[ccp4bb] PDF opening for membrane protein production for structural studies

[M. Joanne Lemieux]

*Lemieux lab, MITACS funded PDF advertisement, 2022 *



Applications are invited for an immediate opening for a postdoctoral
position to work on expression of eukaryotic membrane proteins. The
candidate must be within five years of attaining a PhD degree in
biochemistry or a related field. Experience in baculovirus, Expi293 (or
Freestyle) expression, and crystallography is desired. In addition, the
successful candidate should be well versed in one or more of the following
areas: molecular biology, protein purification, and membrane protein
biochemistry. This is a joint position with industry through the MITACS
program.



This is an opportunity to join a lab experienced in the expression and
crystallization of various membrane proteins (See *PNAS *(2007)
104(3):750-4, and *Science, *(2003)*. *301:616-620), and viral proteases (*Nat
Comm 2020, J Med Chem 2021*: (http://www2.biochem.ualberta.ca/LemieuxLab/).
The University of Alberta, located in Edmonton, Alberta (Canada), is home
to a large and interactive community of biomedical scientists, and
facilities for structural biology are excellent. Our department provides
interaction with numerous crystallographers. The Canadian Light Source
(CLS) synchrotron facility is located a short drive away. In addition, the
membrane protein research group provides a dedicated forum for membrane
protein research at the University of Alberta (http://www.mpdrg.com).

Edmonton, having a population of over 1 million, offers a
cosmopolitan environment with world-class performing arts, sports, culinary
and recreational opportunities.  In addition, the city’s proximity to the
Rocky Mountains including the towns of Jasper and Banff is an additional
bonus.

Salary is commensurate with training and experience at the MITACS standard
rates. A medical and dental benefit package is included with salary. The
University of Alberta hires on the basis of merit. We are committed to the
principle of equity in employment. We welcome diversity and encourage
applications from all qualified women and men, including persons with
disabilities, members of visible minorities, and Aboriginal persons. The
records arising from this competition will be managed in accordance with
provisions of the Alberta Freedom of Information and Protection of Privacy
Act (FOIPP).



Please direct CV, statement of interests including proteins expressed and
system used, and if applicable structures previously solved, and a list of
three references to Dr. M. Joanne Lemieux at the following email address:
joanne.lemi...@ualberta.ca  with the subject
header: *PDF application*.



M. Joanne Lemieux, Ph.D.

Professor and Director of the Membrane Protein Disease Research Group

Department of Biochemistry

University of Alberta

Medical Science Bldg, Rm 453a

Edmonton, AB, Canada

T6G 2H7



http://www.mpdrg.com 

http://www.biochem.ualberta.ca/home.php



**
M. Joanne Lemieux, Ph.D.
Professor
Director, Membrane Protein Disease Research Group
Department of Biochemistry
College of Health Sciences
Faculty of Medicine & Dentistry
University of Alberta
Medical Sciences Bldg.
Office 4-53
Lab4-51
University of Alberta
Edmonton AB, T6G 2H7

office phone: 780-492-3586
lab phone:780-492-3465
fax: 780-492-0886

CSMB 2022 meeting: https://event.fourwaves.com/2022csmb/pages


Lab web pages:
*https://lemieuxlab.biochem.ualberta.ca/
*
http://www2.biochem.ualberta.ca/LemieuxLab

Membrane Protein Disease Research Group:
http://www.mpdrg.com

NSERC Membrane Protein International Research Training Group:
http://www.mpdrg.com/index.php/international-linkages/

The University of Alberta is located in ᐊᒥᐢᑿᒌᐚᐢᑲᐦᐃᑲᐣ (Amiskwacîwâskahikan) on
Treaty 6 territory, the territory of the Papaschase, and the homeland
of the Métis
Nation.

CONFIDENTIALITY WARNING
This communication is intended for the use of the recipient to which it is
addressed, and may contain confidential, personal, and/or privileged
information. Please contact me immediately if you are not the intended
recipient of this communication, and do not copy, distribute, or take
action relying on it. Any communication received in error, or subsequent
reply, should be deleted or destroyed.



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[ccp4bb] Scientific/Bioinformatics Software Developer position at RCSB PDB (Rutgers)

[Jasmine Young]

Dear CCP4bb,

RCSB Protein Data Bank is seeking highly motivated, scientific software 
developers with domain experience in structural biology, bioinformatics 
or related fields. The candidate should be interested in structural 
biological data and enjoy engaging with other programmers and scientists 
in a collaborative team environment.



   Responsibilities:

 * Design, development, and deployment of modern data-intensive
   scientific applications, within a microservice architecture
 * Integration of complex bioinformatics data, implementation of
   specialised algorithms for search/data analysis and use of AI tools
 * Design and implementation of cloud-ready deployments using
   containerization and modern cloud technologies
 * Analysis, refactoring and adaptation of legacy code to conform to
   new architecture designs
 * Debugging, testing, troubleshooting


   Qualifications:

 * PhD or Master’s degree in Computer Science, Biochemistry,
   Bioinformatics, or a related discipline, or a comparable combination
   of education and experience developing modern scientific data
   applications
 * Excellent interpersonal, verbal, and written communication skills
 * Experience with Python, document databases (e.g., MongoDB), search
   and data access tools (e.g., ElasticSearch and GraphQL)

Scientific background in any of the following areas would be considered 
a major plus: Molecular Biology, Bioinformatics, Cheminformatics, 
Biochemistry, Chemistry, Genomics.


Experience working with large and complex scientific datasets would also 
be considered a plus.



   Outstanding Benefits Package

RCSB PDB is a friendly and collaborative working environment with 
excellent professional development opportunities. At Rutgers, this 
academic position offers New Jersey state benefits and a faculty-level 
salary. There are personal rewards including comprehensive health and 
retirement plan options.



   About RCSB PDB:

The work at RCSB PDB (rcsb.org) focuses on data analysis, integration, 
and transformation, and the presentation and visualization of data using 
complex interactive graphical user interfaces. An important aspect is to 
provide users with the ability to search and explore the PDB data 
archive. Solutions are implemented using a wide range of components 
developed and maintained in-house, in addition to third-party tools, 
libraries, frameworks and technologies. The candidate should be 
comfortable working in a dynamic environment, and able to demonstrate an 
ability to think creatively, generate new ideas, and implement 
solutions. The candidate should also show an eagerness to learn new 
skills and technologies.



   Apply at Rutgers:

https://jobs.rutgers.edu/postings/142529


--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===



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[ccp4bb] Suggestion for molecular biology/recombinant DNA methodology primer for beginner trainees

[Anirban Banerjee]

Dear all,

Apologies for the off-topic post. Might you have a suggestion for a
book/online tutorial that can serve as a primer for someone with no formal
college level biology courses but with a good understanding of chemistry ?
The goal is to become self-sufficient in molecular biology techniques
pertaining to the common fields of interest of this community.

I used Recombinant DNA by Watson as a graduate student but that was a while
ago. I thought there may be newer material I don't know of.

Many thanks in advance for any pointers at all.

Warm regards,

Anirban



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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2022

[Manfred S. Weiss]

Dear all,


the next MX-proposal application deadline: March 01, 2022 is approaching

NEW: REMOTE OPERATION IS NOW THE PREFERRED MODE AT BLs14.1 AND 14.2.
PARTICPATION IN REMOTE TRAINING COURSE IS REQUIRED.

As usual, all proposals will be handled by our electronic user portal GATE,
https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2022-12/2022). Please note that in 2022 we are facing an very
long summer shutdown (May-August 2022, weeks 18-34).

In order to apply for beamtime, please register in GATE and submit
a new beam time application proposal.

Please note that we now expect from each research group only ONE proposal,
which can contain up to 20 individual projects.

IMPORTANT: If you have a running 2020-2 or a running 2021-2 proposal, you
may ask for extension. For a 2021-2 proposal, an interim report is necessary,
and for a 2020-2 proposal a full report including highlights. You will also
be able to edit and modify your proposals by adding and deleting projects.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with almost 4000 PDB depositions in total. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position
 (0.04-1 sec exposure time per frame)
- PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. 
distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 9 Unipucks, i.e. 144 sample storage capacity
- User defined beam shaping from 50 µm-100 µm diameter possible
- Multi-core XEON-CPU server, with 10GB uplink to Pilatus 6M
- Data collection control via MXCuBE2
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP3
- Remotely controlled cryo-shutter for crystal annealing
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out UV-RIP experiments at BL14.1. For further information,
please visit:
https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.6x10¹¹ Phot/sec x 100 mA at sample position
 (0.05-1 sec exposure time per frame)
- PILATUS3 S 2M detector with 1000 µm Si sensor thickness,
 85 mm - 800 mm distance from the sample (a special mode with
 56 mm distance is also available upon request)
- Nanodiffractometer with fast air-bearing axis and on-axis sample
 microscope
- User defined beam shaping from 30 µm-150 µm diameter possible
- Data collection control via MXCuBE2
- G-ROB sample changer for SPINE support
PLEASE NOTE: From September 2022 onwards, only Unipucks will be supported.
- Multi-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- AMPTEK-XRF detector and XFEPLOT software available
- UV-Microsprectrophotometer offline setup available

If you need atomic resolution or better, BL14.2 is the beamline
of choice for you!!

BL14.3:
- Fixed photon energy: 13.8 keV (wavelength: 0.89 A)
- Photon flux: 1.6x10exp10 Phot/sec x 100mA at sample position
 (3-20 sec exposure time per frame)
- PILATUS 6M detector, 54 mm-450 mm distance from the sample
- MD2S microdiffractometer with mini-kappa goniometer
- RT data collection
- Data collection at 50 K using a He cryostat
- Multi-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Data collection control via MXCuBE2
- Common MX software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- REX rapid nozzle exchanger
- HC-Lab dehydration device installed (please specify HC-Lab-beamtime
 in your proposal if needed)
- AMPTEK-XRF detector and XFEPLOT software available

Other facilities:
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpix CCD-camera
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)

S1-biolab facilities (separate registration required):
- Protein production and purification