Researchers generate first complete 3-D structures of bacterial chromosome

A team of researchers at the University of Massachusetts Medical School, Harvard Medical School, Stanford University and the Prince Felipe Research Centre in Spain have deciphered the complete three-dimensional structure of the bacterium Caulobacter cresc ...

Source: University of Massachusetts Medical School 

A QuantuMDx Leap for Handheld DNA Sequencing

"October 17, 2011 | MONTREAL – Speaking for the first time in his life as a commercial consultant rather than a public servant, Sir John Burn, a highly respected clinical geneticist in the United Kingdom, provided the first glimpse at a nanowire technology for rapid DNA genotyping that could eventually mature into the world’s first handheld DNA sequencer.  

Burn previewed a potentially disruptive genome diagnostic technology in a presentation on the closing day of the International Congress of Human Genetics in Montreal last weekend. 

One day a week, Burn, professor of clinical genetics at Newcastle University, serves as medical director for QuantuMDx (QMDx), a British start-up co-founded by molecular biologist Jonathan O’Halloran and healthcare executive Elaine Warburton."

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Drug2Gene

Drug2Gene is a free knowledge integrated data repository unifying a number of popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. It allows user's interactive management by the ability to flag, comment and update relations, to import new drug-gene relations valuable for a specific project. Gene orthology and similarity information is matched to certain relationship entries assisting the prediction of new unreported drug-gene associations. You can go to the original source of the reported relation and explore for more facts, details and evidences. 

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Gamers succeed where scientists fail

"Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, an online game that allows players to collaborate and compete in predicting the structure of protein molecules."

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mz5: Space- and time-efficient storage of mass spectrometry data sets

"Across a host of mass spectrometry (MS)-driven -omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS datasets and the need for their compact yet efficiently accessible storage has become clear.
The HUPO proteomics standard initiative (PSI) has defined an ontology and associated controlled vocabulary that specifies the contents of MS data files in terms of an open data format. Current implementations are the mzXML and mzML formats (mzML specification), both of which are based on an XML representation of the data. As a consequence, these formats are not particular efficient with respect to their storage space requirements or I/O performance.
This contribution introduces mz5, an implementation of the PSI mzML ontology that is based on HDF5, an efficient, industrial strength storage backend.
Compared to the current mzXML and mzML standards, this strategy yields an average file size reduction of a factor of ~2 and increases I/O performace ~3-4 fold.
The format is implemented as part of the ProteoWizard project."
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Gamers Unlock Protein Mystery That Baffled AIDS Researchers For Years

"In just three weeks, gamers deciphered the structure of a key protein in the development of AIDS that has stumped scientists for years. According to a studypublished Sunday in the journal Nature Structural & Molecular Biology, the findings could present a significant breakthrough for AIDS and HIV research.

Using an online game called Foldit, players were able to predict the structure of a protein called retroviral protease, an enzyme that plays a critical role in the way HIV multiplies. Unlocking the build of the protein could theoretically aid scientists in developing drugs that would stop protease from spreading.

Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to produce accurate models of the protein,” the study reads. “Remarkably, Foldit players were able to generate models of sufficient quality for successful molecular replacement and subsequent structure determination. The refined structure provides new insights for the design of antiretroviral drugs.”

Developed by researchers at the University of Washington, Foldit turns scientific problems into competitive games. Players were charged with using spatial and critical thinking skills to build 3D models of protease. Few of these players had any kind of background in biochemistry.

According to Fox, it took players a matter of days to come up with models that were solid enough for researchers to translate into scientific rendering of the protein.

“People have spatial reasoning skills, something computers are not yet good at,” Foldit’s lead designer Seth Cooper said in a statement. “Games provide a framework for bringing together the strengths of computers and humans.”

Foldit has not only made this breakthrough with AIDS research, but it has also aided in Cancer and Alzheimer’s research. For more, read the study in its entirety here.

HPLC 2011 highlights chromatography technologies

Thermo Fisher Scientific is to highlight its expanded offering of chromatography instruments, software and consumables, including the Accucore HPLC column range, at the HPLC 2011 event in Budapest.

The Accucore HPLC column range is said to enhance laboratory workflow and efficiency by providing increased sensitivity and peak resolution in columns that are compatible with almost any instrument.

Thermo Fisher Scientific will also showcase the Easy-NLC 1000 split-free nano-flow system for advanced proteomics research at HPLC 2011.

This system is said to increase chromatographic resolution and, as a result, protein and peptide identifications, with ultra-high-pressure operation.

The company will also highlight the Velos Pro linear ion trap and the Orbitrap Velos Pro hybrid FTMS mass spectrometers.

These systems are said to provide improved quantitative performance, faster scanning, trap higher energy collision dissociation (HCD) and enhanced robustness.

Thermo Fisher Scientific will also introduce the Q Exactive high-performance benchtop quadrupole-Orbitrap LC-MS/MS, which combines quadrupole precursor selection and high-resolution accurate mass (HR/AM) Orbitrap mass analysis to deliver high-confidence quantitative and qualitative workflows.

With the HR/AM Quanfirmation capability, the Q Exactive mass spectrometer can identify, quantify and confirm more trace-level peptides and proteins in complex mixtures in one analytical run.

The Orbitrap Elite hybrid mass spectrometer is said to provide the resolution and sensitivity required to improve the determination of the molecular weights of intact proteins within laboratories, as well as enable greater proteome coverage through improved protein, PTM and peptide identification, even at low abundances.

Read more: http://www.laboratorytalk.com/news/tel/tel185.html#ixzz1RfGDUTMa