‘Start Codons’ in DNA and RNA May Be More Numerous Than Previously Thought


For decades, scientists working with genetic material have labored with a few basic rules in mind. To start, DNA is transcribed into messenger RNA (mRNA), and mRNA is translated into proteins, which are essential for almost all biological functions. A central principle regarding translation has long held that only a small number of three-letter sequences in mRNA, known as start codons, could trigger the production of proteins. But researchers might need to revisit and possibly rewrite this rule, after recent measurements from a team including scientists from the National Institute of Standards and Technology (NIST)

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President Obama Honors Federally-Funded Early-Career Scientists, Including JIMB Team Member Justin Zook

The White House

Office of the Press Secretary

For Immediate Release

January 09, 2017

President Obama Honors Federally-Funded Early-Career Scientists

Today, President Obama named 102 scientists and researchers as recipients of the Presidential Early Career Awards for Scientists and Engineers (PECASE), the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers.
“I congratulate these outstanding scientists and engineers on their impactful work,” President Obama said. “These innovators are working to help keep the United States on the cutting edge, showing that Federal investments in science lead to advancements that expand our knowledge of the world around us and contribute to our economy.”
The Presidential Early Career Awards highlight the key role that the Administration places in encouraging and accelerating American innovation to grow our economy and tackle our greatest challenges. This year’s recipients are employed or funded by the following departments and agencies: Department of Agriculture, Department of Commerce, Department of Defense, Department of Education, Department of Energy, Department of Health and Human Services, Department of the Interior, Department of Veterans Affairs, Environmental Protection Agency, National Aeronautics and Space Administration, National Science Foundation, Smithsonian Institution, and the Intelligence Community. These departments and agencies join together annually to nominate the most meritorious scientists and engineers whose early accomplishments show the greatest promise for assuring America’s preeminence in science and engineering and contributing to the awarding agencies' missions.
The awards, established by President Clinton in 1996, are coordinated by the Office of Science and Technology Policy within the Executive Office of the President. Awardees are selected for their pursuit of innovative research at the frontiers of science and technology and their commitment to community service as demonstrated through scientific leadership, public education, or community outreach.
The newest recipients are:
Department of Agriculture
Michelle Cilia, USDA Agricultural Research Service
Pankaj Lal, Montclair State University
Michael Ulyshen, USDA Forest Service
Department of Commerce

Nicholas Butch, NIST Center for Neutron Research
Mandy Karnauskas, NOAA Fisheries
Anne Perring, University of Colorado, Boulder
Corey Potvin, University of Oklahoma
John Teufel, NIST Physical Measurement Laboratory
Justin Zook, NIST Material Measurement Laboratory
Department of Defense
Michael Bell, Colorado State University
Nurcin Celik, University of Miami
Kaushik Chowdhury, Northeastern University
Shawn Douglas, University of California, San Francisco
Christopher Dyer, DeepMind and Carnegie Mellon University
Aaron Esser-Kahn, University of California, Irvine
Sinan Keten, Northwestern University
Jonathan Fan, Stanford University
Danna Freedman, Northwestern University
Thomas Harris, Northwestern University
David Hsieh, California Institute of Technology
Osama Nayfeh, Space and Naval Warfare Systems Center-Pacific
Olukayode Okusaga, Johns Hopkins Applied Physics Laboratory
Joseph Parker, U.S. Naval Research Laboratory
Adam Pilchak, Air Force Research Laboratory
Harris Wang, Columbia University
Department of Education
Daphna Bassok, University of Virginia
Shayne Piasta, The Ohio State University
Department of Energy
Jonathan Belof, Lawrence Livermore National Laboratory
Carl Dahl, Northwestern University
Eric Duoss, Lawrence Livermore National Laboratory
Anna Grassellino, Fermi National Accelerator Laboratory
Jacqueline Hakala, National Energy Technology Laboratory
Stephanie Hansen, Sandia National Laboratories
Kory Hedman, Arizona State University
Alan Kruizenga, Sandia National Laboratories
Wei Li, Rice University
Guglielmo Scovazzi, Duke University
Michael Tonks, Penn State University
Jenny Yang, University of California, Irvine
John Yeager, Los Alamos National Laboratory
Department of Health and Human Services
Gregory Alushin, Rockefeller University
Manish Arora, Icahn School of Medicine at Mount Sinai
Dawn Cornelison, University of Missouri
Kashmira Date, Centers for Disease Control and Prevention
Craig Duvall, Vanderbilt University
Nicholas Gilpin, Louisiana State University Health Sciences Center
Anna Greka, Brigham and Women's Hospital
Pamela Guerrerio, National Institutes of Health
Gery Guy, Jr., Centers for Disease Control and Prevention
Christine Hendon, Columbia University
Catherine Karr, University of Washington
Maria Lehtinen, Boston Children's Hospital
Adriana Lleras-Muney, University of California, Los Angeles
Mary Kay Lobo, University of Maryland School of Medicine
Michael McAlpine, University of Minnesota
Eric Morrow, Brown University
Daniel O'Connor, Johns Hopkins University
Aimee Shen, Tufts University
Cui Tao, University of Texas
Jacquelyn Taylor, Yale School of Nursing
Benjamin Voight, University of Pennsylvania
Matthew Wheeler, Centers for Disease Control and Prevention
Blake Wiedenheft, Montana State University
Department of Interior
Nathaniel Hitt, U.S. Geological Survey
Sarah Minson, U.S. Geological Survey
Diann Prosser, U.S. Geological Survey
Department of Veterans Affairs
Adam Rose, RAND Corporation and Boston Medical Center
Nasia Safdar, Middleton Memorial Veterans Hospital
Joshua Yarrow, U.S. Department of Veterans Affairs
Environmental Protection Agency
Havala Pye, Environmental Protection Agency
Sala Senkayi, Environmental Protection Agency
Intelligence Community
Matthew Dicken, U.S. Army
Josiah Dykstra, National Security Agency
James Kang, National Geospatial-Intelligence Agency
Jason Matheny, Office of the Director of National Intelligence
David Moehring, IonQ, Inc.
R. Jacob Vogelstein, Intelligence Advanced Research Projects Activity
National Aeronautics and Space Administration
Jeremy Bassis, University of Michigan
Othmane Benafan, NASA Glenn Research Center
Dalia Kirschbaum, NASA Goddard Space Flight Center
Marco Pavone, Stanford University
Miguel Roman, NASA Goddard Space Flight Center
National Science Foundation
Alicia Alonzo, Michigan State University
Randy Ewoldt, University of Illinois at Urbana-Champaign
Emily Fox, University of Washington
Jacob Fox, Stanford University
Eric Hudson, University of California, Los Angeles
Shawn Jordan, Arizona State University
Ahmed Khalil, Boston University
Oleg Komogortsev, Texas State University, San Marcos
John Kovac, Harvard University
Bérénice Mettler, University of Minnesota and icuemotion, LLC
Jelani Nelson, Harvard University
Elizabeth Nolan, Massachusetts Institute of Technology
Michael Rotkowitz, University of Maryland, College Park
Andrea Sweigart, University of Georgia
Chuanbing Tang, University of South Carolina
Aradhna Tripati, University of California, Los Angeles
Franck Vernerey, University of Colorado, Boulder
Juan Pablo Vielma Centeno, Massachusetts Institute of Technology
Makeba Wilbourn, Duke University
Smithsonian Institution
Nicholas Pyenson, Smithsonian Institution



We're Hiring: Principal Investigators

The Joint Initiative for Metrology in Biology (JIMB), a collaboration between the National Institute of Standards & Technology (NIST) and Stanford University, invites applications for Principal Investigators. Applicants must have a doctorate in an engineering or science discipline.  Successful candidates will be appointed as NIST Staff with Principal Investigator status and as Adjunct Faculty in the most appropriate Stanford University department (e.g., bioengineering, genetics, pathology, etc.).  Appointees will receive significant intramural funding from NIST, and are expected to develop and conduct world-leading research in metrology (the science of measurement) with a focus on genomics or synthetic biology. Appointees will contribute to and be an integral part of the JIMB and broader Stanford and NIST communities.

JIMB’s mission is to advance the science of measuring biology (biometrology). JIMB is pursuing fundamental research, standards development, and the translation of products that support confidence in biological measurements and reliable reuse of materials and results. JIMB is particularly focused on measurements and technologies that impact, are related to, or enabled by ongoing advances in and associated with the reading and writing of DNA. 

JIMB enthusiastically invites applications especially from junior investigators, women, and members of underrepresented groups; applicants must be U.S. citizens. Complete applications should be emailed to jimbscientist@lists.stanford.edu and must include a brief cover letter addressed to the JIMB Search Committee, a research plan of up to three pages, a brief statement of teaching interests, a detailed curriculum vitae, and the names and addresses for at least four references. The candidate selection process will start on 18 December 2016.

NIST Releases New 'Family' of Standardized Genomes

With the addition of four new reference materials (RMs) to a growing collection of “measuring sticks” for gene sequencing, the National Institute of Standards and Technology (NIST) can now provide laboratories with even more capability to accurately “map” DNA for genetic testing, medical diagnoses and future customized drug therapies. The new tools feature sequenced genes from individuals in two genetically diverse groups, Asians and Ashkenazic Jews; a father-mother-child trio set from Ashkenazic Jews; and four microbes commonly used in research.

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BioRxiv Pre-Print: Genome-wide reconstruction of complex structural variants using read clouds

Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cloud approaches represent a powerful, accurate, and cost-effective alternative to single-molecule long-read sequencing. We developed software, GROC-SVs, that takes advantage of read clouds for structural variant detection and assembly.

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BioRxiv Pre-Print: Measurements of translation initiation from all 64 codons in E. coli

Our understanding of translation is one cornerstone of molecular biology that underpins our capacity to engineer living matter. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are typically considered as the start codons for translation initiation in Escherichia coli (E. coli). Translation is typically not thought to initiate from the 61 remaining codons. Here, we systematically quantified translation initiation in E. coli from all 64 triplet codons. We detected protein synthesis above background initiating from at least 46 codons. Translation initiated from these non-canonical start codons at levels ranging from 0.01% to 2% relative to AUG. Translation initiation from non-canonical start codons may contribute to the synthesis of peptides in both natural and synthetic biological systems.

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Journal of the American Chemical Society Publication: In Vivo Site-Specific Protein Tagging with Diverse Amines Using an Engineered Sortase Variant

Chemoenzymatic modification of proteins is an attractive option to create highly specific conjugates for therapeutics, diagnostics, or materials under gentle biological conditions. However, these methods often suffer from expensive specialized substrates, bulky fusion tags, low yields, and extra purification steps to achieve the desired conjugate. Staphylococcus aureus sortase A and its engineered variants are used to attach oligoglycine derivatives to the C-terminus of proteins expressed with a minimal LPXTG tag. This strategy has been used extensively for bioconjugation in vitro and for proteinprotein conjugation in living cells. Here we show that an enzyme variant recently engineered for higher activity on oligoglycine has promiscuous activity that allows proteins to be tagged using a diverse array of small, commercially available amines, including several bioorthogonal func- tional groups. This technique can also be carried out in living Escherichia coli, enabling simple, inexpensive production of chemically functionalized proteins with no additional purification steps. 

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ACS Synthetic Biology Publication: When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins

The abundance of bacteria in liquid culture is commonly inferred by measuring optical density at 600 nm. Red fluorescent proteins (RFPs) can strongly absorb light at 600 nm. Increasing RFP expression can falsely inflate apparent cell density and lead to underestimations of mean per-cell fluorescence by up to 10%. Measuring optical density at 700 nm would allow estimation of cell abundance unaffected by the presence of nearly all fluorescent proteins. 

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