> Hi, I found that my protein bound ethidium bromide in an agarose gel. I tested that by treating my protein with protease and DNAse in two different tubes and running a gel. The band in the agarose gel disappeared only when the protein was treated with protease. It is worth trying. I hope that helps,
Chiara > Pramod, > > You already got good suggestions on how to handle DNA contamination in > protein preparations. > > Let me point out briefly that you haven't demonstrated yet that your > contamination is DNA. > > I had the same observation when purifying UvsX. A very persistent and strong > contamination in all my preps at ~500kb. To test weather it was DNA or RNA I > boiled the protein 30 minutes and incubated it with DNAase and RNAse and > result was the same. I concluded it was neither RNA nor DNA and continued as > if nothing had happened. > > This publication is reporting the same observation: > > Formosa and Alberts (1986) "Purification and characterization of the T4 > bacteriophage uvsX protein." J Biol Chem. 1986 May 5;261(13):6107-18. > > If you ever find out what it is that runs like 500kb DNA on Agarose, please > let me know. > S. > > ------------------------------ > > Date: Sat, 27 Jun 2015 04:39:45 +0100 > From: Stefan Gajewski <sgajew...@gmail.com <mailto:sgajew...@gmail.com>> > Subject: Re: Interesting DNA contamination > > Correction, > > I meant to say 0.5kb, not 500kb > > sorry for that. > S. > > ------------------------------ > > Date: Sat, 27 Jun 2015 16:52:06 +0000 > From: "Rose, Peter" <pwr...@ucsd.edu <mailto:pwr...@ucsd.edu>> > Subject: Postdoctoral Fellows in Big Data/Structural Bioinformatics at > University of California, San Diego > > Summary: We are looking for two highly motivated post-docs as part of our new > project “Compressive Structural Bioinformatics” funded by the US National > Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. > > The Challenge: To enable efficient research on the rapidly growing number of > 3D molecular structures of ever increasing size and complexity. Develop > highly scalable 3D structural search, analysis, workflow, data-exchange, and > visualization tools. > > Qualifications: Ph.D. in structural bioinformatics, structural biology, > bioinformatics, computational biology or chemistry, computer science, or > related discipline. Experience with scientific software development as > demonstrated by publications or participation in open source software > projects. Experience with several programming languages, including Java, > JavaScript, C++, or Python, and software development tools. Strong skills in > applied mathematics and algorithm design are required. Experience with > distributed parallel computing or 3D visualization applications are a plus. > Excellent interpersonal, written, and oral presentation skills are essential. > > Note, this position is reviewed annually on the basis of performance and can > be renewed for a maximum of three years. > > Our Environment: > > The Structural Bioinformatics Group > (http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/> > <http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/>>) at the San > Diego Supercomputer Center (SDSC) (http://www.sdsc.edu<http://www.sdsc.edu/> > <http://www.sdsc.edu<http://www.sdsc.edu/>>) is involved in research and > development activities centered around 3D structures of proteins and nucleic > acids, the integration of structural data with other domains such as > Medicine, Genomics, Biology, Drug Discovery, and the development of scalable > solution to Big Data problems in Structural Bioinformatics. Our group leads > the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB > (http://www.rcsb.org<http://www.rcsb.org/> > <http://www.rcsb.org<http://www.rcsb.org/>>) represents the preeminent source > of experimentally determined macromolecular structure information for > research and teaching in biology, biological chemistry, and medicine. With > over 300,000 unique users from over 160 countries around the world, the RCSB > PDB is one of the leading worldwide Biological Databases. Our group is > involved in the National Institutes of Health (NIH) Big Data to Knowledge > (BD2K) initiative. > > As an Organized Research Unit of UC San Diego, SDSC is a world leader in > data-intensive computing and cyber infrastructure, providing resources, > services, and expertise to the national research community, including > industry and academia. > > To apply, please send cover letter and resume to Dr. Peter Rose > (pwr...@ucsd.edu <mailto:pwr...@ucsd.edu>). > > -- > Peter Rose, Ph.D. > Site Head, RCSB Protein Data Bank West > (http://www.rcsb.org<http://www.rcsb.org/> > <http://www.rcsb.org<http://www.rcsb.org/>>) > Principal Investigator, Structural Bioinformatics Laboratory > (http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/> > <http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/>>) > San Diego Supercomputer Center (http://www.sdsc.edu<http://www.sdsc.edu/> > <http://www.sdsc.edu<http://www.sdsc.edu/>>) > University of California, San Diego > +1-858-822-5497<file://localhost/tel/%252B1-858-822-5497 > <file:///tel/%252B1-858-822-5497>> > > ------------------------------ > > Date: Sat, 27 Jun 2015 17:00:08 +0000 > From: "Rose, Peter" <pwr...@ucsd.edu <mailto:pwr...@ucsd.edu>> > Subject: Web Developers at RCSB PDB at University of California, San Diego > > The RCSB PDB is seeking exceptional Developers, and we know we're not alone > in our search. So why choose to work with us? Our team values open discussion > and contribution. Starting from your first day, you will shape software and > services used by thousands of people around the world. Our organization can > trace its lineage back to the 1970's, but we still operate like a start up. > Have a great idea, let's hear it. Want to try a new technology, let's learn > it. Want to write code at scale, let's do it. Everyone at our organization is > passionate about what we do, and that is why we are leaders in our field. We > want to hear from skilled Developers, people passionate about their craft and > what they can bring to the field. > We are looking for two experienced Developers to join our team of agile > software Developers at the University of California, San Diego. By joining > our team, a successful applicant would be able to contribute to a variety of > projects ranging from: > > * Front end development using HTML, CSS, Javascript, JSP, and NodeJS > * Our core business is our website and web services > * Middleware development that leverages Memcached, Hibernate and RabbitMQ > * How we scale to meet tens of thousands of unique users every day > * Back end development using Java, MySQL/MariaDB, and NoSQL solutions > * How we incorporate and add value to the scientific community > * Special projects > * Search using Apache Solr > * Scalable solutions built on top of OpenStack, Hadoop, and Spark > > The RCSB Protein Data Bank (www.rcsb.org > <http://www.rcsb.org/><http://www.rcsb.org/ <http://www.rcsb.org/>>) is one > of the world’s leading biological databases with more than 300,000 unique > users per month from over 160 countries. It enables access to the singular > global archive of the three-dimensional structures of proteins and nucleic > acids and is a key resource for the design of new medicines, biofuels, > nanomaterials, and enables fundamental discoveries in biology and medicine. > Requirements: > > * BS degree in Computer Science or related field > * A minimum of 2 years of experience developing dynamic, highly scalable, > database-driven web applications using HTML, CSS, JavaScript and Java/JSP > * Demonstrable experience with database design and systems > * Experience with NoSQL database systems, object-relational mapping > using Hibernate and distributed parallel computing is a plus > * Citable experience using agile software development and test-driven > design > > For more requirements or to apply, please view the UCSD job > page<https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=75896 > > <https://jobs.ucsd.edu/bulletin/job.aspx?cat=new&sortby=post&jobnum_in=75896>>. > > ------------------------------ > > End of CCP4BB Digest - 26 Jun 2015 to 27 Jun 2015 (#2015-182) > *************************************************************
