[ccp4bb] Postdoctoral Positions in Structural RNA Biology at the NIH

[Eugene Valkov]

The Messenger RNA Regulation and Decay Section, RNA Biology Laboratory
(RBL), Center for Cancer Research (CCR), National Cancer Institute (NCI),
National Institutes of Health (NIH), Department of Health and Human
Services (DHHS), is seeking postdoctoral candidates with training/expertise
in RNA/protein structural biology/biochemistry. Research experience in RNA
biology or structural/biophysical techniques will be considered
advantageous. Strong work ethic, excellent communication skills and ability
to work in a multidisciplinary team are essential.



The focus of our research is to understand the mechanisms by which the
function of messenger RNA is regulated. We are especially interested in
exploring in molecular detail the processes of deadenylation and decapping
as well as the connections in the metazoan 5´-to-3´ cytoplasmic degradation
pathway. Recently, we have described the biochemical reconstitution of
human CCR4-NOT deadenylation complex and uncovered new links between decay
factors. The next stage will be to take structural approaches, especially
high-resolution cryoEM, in combination with other biophysical techniques
toward the study of the human mRNA decay machinery. Significant preliminary
data has already been generated for several projects and candidates will
join an established research program.



For high-resolution cryoEM, a Talos Arctica equipped with a K3 detector
together with a Vitrobot plunger is available on site together with a Talos
L120C for screening. Titan Krios microscopes are also locally accessible at
dedicated facilities on the NIH campuses in Frederick and Bethesda. For
crystallography, there is regular access to synchrotron beamlines at the
Argonne National Laboratory. Automated crystallization platforms and
automated imagers for crystal detection are available in the neighboring
Structural Biophysics Laboratory. In addition, a biophysics core facility
contains an array of instruments for biophysical characterization.
High-performance computational resources including a GPU-enabled cluster
are also provided. Further information about the core facilities can be
found here: https://ostr.ccr.cancer.gov/resources/core.



For relevant recent publications please see: Raisch et al. (2019) Nature
Communications, Chang et al. (2019) Nucleic Acids Research, Valkov et al.
(2016) Nature Structural & Molecular Biology.



We are looking for enthusiastic, imaginative and dedicated scientists to
join our research team working on exciting RNA structural biology projects.
The NIH intramural program provides ample opportunities for advanced
training to early-career scientists to develop valuable research and
transferable skills. A vibrant and collegiate NIH community with diverse
expertise in RNA, chemical and structural biology ensures a unique research
environment with excellent collaborative opportunities. NIH offers a
competitive salary and comprehensive health insurance as well as a host of
other benefits. Candidates must have a doctoral degree or expect to receive
their degree shortly. Appointments will be for one year initially and
renewable for up to a maximum of 5 years.  The NIH is dedicated to building
a diverse community in its training and employment programs.  This position
is subject to a background investigation.



Applicants should send their CV and contact details for three references to
Dr. Eugene Valkov: eugene.val...@nih.gov. Informal inquiries are welcome.
More information can be found at
https://ccr.cancer.gov/RNA-Biology-Laboratory/eugene-valkov. The RNA
Biology Laboratory is located on the Frederick campus of the National
Cancer Institute in Maryland, U.S.A.



*DHHS, NIH, and NCI are Equal Opportunity Employers*


-- 

Eugene Valkov, Ph.D.

NIH Stadtman Investigator

Head, Messenger RNA Regulation and Decay Section

RNA Biology Laboratory

Center for Cancer Research

National Cancer Institute

Building 560, Room 11-84

Frederick, MD, 21702-1201, U.S.A.

Ph  +1-301-846-1823

Email eugene.val...@nih.gov

Web https://ccr.cancer.gov/RNA-Biology-Laboratory/eugene-valkov



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[ccp4bb] 6th International Symposium on Diffraction Structural Biology

[Leighton Coates]

Dear Colleague

You are invited to the 6th International Symposium on Diffraction
Structural Biology which will take place at the University of Osaka in
Japan. The early bird registration and abstract submission deadline of
31st August 2019 is rapidly approaching.

Start Date: 17th Oct 2019
End Date:  20th Oct 2019

URL:  https://isdsb2019.symposium-hp.jp/

The 6th International Symposium on Diffraction Structural Biology
(ISDSB2019) is an international symposium organized by the Japan
Society for the Promotion of Science, University-Industry Research
Cooperative Research Committee, 169th Committee on Structural Biology
using Diffraction Techniques. This symposium is positioned as an
interface between academic researchers and industry researchers, as
well as an interface between diffraction techniques and other related
techniques in the field of structural biology. Symposium topics will
include Macromolecular crystallography, CryoEM, software and databases
and drug discovery, registration and abstract submission for the
symposium is now open and costs 25,000 Japanese yen for academics.

Confirmed Speakers are

 Nobel Lecture

Joachim Frank, Columbia University, USA (Nobel Prize in Chemistry 2017)

Plenary Lectures

  Stephen K. Burley, RCSB Protein Data Bank, Rutgers University and UC
San Diego, USA
  Yoshinori Fujiyoshi, Tokyo Medical and Dental University, Japan
  Ian Wilson, The Scripps Research Institute, USA

Invited Speakers

  Shinichi Adachi, Institute of Materials Structure Science (IMSS), KEK, Japan
  Terese Bergfors, Uppsala University, Sweden
  Caterina Biscari, ALBA Synchrotron, Spain
  Gérard Bricogne, Global Phasing Limited, UK
  Jacqui Gulbis, Walter and Eliza Hall Institute of Medical Research
  Vadim Cherezov, University of Southern California, USA
  Leighton Coates, Oak Ridge National Laboratory, USA
  Michael Henning, LeadXpro, Switzerland
  Roderick E. Hubbard, York University, UK
  Tamir Gonen, UCLA, USA
  Jie-Oh Lee, KAIST, Korea
  Mei Li, Institute of Biophysics, Chinese Academy of Science, P.R.China
  Jose A. Márquez, EMBL, France
  Yukihiko Sugita, Institute for Protein Research, Osaka University
  Marjolein Thunnissen, Max IV, Lund University, Sweden
  Leann Tilley, University of Melbourne, Australia

Contact:   Atsushi Nakagawa (Osaka University)
Email: isdsb2...@gmail.com
URL:   https://isdsb2019.symposium-hp.jp/



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[ccp4bb] New release of iMosflm (version 7.3.0)

[Andrew Leslie]

A new release (version 7.3.0) of the data processing program iMosflm is now 
available for the MRC website:
https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm 


The most significant difference to the previous version (7.2.2) is the ability 
to read Dectris HDF5 files directly, rather than having to convert them to CBF 
files (using eiger2cbf). These changes were implemented by Harry Powell (now an 
independent software consultant) with financial support from Dectris, Diamond 
Light Source and CCP4. When reading HDF5 files, there is the option to sum 
images prior to processing, which may give improved performance if the 
oscillation angle is very small. 

Images from the new Dectris Eiger2 and Dectris Quadro detectors and Rigaku 
Pilatus and Eiger image formats are also handled.

A bug in version 7.2.2 meant that MTZ files produced when using the multi 
lattice integration option could not be read correctly by any downstream 
programs (POINTLESS etc). this has been corrected. There have also been minor 
changes to the integration of very weak images (where many pixel values are 
zero) to avoid bias in the intensity estimation.

There have been numerous additional minor improvements and bug fixes, a full 
list is given on the web site (Under “changes since 7.2.2").

The reading of HDF5 format images has been tested with files from ESRF and 
Diamond Light Source. Because there is not yet a universally agreed format for 
the header information, there may be issues with reading the metadata (phi 
values, detector distance, wavelength etc) from files produced elsewhere, 
please let me know if this is the case.

This latest version will be released as part of the CCP4 package in due course.

Andrew Leslie


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Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Markus Heckmann]

Dear Flemming,

On 8/21/19, Flemming Goery  wrote:
> I find the message in my original e-mail has changed, perhaps by hackers,

What do u mean by 'hackers' BTW!!!


>
> Dear all:
> A has sought a job in the lab of B. B invited A for a interview with a PPT
> oral presentation, as requested A has sent the PPT on the structural biology
> research of XXX to B by e-mail, and presented in front of B and his
> postdoctoral researcher.
>
> After interview, B requested all research documents (including detailed
> reports, all done by A) on XXX to be sent by A to B by e-mail, A sent,
> including 2 sets of pdb for the same structure, one set with solvent, one
> without. A told B all intellectual property of the Documents and the
> research belonged to A, based on the regulation of A's institute.
>

Who was the boss/PI of A?

If  A  did transfer all  intellectual property to B then it is already
'game over for A'.


> B sought a referee from A's institute, to someone A did not agree. It seems
> the referee told B one set of PDB has been deposited (the one without
> solvent, also completed by A)
>
> Then B did not give the offer to A. A joined Institute D, without
> independent funding for the writing (in fact, no salary to support this
> writing, and no fee for publication of this work).

While one could sympathize A, it has no real effect on the claim.

>
> Several years later, A found B's paper, i.e., the concerned paper published

> in Journal C. In the paper, B has used the information from deposited PDB
> for 9 times (already a significant paprt of the paper, not to say the
> message from the other Documents sent to B by A). In the paper, it write
> something like, 'based on our work on the structure of  (folowed by 4 letter
> pdb code)', which implied the structure was solved by the authors of the
> paper, rather than by A.
>
> A contacted Journal C, Journal C contacted B, B claimed the deposited PDB
> was a public domain knowldge. Journal C took the action to add the reference
> to the deposited pdb in the paper.

--> Wait - who deposited the model?
--> Did B deposit model without including A?
--> Can you mention the PDB code?  :-)

> As mentioned, the paper has mentioned and used the message from the
> deposited pdb 9 times, and in the paper the reference mark was not added to
> the first occurence of the mentioning of the deposited pdb, but added (only
> once in total for the 9 occurences of depositation code) to a paragraph
> where it can be concluded that the authors have used the undeposited pdb
> with the solvent. In another word, although reference to the deposited pdb
> was added by a correction, from where the reference mark was added, it
> cannot show they have refered to the cited pdb (completed by A), not to say
> the undeposited pdb with solvent which they used based on the paragraph
> information.
>
> A's concern was that: A cannot exclude the possibility that the research in
> the paper other the part related to PDB, i.e., the part done in B's lab used
> in the paper, were fabricated by the current paper authors, thus A request
> paper retraction as the major claim.

Not sure about that. May be you contact people at
 https://retractionwatch.com/
https://twitter.com/retractionwatch
They may have more experience with these issues.



> If cannot retratcted, A request to be the correspondence author (sometimes
> requets co-first author, sometimes request both co-first author and
> co-correspondence author), as without A's work (the PPT presentation, 2 sets
> of pdb, all documents), the work in the concerned paper cannot be done. A
> regard as having contributed to the initiation of the paper, thus A prefer
> to be add as a co-correspondence author if appropriate.
>
> First, can the paper deserve a retraction, and second, can A deserve a
> co-author?



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