[ccp4bb] Postdoctoral position to study protein synthesis at a molecular level at the University of Texas Med. Branch (UTMB)

[Gagnon, Matthieu]

There is an open postdoctoral opportunity in my laboratory in the Department of 
Microbiology and Immunology at the University of Texas Medical Branch (UTMB). 
The Gagnon laboratory focuses on structural studies of ribosome functional 
complexes and associated translation factors. We take a combined 
structure-function approach to study mechanisms of protein synthesis and 
address how specific ligands, such as translation factors and antibiotics, 
modulate gene expression by interacting with the translation machinery.

Our laboratory was recently featured on the UTMB Facebook page at:
https://www.facebook.com/notes/utmb-office-of-the-provost/faculty-spotlight-matthieu-g-gagnon-phd/2263201517258845/

The advertisement for this position is below.


Postdoctoral position at The University of Texas Medical Branch (UTMB)

We have an immediate opening for a talented, highly motivated postdoctoral 
scholar in my laboratory at The University of Texas Medical Branch (UTMB) 
located in Galveston, TX (USA) to study the structure and function of ribosome 
functional complexes (https://microbiology.utmb.edu/faculty/matthieu-gagnon). 
The successful candidate will be involved in the characterization of 
prokaryotic and eukaryotic ribosomes, translation factors and other RNA/protein 
complexes. The research in our laboratory aims to elucidate the mechanisms of 
protein synthesis, antibiotic resistance and regulation of translation at a 
structural level using a combination of macromolecular X-ray crystallography, 
single-particle cryo-electron microscopy (cryo-EM) and biochemical techniques.

The desired qualifications are:
• Ph.D. in biochemistry, chemistry, biophysics, or a related field;
• Practical skills in molecular biology, protein expression/purification, and 
various biochemical techniques;
• Experience in structural biology (cryo-EM and/or X-ray crystallography);
• Strong interest and motivation to elucidate the molecular mechanisms of 
protein synthesis and antibiotic resistance through structure determination.

The successful candidate will have an excellent track record and is expected to 
drive forward the projects, act independently or semi-independently, compile, 
analyze and write up data for publication, assist with the training of graduate 
students and work co-operatively with others.

Structural biology facilities at UTMB are outstanding 
(https://www.utmb.edu/core). Our cryo-electron microscopy (cryo-EM) core 
facility recently acquired the FEI Titan Krios high-voltage (300 kV) electron 
microscope equipped with two direct detector cameras, Falcon 3 (ThermoFisher) 
and K3 (Gatan), ideal setup for high-resolution structure visualization. Other 
cryo-EM resources include a JEOL 2200FS cryo-EM microscope equipped with a DE20 
direct electron detector for high-resolution imaging work and a liquid nitrogen 
autofilling system allowing week-long experiments, a cryo-microscope JEOL 2100, 
an FEI vitrobot cryo-plunger, a Leica EM-GP2 cryo-plunger, a Gatan Solarus 
plasma cleaner. X-ray crystallography resources include two X-ray area detector 
systems, a Phoenix crystallization robot, a Minstrel crystal imaging robot, the 
Alchemist and epMotion liquid handling robots. Other state-of-the-art 
facilities include NMR, next-generation sequencing, molecular genomics, 
high-throughput screening, solution biophysics, optical microscopy and 
computational biology.

Ample opportunities exist at UTMB for interactions with centers of scientific 
excellence in structural biology and molecular biophysics, biodefense, 
molecular medicine, cancer biology, infectious diseases, environmental health, 
aging, and translational sciences (https://www.utmb.edu/centers). Moreover, 
UTMB boasts a renowned, vibrant and highly active community of infectious 
disease researchers and clinicians, providing ample opportunities for broader 
collaborations and development.

Review of applications will begin immediately and will continue until the 
position is filled. Interested applicants should send their CV along with a 
cover letter briefly describing their research accomplishments, current 
research interests and contact information for three references in a single PDF 
directly to Dr. Matthieu Gagnon at magag...@utmb.edu.

Sincerely,
---
Matthieu G. Gagnon, Ph.D.
Assistant Professor
Department of Microbiology & Immunology
Sealy Center for Structural Biology & Molecular Biophysics
The University of Texas Medical Branch
301 University Blvd., Galveston, TX 77555-1019
4.104C Medical Research Building
Email: magag...@utmb.edu
Phone: 409-772-2326
https://microbiology.utmb.edu/faculty/matthieu-gagnon
https://scsb.utmb.edu/faculty/Gagnon.asp



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] PhD position in biomolecular solid-state NMR - Groningen, Netherlands

[P.C.A. van der Wel]

PhD position in Structural biology of Huntington’s disease using solid-state NMR

University of Groningen, Zernike Institute for Advanced Materials (Netherlands)
Van der Wel Solid-state NMR Group



We are looking to fill a PhD position for an exciting new project in our lab at 
the University of Groningen. This project is funded by a grant from the 
Netherlands’ Campagneteam Huntington – a community-driven effort to fund 
Huntington’s disease (HD) research in the Netherlands.

The researcher will use solid-state NMR and electron microscopy for molecular 
studies of the central protein misfolding event behind the neurodegenerative 
disease HD. Tailor-made solid-state NMR experiments will be used to provide an 
atomic view of the protein aggregates. For an integrated 
structure/toxic-function analysis, the project will include toxicity assays in 
human neuronal cells and aggregation modulation studies. The PhD researcher 
will perform the cellular assays with the group of Prof. Amalia Dolga, our 
close collaborator in the Groningen Research Institute of Pharmacy. The 
interdisciplinary studies are designed to yield a new understanding of this 
devastating disease, with likely implications for other neurodegenerative 
disorders associated with protein aggregation.

Recent HD research papers from the lab:
• Hoop et al. (2016) Huntingtin exon 1 fibrils feature an interdigitated 
β-hairpin–based polyglutamine core. PNAS 113(6):1546–51.

• Lin et al. (2017) Fibril polymorphism affects immobilized non-amyloid 
flanking domains of huntingtin exon1 rather than its polyglutamine core. Nat 
Commun. 8:15462.

• Smith et al. (2018) Structural fingerprinting of protein aggregates by 
dynamic nuclear polarization-enhanced solid-state NMR at natural isotopic 
abundance. J Am Chem Soc 140(44): 14576-14580.

The candidate is expected to have a Master’s degree (or potentially a BSc 
degree with demonstrable research experience*) in bio- or physical chemistry, 
(bio)physics or another field of science relevant for the position. Experience 
with NMR, and especially solid-state NMR, is an important consideration, but 
may not be essential (depending on the background of the candidate). Applicants 
with a background and interest in protein biophysics or protein aggregation are 
encouraged to apply.

For information or questions about the project, application procedure, and 
requirements, potential applicants should contact Dr Van der Wel at  
p.c.a.van.der@rug.nl 
Additional background information about the lab is also available on our 
website https://www.vanderwellab.org/ 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Java based structural database websites

[Jose Duarte]

Indeed java in the browser was killed a long time ago.

But the good news is that plenty of alternatives exist, written in native
(to the browser) javascript. Wikipedia has a nice compilation of the
different viewers, under the "Web-based systems" section:

https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems

I would particularly recommend the Mol* project:

https://molstar.org/

Jose


On Tue, 19 Mar 2019 at 10:37, Robbie Joosten 
wrote:

> Hi Nick,
>
> A bit of a hack I suppose, but you could use a (single use) VM with some
> old windows version that still works.
> E-mailing the developers directly is the way to go to figure out whether
> you can expect an update.
>
> We had a similar problem with our own webserver (the Crystallographic
> Construct Designer ccd.rhpc.nki.nl) which was completely a java applet.
> The only real solution was a full rewrite. But that requires funding which
> we luckily got from the West-Life project.
> Keeping websites online is is not easy with changing technology and
> getting funding is hard because it is not new science.
>
> Cheers,
> Robbie
>
>
>
> On 19 Mar 2019 17:43, Nicholas Keep  wrote:
>
> This is slightly off topic but I suspect people from PDBe etc read this
> bulletin board.
>
> Quite a number of very useful structural biology web sites (Olderado,
> Vivaldi, EMDB to name but a few) require java based viewers and hence no
> longer have full (or in the case of vivaldi any) functionality on up to
> date browsers.
>
> On a new computer it may prove hard or even impossible to find a browser
> that will work
>
> Are there plans to update these websites and is there any suggeted time
> scale?
>
> Any work rounds?
>
> Best wishes
>
> Nick
>
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the crystallography
> entrance
> and ring me or the department office from the internal phone by the door
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Java based structural database websites

[Robbie Joosten]

Hi Nick,

A bit of a hack I suppose, but you could use a (single use) VM with some old 
windows version that still works.
E-mailing the developers directly is the way to go to figure out whether you 
can expect an update.

We had a similar problem with our own webserver (the Crystallographic Construct 
Designer ccd.rhpc.nki.nl) which was completely a java applet. The only real 
solution was a full rewrite. But that requires funding which  we luckily got 
from the West-Life project.
Keeping websites online is is not easy with changing technology and getting 
funding is hard because it is not new science.

Cheers,
Robbie



On 19 Mar 2019 17:43, Nicholas Keep  wrote:

This is slightly off topic but I suspect people from PDBe etc read this
bulletin board.

Quite a number of very useful structural biology web sites (Olderado,
Vivaldi, EMDB to name but a few) require java based viewers and hence no
longer have full (or in the case of vivaldi any) functionality on up to
date browsers.

On a new computer it may prove hard or even impossible to find a browser
that will work

Are there plans to update these websites and is there any suggeted time
scale?

Any work rounds?

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
   020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Java based structural database websites

[Nicholas Keep]

This is slightly off topic but I suspect people from PDBe etc read this 
bulletin board.


Quite a number of very useful structural biology web sites (Olderado, 
Vivaldi, EMDB to name but a few) require java based viewers and hence no 
longer have full (or in the case of vivaldi any) functionality on up to 
date browsers.


On a new computer it may prove hard or even impossible to find a browser 
that will work


Are there plans to update these websites and is there any suggeted time 
scale?


Any work rounds?

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Postdoc position MAX IV, Lund, Sweden for Fragment screening development within the MX-group

[Uwe Müller]

Postdoctoral fellow/temporary scientist FragMAX project (2 years)
Login and 
apply

Lund University was founded in 1666 and is repeatedly ranked among the world’s 
top 100 universities. The University has 40 000 students and 7 400 staff based 
in Lund, Helsingborg and Malmö. We are united in our efforts to understand, 
explain and improve our world and the human condition.

MAX IV is a Swedish national large-scale research laboratory hosted by Lund 
University. It provides scientists from Sweden as well as internationally, with 
state-of-the-art instrumentation for research in areas such as engineering, 
physics, structural biology, chemistry and nanotechnology. Fully developed it 
will receive more than 2 000 scientists annually, conducting ground-breaking 
experiments in materials and life sciences using the brilliant X-ray light. As 
a national laboratory, MAX IV is operated in agreement with governmental 
regulations, and in compliance with major funders such as the Swedish Research 
Council (VR) and the Wallenberg Foundation. 250 people are currently employed 
at MAX IV Laboratory, and 16 beamlines are funded. The facility is in a ramp-up 
phase with 3 beamlines now receiving users and 13 more scheduled to be 
commissioned and built to receive users within the next few years. The facility 
is dimensioned for 25-28 beamlines.

Tasks
You are developing, implementing, testing and using the FragMAX screening 
platform for efficient fragment screening at BioMAX. This includes the 
implementation of sample handling at the LP3 laboratory, the constant 
development of relevant processes to carry out the fragment screening at all 
levels of our support chain and the support of users during screening 
experiments and standard beamline support. You play a responsible role to 
develop and utilize our internal fragment library, FragMAXlib.
You are expected to work both independently and in close collaboration with the 
entire BioMAX team, the FragMAX project group, industrial collaboration 
partners as well as other international collaborators and future FragMAX user 
communities.

Qualifications
Essential requirements:

  *   PhD in relevant scientific field for the FRAGMAX project
  *   Demonstrated experiences in protein crystallography or other structural 
biology methods
  *   Demonstrated experiences in protein crystallisation
  *   Demonstrated experiences in biological laboratory based automated liquid 
handling
  *   Very good command of English, both written and spoken

Additional requirements:

  *   Experiences in protein-ligand interactions
  *   Experiences in ligand library design
  *   Experiences in synchrotron based structural biology experiments

On call services may apply in the future.

Lund University welcomes applicants with diverse backgrounds and experiences. 
We regard gender equality and diversity as a strength and an asset. We kindly 
decline all sales and marketing contacts.

Type of employment  Temporary position longer than 6 months
Contract type   Full time
First day of employment As per agreement
Salary  Monthly salary
Number of positions 1
Working hours   100
CityLund
County  Skåne län
Country Sweden
Reference numberPA2019/894
Contact

  *   Marjolein Thunnissen, +46766320417
  *   Uwe Müller, +46730655268


Union representative

  *   OFR/ST:Fackförbundet ST:s kansli, 046-222 93 62
  *   SACO:Saco-s-rådet vid Lunds universitet, 046-222 93 64
  *   SEKO: Seko Civil, 046-222 93 66


Published   13.Mar.2019
Last application date   07.Apr.2019 11:59 PM CET




Uwe Mueller
Group manager Macromolecular Crystallography
BioMAX beam line manager

MAX IV Laboratory
Lund University
Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 224 84 Lund, Sweden
Mobile:  +46(0)730-655268
E-mail: uwe.mul...@maxiv.lu.se
Url: www.maxiv.se
VAT No.: SE 2021 0032 1101









To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] IMCBio International PhD Program Call 2019

[Abhishek Anan]

On 3/19/19, Albert Weixlbaumer  wrote:
> Hi everyone,
>
> This is a friendly reminder to draw your attention to a call for the
> International PhD program of the Integrative Molecular and Cellular Biology
> (IMCBio) graduate school at the University of Strasbourg, France:
> http://imcbio-phdprogram.unistra.fr
>
> The IMCBio graduate school builds on the strong research developed in four
> different institutes. This includes the IGBMC, which is a European Instruct
> center and thus houses state-of-the-art facilities for structural biology
> (NMR, X-ray crystallography, SAXS, and latest instrumentation for Cryo-EM).
>
> Structural biology at the IGBMC has a long tradition and focus on large
> macromolecular machines involved in gene expression (transcription and
> translation machineries), Chromatin organization, stability, and epigenetics
> (epigenetic regulators, topoisomerases, retroviral integrases, histone
> chaperones and deacetylases, methyltransferases), viral oncoproteins, motor
> proteins, and nuclear receptors.
> Strasbourg is a cosmopolitan city in the heart of Europe. The IGBMC is a
> vibrant and highly international institute (over 45 nationalities, working
> language is English) with about 250 PhD students:
> http://igbmc.fr/igbmc/vie_etudiante/
>
> Registration for the PhD program needs to be done until March 22nd, the
> deadline to complete the application is March 29th, 2019
>
> Please forward this to any interested candidate.
>
> Thanks,
> Albert
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] IMCBio International PhD Program Call 2019

[Albert Weixlbaumer]

Hi everyone,
 
This is a friendly reminder to draw your attention to a call for the 
International PhD program of the Integrative Molecular and Cellular Biology 
(IMCBio) graduate school at the University of Strasbourg, France: 
http://imcbio-phdprogram.unistra.fr

The IMCBio graduate school builds on the strong research developed in four 
different institutes. This includes the IGBMC, which is a European Instruct 
center and thus houses state-of-the-art facilities for structural biology (NMR, 
X-ray crystallography, SAXS, and latest instrumentation for Cryo-EM).

Structural biology at the IGBMC has a long tradition and focus on large 
macromolecular machines involved in gene expression (transcription and 
translation machineries), Chromatin organization, stability, and epigenetics 
(epigenetic regulators, topoisomerases, retroviral integrases, histone 
chaperones and deacetylases, methyltransferases), viral oncoproteins, motor 
proteins, and nuclear receptors.
Strasbourg is a cosmopolitan city in the heart of Europe. The IGBMC is a 
vibrant and highly international institute (over 45 nationalities, working 
language is English) with about 250 PhD students: 
http://igbmc.fr/igbmc/vie_etudiante/
 
Registration for the PhD program needs to be done until March 22nd, the 
deadline to complete the application is March 29th, 2019
 
Please forward this to any interested candidate.
 
Thanks,
Albert



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Unknown anomalous scatterer

[Leonarski Filip Karol (PSI)]

Dear Aleix,

From what you say, it is also possible, that you see anomalous scattering of 
native elements present in your complex - your DNA contains P atoms, there 
might be also S in protein part and K+/Ca2+ in solvent. The signal is very weak 
at 12667 keV, but could give high anomalous correlation in lowest resolution 
shells.

What is the value of SigAno (column next to anomalous correlation) at 5.0 A 
resolution? What is the resolution of your complex (is 5 A close to diffraction 
limit or far)?

Best,
Filip

From: CCP4 bulletin board  on behalf of Aleix Tarrés 
Solé 
Reply-To: Aleix Tarrés Solé 
Date: Friday, 15 March 2019 at 22:17
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Unknown anomalous scatterer

Dear colleagues:
Hereby, I would like to expose a problem I encountered during the data 
processing of one of my crystals. Recently I collected a full dataset of a 
native protein-DNA crystal at an energy of 12667KeV. To my surprise, after 
processing with XDS I can see that I have significant values of anomalous 
correlation up to 5 Angstrom resolution. Using the fluorescence scan on the 
beam, I could discard the presence of the following heavy atoms that could have 
ended up in my drop due to cross-contamination; Se, As, Fe, Zn and Pr. So far, 
my attempts to use this dataset for phasing have been sadly unsuccessful. I 
would like to know if somebody has experience in this kind of problem and can 
gently help with some advices.

Thank you all in advance

Aleix




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1