Several baffling puzzles in protein molecular structure solved with new method

The structures of many protein molecules remain unsolved even after experts apply an extensive array of approaches. An international collaboration has led to a new, high-performance method that rapidly determined the structure of protein molecules in several cases where previous methods had failed.

The usefulness of the new method is reported May 1 inNature advanced online publication. The lead authors are Dr. Frank DiMaio of the University of Washington (UW) in Seattle and Dr. Thomas C. Terwilliger of Los Alamos National Laboratory in New Mexico. The senior author is Dr. David Baker, of the UW Department of Biochemistry.

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2D Gel Image Analyser at Major Ophthalmology Centre

Syngene, a world-leading manufacturer of image analysis solutions, is pleased to announce its Dyversity 2D gel imaging system is being used by scientists at one of Latin America’s most prestigious Ophthalmological Institutions, the Institute of Ophthalmology “Fundación Conde de Valenciana” in Mexico, to study which proteins are associated with ocular diseases. 

Researchers in the Microbiology and Ocular Proteomics Area at the Institute of Ophthalmology “Fundación Conde de Valenciana” are using the Dyversity, Syngene’s 2D gel imaging system to accurately visualise proteins stained with either silver stain or Coomassie blue on 2D and 1D gels. The system is also being used to analyse chemiluminescent protein arrays and Western blots. The information from the gels and blots is helping detect which proteins are responsible for a range of ocular diseases, and it is hoped that determining the molecular basis of these conditions, may help find new therapies to treat them. 

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Thermo Fisher Scientific Introduces Peptide Calibration Reagent to Optimize Liquid Chromatography Performance

"Thermo Fisher Scientific, the world leader in serving science, today announced the availability of the Thermo Scientific Pierce Peptide Retention Time Calibration Mixture for the prediction of peptide retention times on reversed-phase high-performance liquid chromatography (HPLC) columns. 
The convenient, ready-to-use Pierce® Peptide Retention Time Calibration Mixture contains 15 synthetic, heavy peptides mixed at an equimolar ratio to elute across the chromatographic gradient. It can be used with Thermo Scientific Pinpoint Software to predict peptide retention time from sequence alone, using hydrophobicity factors, or to predict peptide retention time between instrument platforms. 

The Pierce Peptide Retention Time Calibration Mixture streamlines the transition from qualitative protein discovery results to the development of targeted mass spectrometry (MS) assays on Thermo Scientific Triple Quadrupole, Orbitrap and Exactive Instruments and all other mass spectrometers. It also saves time in peptide purification by increasing the prediction efficiency of peptide retention profiles. The mixture is useful in evaluating different reversed-phase column and gradient options, monitoring for autosampler and HPLC column performance characteristics and normalizing results between experiments and over time."

In Vivo Imaging From Whole Organ to Single Cell

UVP, LLC announces the release of the new iBox® Explorer™ Fluorescence Microscope at ASM. The Explorer system combines the technology from its macro imager, the iBox Scientia™ Imaging System, with new micro imaging technology that incorporates imaging tissues, tissue margins and individual cells. The Explorer provides breakthrough advances in its dual lighting system and software controlled objectives. The Explorer system supplies the benefit of using one complete system for macro and micro in vivo animal fluorescent imaging. 
"The iBox Explorer is significant for speed and versatility," according to Sean Gallagher (VP and CTO UVP). "Enabling the rapid and multiplexed fluorescence detection of tumor margins and micro metastasis, the Explorer cleanly separates normal from cancer tissues via the cell's fluorescent signature. Operating in the visible and NIR wavelengths, the Explorer yields detailed images of tissues and cells or, using the joy stick, 'flies' across an area such as the open abdominal region or skin flap of a mouse for rapid screening." In addition to imaging both the whole organ and cells of small animals, the Explorer delivers optical configurations that are parcentered and parfocal, allowing seamless imaging through the magnification ranges. 

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A window into third-generation sequencing

First- and second-generation sequencing technologies have led the way in revolutionizing the field of genomics and beyond, motivating an astonishing number of scientific advances, including enabling a more complete understanding of whole genome sequences and the information encoded therein, a more complete characterization of the methylome and transcriptome and a better understanding of interactions between proteins and DNA. Nevertheless, there are sequencing applications and aspects of genome biology that are presently beyond the reach of current sequencing technologies, leaving fertile ground for additional innovation in this space. In this review, we describe a new generation of single-molecule sequencing technologies (third-generation sequencing) that is emerging to fill this space, with the potential for dramatically longer read lengths, shorter time to result and lower overall cost.
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NSF Gives Three Life-Science Projects $1.2M Grant to Test Microsoft’s Azure Cloud

Three life-science projects are among 13 teams that will have free access to Microsoft’s Azure cloud-computing platform for two years as part of an agreement between Microsoft and the National Science Foundation.

The life-science projects, led by researchers at Virginia Polytechnic Institute; the University of North Carolina, Charlotte; and the J. Craig Venter Institute, were awarded a total of $1.2 million in grants under the program, which kicked off in 2010 (BI02/10/2010). The awardees were announced last week.

In addition to providing access to the cloud, Microsoft will provide a support team, tools, applications, and data collections to help the scientists integrate cloud technology into their research.

An NSF review board considered the “appropriateness” of each proposal to the Azure platform’s capabilities, Reed Beaman, a program director at the agency, told BioInform.

For example, he said, the reviewers considered the fact that the platform is very strong in so-called “embarrassingly parallel” computations and in its ability to deploy web services.

He observed that in addition to providing Microsoft an opportunity to test the limits of its cloud computing platform, the partnership saves research dollars that would otherwise have been spent on hardware.

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Get SMRT: Pacific Biosciences Unveils Software Suite with Commercial Launch

April 29, 2011 | Third-generation sequencing company Pacific Biosciences (PacBio) began commercial shipment of its PacBio RS single-molecule sequencer this week. The instrument has been in beta testing at 11 institutions in North America and elsewhere for the past year. A notable success was the recent sequencing and identification of the cholera strain sweeping Haiti after the devastating 2010 earthquake.  

In a briefing with Bio-IT World, PacBio staffers Kevin Corcoran, Jon Sorenson and Edwin Hauw previewed the new suite of software tools on the RS sequencer. The SMRT (single molecule/real time) Analysis software suite features web-based software, an analysis pipeline framework, and algorithms for sequence alignment and de novo assembly.  

“We’re accelerating the development of software with the community,” says Kevin Corcoran. “A key feature of third-generation sequencing is that [the technology] doesn’t match up with what’s out there now. The key features of the PacBio system include fast time to result, high granularity, long read lengths, and new sequencing modes, including a circular mode and strobe sequencing.”  

PacBio’s single-molecule sequencing system offers significantly longer read lengths (1,000 bases on average) than its second-generation sequencing rivals, and faster run times. That said, the total sequence throughput per run is currently less than other commercial platforms. The single-read accuracy hovers in the 85-90% range.   

A revelatory feature of the SMRT software portal is that it captures kinetic information – the time for each registered nucleotide to be captured and incorporated into the growing DNA strand. “This is the first time you can watch DNA polymerase in real time, so that kinetic information will provide additional applications that have never been enabled before,” says Corcoran.   

The genome browser is called SMRT View. “This takes advantage of our longer reads and kinetic information,” says Sorenson. It includes strobe and consensus sequence modes, allowing the user tovisualize and interact with secondary analysis sequence data. PacBio says the interactive graphical representations of variants, quality values, and other metrics is the first data visualization application that can visualize kinetics and structure information unique to PacBio's SMRT technology.

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