A lack of structure facilitates protein synthesis

Texts without spaces are not very legible, as they make it very difficult for the reader to identify where a word begins and where it ends. When genetic information in our cells is read and translated into proteins, the enzymes responsible for this task face a similar challenge. They must find the correct starting point for protein synthesis. Therefore, in organisms with no real nucleus, a point exists shortly before the start codon, to which the enzymes can bind particularly well. This helps them find the starting point itself. However, genes that do not have this sequence are also reliably translated into proteins. Scientists from the Max Planck Institute of Molecular Plant Physiology in Potsdam have discovered that the structure of the messenger RNA probably plays a crucial role in this process.

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Predicting liver transplant rejection

"The survival rate of liver transplant patients one year after treatment has improved from about 30% in the 1970s to more than 80%, with acute cellular rejection (ACR) the most common complication. It occurs in about 30% of cases and is generally arrested by drug treatment. However, if ACR occurs more than one year after the transplant, survival rates plummet.

The diagnosis of ACR requires a tissue biopsy, which is risky and uncomfortable for the patient. Even then, the interpretation of samples is difficult because the three clinical predictors are not always present.

These problems have prompted scientists in the US to look for a non-invasive alternative diagnosis for ACR and they turned to proteomics for the solution. Michael Charlton and colleagues from the Mayo Clinic and Foundation, Rochester, MN, and the University of Alabama at Birmingham decided to look at the serum proteome to see if any indicators of ACR were detectable.

Human serum contains many high-abundant proteins but, if they are removed before protein analysis, it is possible to detect low-abundant proteins which are transiently present in serum.

So, proteins secreted by cells or produced during cell destruction become visible. These include hormones and cytokines which are transported in serum to their destinations within the human body."

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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

Scientists welcome bioinformatics bonanza

AUSTRALIAN researchers now have free access to one of the world's most comprehensive database resources.

Launched last month, a mirror facility at the University of Queensland in Brisbane means scientists can use their computers to enter the most used data services of the British arm of the European Molecular Biology Laboratory's European Bioinformatics Institute.

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Roche´s xCELLigence RTCA HT System: Fully-automated Measurement of Therapeutic Targets` Cellular Activity

"Label-free technologies have entered the stage of cellular drug discovery and high-throughput screening (HTS). For the measurement of G protein-coupled receptor (GPCR) activation electrical impedance represents an excellent universal readout technology, since different signaling pathways can be measured in one assay format using recombinant as well as primary cells. The recently developed xCELLigence RTCA HT Instrument from Roche Applied Science now allows to perform fully-automated impedance screens for GPCRs and other targets in the 384-well high-throughput format.
In a recent case study, Urs Lüthi and John Gatfield from Actelion Pharmaceuticals Ltd., Allschwil, Switzerland, integrated 2 RTCA HT (real-time cell analyzer for high-throughput) Instruments on an automated high-throughput screening platform from Agilent Technologies (Santa Clara, US). 263 antagonist hits of the orexin type 1 (Ox1) GPCR that had been identified in a classical calcium flux (FLIPR) HTS were screened for Ox1 inhibition in fully-automated RTCA HT assays. The overall performance, the quality of E-Plates 384 and intra- and inter-assay reproducibility were evaluated. 65% of the 263 antagonist hits were confirmed to be Ox1 receptor antagonists after impedance measurements. According to the researchers, the RTCA HT Instrument could be readily integrated into automated workflows and delivered a highly reproducible data set, making the RTCA HT Instrument a powerful screening technology. 

Compared to standard readout technologies one of the major advantages of label-free technologies is that cellular processes are measured in real-time kinetics in a non-invasive manner. The xCELLigence System uses gold electrodes at the bottom surface of microplate wells as sensors to which an alternating current is applied. Cells that are grown as adherent monolayers on top of such electrodes influence the alternating current at the electrodes by changing the electrical resistance (impedance). The degree of this change is primarily determined by the number of cells, strength of the cell-cell interactions, interactions of the cells with the microelectrodes and by the overall morphology of the cells."

MSE from Waters - the ultimate technology for reproducible profiling

"Waters mass spectrometers provide a method of data acquisition - known as MS^E - that records exact mass precursor and fragment ion information from every detectable component in a sample. This method rapidly alternates between two functions: the first acquiring low-energy exact mass precursor ion spectra, the second acquiring elevated-energy exact mass fragment ion spectra. Every mass is measured, and spectra for each component aligned in retention time. This patented method records data without discrimination or pre-selection so your samples are completely catalogued in a single analysis.



When compared to Data Directed Analysis (DDA), MS^E maximizes instrument duty cycle by ensuring that exact mass precursor and fragment ion information data are obtained for the entire peak complement of a chromatogram, making it ideal for fast analysis and narrow, rapidly eluting peaks. DDA results in both a loss of data in the MS mode when MS/MS data are being acquired, and poor duty cycle. MS^E data is collected fast enough to accurately define the LC peaks for every detectable component.



MS^E is faster than traditional MS followed by MS/MS analysis, and provides data that is not readily obtained by DDA, as both MS and MS/MS data for all detectable components in the chromatogram are generated. MS^E can generate both precursor and product ions in a single analytical run thereby eliminating the need to rerun the samples to obtain further MS/MS spectra. To see MS^E in action and hear what scientists have to say about it, visit www.waters.com/MS^E."

Bruker Announces Release of Breakthrough CaptiveSpray(TM) Nano/Capillary Electrospray Ion Source for Proteomics at ASMS 2011

At ASMS 2011, Bruker is introducing the breakthrough, proprietary CaptiveSpray electrospray ion source for nano-HPLC applications in proteomics. Using CaptiveSpray technology in many cases increases bottom-up protein identifications significantly, and CaptiveSpray is presently the best available technology for robust, reproducible protein ID or quantitative proteomics applications, with excellent, stable sensitivity over long time periods.
Unlike a traditional pulled nanospray tip, the Etch-Taper™ technology employed by CaptiveSpray ensures that the internal diameter of the spray tip remains constant, thereby reducing tip clogging, and providing excellent spray stability over the entire LC gradient and robust operation for long time periods, even with heavy proteomics samples loads. A key proprietary feature of the CaptiveSpray is its novel gas-flow focusing technology for dramatic sensitivity gains compared to normal electrospray. The CaptiveSpray source delivers nanospray sensitivity without the need for complex and time consuming spray tip adjustments, while its innovative plug-and-play design fits all current Bruker LC-MS instruments, including the latest maXis UHR-Qq-TOF systems, solariX FTMS systems and amaZon ETD ion trap mass spectrometers. 
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