4 weeks or more before
adults eclosed (rather than the expected 3 weeks). Some stocks were
unaffected.

We bought new maize (March 09), and the problem went away, BUT, over the
next few months (june/july) it came back... So, we thought it was due
to maize going off, and switched to another batch, this one had been
bought a while ago, used with no problems and stored at -20, so should
stay fresh. Again, initially (july) everything was fine, but now the
stocks are slowing their generation times / dying off again.

We have had the first batch of maize tested for pesticide residue but it
came back negative. We have also tested it for Bt spore contamination
(yes it is organic...), by heating a maize /water mix to 80C for 15
minutes and plating on media suitable for Bt. we do not get Bt growth,
however there is growth of something (fungal). we have tested this with
flies in a laying bottle and it does not seem to retard egg hatching,
neither is it toxic to adults or larvae (indeed the larvae love it...).

So, does anyone out there have any ideas what could be causing the
problem, and most importantly, how to make it go away? The only things
we can think of are the temperature the food gets to after adding the
maize/ sugar/ yeast mixture (might it have to get up to 85C?, ours
probably only gets to 80C), should we add the nipagen earlier (could the
ethanol be causing the problem?).

Yours in desperation

Helen

--
Dr Helen White-Cooper
School of Biosciences
Museum Avenue
Cardiff University
Cardiff
CF10 3AX

Tel 029 20875492

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Food issues, please help

2009-09-15T06:38:35Z

Dear all,

We have recently had serious problems with some of our fly stock
cultures, and would really like some input into what could be the
problem, and how to solve it.

We use a standard maize/dextrose/yeast/agar recipe. cooking is done in
a large food cooker, typically 40-50 litres per batch. We add propionic
acid and nipagen (dissolved in ethanol) just before dispensing. We cook
every 3-4 weeks. After dispensing we leave the vials/bottles overnight
before plugging. We store cooked food wrapped in autoclave bags at 4C.
We leave the food to come to room temperature before use. Fly stocks
are cultured in an 18C room, or at room temperature.

Last year (september) we bought a new batch of maize. Initially the
food was good and all the flies were happy. Over the next few months
the quality of the food declined, and stocks began to suffer. By March
this year we had big problems. In the most seriously affected stocks
the adults died after being put on the new food. In other stocks the
flies were alive, laid eggs, but no eggs hatched. In many stocks eggs
hatched (at least some did), but it would be 4 weeks or more before
adults eclosed (rather than the expected 3 weeks). Some stocks were
unaffected.

We bought new maize (March 09), and the problem went away, BUT, over the
next few months (june/july) it came back... So, we thought it was due
to maize going off, and switched to another batch, this one had been
bought a while ago, used with no problems and stored at -20, so should
stay fresh. Again, initially (july) everything was fine, but now the
stocks are slowing their generation times / dying off again.

We have had the first batch of maize tested for pesticide residue but it
came back negative. We have also tested it for Bt spore contamination
(yes it is organic...), by heating a maize /water mix to 80C for 15
minutes and plating on media suitable for Bt. we do not get Bt growth,
however there is growth of something (fungal). we have tested this with
flies in a laying bottle and it does not seem to retard egg hatching,
neither is it toxic to adults or larvae (indeed the larvae love it...).

So, does anyone out there have any ideas what could be causing the
problem, and most importantly, how to make it go away? The only things
we can think of are the temperature the food gets to after adding the
maize/ sugar/ yeast mixture (might it have to get up to 85C?, ours
probably only gets to 80C), should we add the nipagen earlier (could the
ethanol be causing the problem?).

Yours in desperation

Helen

--
Dr Helen White-Cooper
School of Biosciences
Museum Avenue
Cardiff University
Cardiff
CF10 3AX

Tel 029 20875492

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Graduate Position: MichiganStateU. Evol. Genetics/Development.

2009-09-14T08:17:08Z

PhD Studentships in Evolutionary Genetics and Integrative
Developmental Biology, Michigan State University, USA.

Four graduate positions in evolutionary genetics/developmental biology
are available in the laboratories of Dr. Alex Shingleton and Dr. Ian
Dworkin in the Department of Zoology and Program in Ecology,
Evolutionary Biology and Behavior at Michigan State University. The
positions are funded as part of three NSF grants working at the
interface of evolution, development and genetics. The Shingleton and
Dworkin laboratories work closely together and employ molecular,
genetic, genomic, physiological and behavioral methods to address
their research questions, using Drosophila as a model organism. More
details on the research being conducted in the laboratories are
available at www.msu.ed/~shingle9 and www.msu.edu/~idworkin. Students
will be immersed in an integrative and collaborative research
experience within the diverse and dynamic life-science community at
Michigan State University.

Potential projects for graduate students include:

1) Elucidating the molecular and developmental regulation of
morphological scaling relationships. Previous research in the
Shingleton lab has identified the insulin-signaling pathway as being
differently regulated in organs that differ in their scaling
relationship with body size. The goal of the project is to elucidate
the molecular basis for this differential regulation.

2) Exploring the evolution of wing-body scaling in Drosophila
populations. This project involves applying artificial selection on
scaling relationships in Drosophila and elucidating the genetic and
developmental basis for the selection response.

3) Examining the role of conditional and pleiotropic genetic effects
in the evolutionary process, and mapping genetic modifiers that
contribute to these effects. Previous work (Dworkin et al. 2009)
demonstrated that a genetic modifier of the allelic effects of a
mutant results in profound difference in phenotypes. The student will
fine map the genetic modifier and examine its potential pleiotropic
contributions in natural populations.

4) Explore the effects of different genetic backgrounds on gene
interactions and ordering of allelic series for mutations that affect
wing development and shape. This work will examine the effects of a
series of mutations in different “wild-type” genetic backgrounds,
across several rearing environments (manipulations of diet and
temperature).

The projects will suit students with an interest in evolutionary
genetics and/or integrative developmental biology. The ideal candidate
should have good general laboratory skills, with a firm grasp of basic
statistical methods.

Michigan State University is a large land-grant institution with an
outstanding faculty and inter-disciplinary programs at the
departmental and university levels. Interested applicants are
encouraged to review additional background on faculty and graduate
programs in Zoology (http://www.zoology.msu.edu), and in the Ecology,
Evolutionary Biology and Behavior (EEBB) program (https://www.msu.edu/~eebb
).

Applicants should submit a statement of interest, a CV, GRE scores and
their cumulative GPA along with names and contact information of three
references (everything as one PDF document) to shingle9@....
Applications will be accepted until the positions are filled. The
start date is September 2010, although applicants who wish to start
sooner should also apply.

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