Friday, September 23, 2011

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.

Friday, September 2, 2011

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:


Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.


We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.


The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing."