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Recent Research Papers of Note: Aug 27, 2010

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Proteomics research papers of note, August 2010

Journal: Journal of Proteome Research, July 28 [Epub ahead of print]

Title: Novel proteomic strategy reveal[s] combined alpha(1) antitrypsin and cathepsin D as biomarkers for colorectal cancer early screening

Authors: Xie LQ; Zhao C; Cai SJ; Xu Y; Huang LY; Bian JS; Shen CP; Lu HJ; Yang PY.

Using methylation isotope labeling assisted gel-enhanced liquid chromatography-mass spectrometry, the researchers compared protein expression levels in early-stage colorectal cancer patients and normal counterparts, identifying 501 proteins showing consistent differential expression, with alpha1 antitrypsin and cathepsin D exhibiting particular promise as potential biomarkers.


Journal: Molecular & Cellular Proteomics, Aug. 6 [Epub ahead of print]

Title: Towards next generation plasma profiling via heat-induced epitope retrieval and array-based assays

Authors: Schwenk JM; Igel U; Neiman M; Langen H; Becker C; Bjartell A; Ponten F; Wiklund F; Grönberg H; Nilsson P; Uhlen M.

The authors demonstrate a high-throughput method of screening patient samples for potential biomarkers using a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval. Several antibodies were found to have altered protein profiles and increased sensitivity upon epitope retrieval at higher temperatures, and a study of prostate cancer patients discovered several proteins with differential profiles.


Journal: Proceedings of the National Academy of Sciences, Aug. 10

Title: Analysis of proteome dynamics in the mouse brain

Authors: Price JC; Guan S; Burlingame A; Prusiner SB; Ghaemmaghami S.

The authors used organism-wide isotopic labeling to measure turnover rates of approximately 2,500 proteins in a variety of mouse tissues. The data represent the most comprehensive in vivo analysis of mammalian proteome turnover to date and could be particularly useful in the analysis of neurodegenerative diseases, they said.


Journal: Journal of Virology, Aug. 11 [Epub ahead of print]

Title: Quantitative proteomic analyses of influenza virus-infected cultured human lung cells.

Authors: Coombs KM; Berard A; Xu W; Krokhin O; Meng X; Cortens JP; Kobasa D; Wilkins J; Brown EG.

The authors used SILAC combined with 2D HPLC-mass spectrometry to investigate quantitative differences in human lung proteins after infection by H1N1, finding that of 4,689 identified proteins, 127 were significantly up-regulated and 153 were significantly down-regulated, with many of the differentially regulated proteins involved in host cell immunity and antigen presentation, cell adhesion, metabolism, protein function, signal transduction, and transcription pathways.


Journal: Environmental Science & Technology, Aug. 17 [Epub ahead of print]

Title: Proteomics analysis of flax grown in Chernobyl area suggests limited effect of contaminated environment on seed proteome

Authors: Klubicová K; Danchenko M; Skultety L; Miernyk JA; Rashydov NM; Berezhna VV; Pret'ová A; Hajduch M.

The land around the Chernobyl Nuclear Power Plant remains contaminated from the plant's 1986 meltdown, but the local ecosystem has been able to adapt. The authors analyzed the proteomes of flax seeds grown in radio-contaminated and control fields near Chernobyl, finding differences in only 35 of 720 protein spots.


Journal: Journal of Proteome Research, Aug. 18 [Epub ahead of print]

Title: Comprehensive profiling of phosphopeptides based on anion exchange followed by flow-through enrichment with titanium dioxide (AFET)

Authors: Nie S; Dai J; Ning ZB; Cao XJ; Sheng QH; Zeng R.

To better isolate phosphopeptides for mass spectrometry the authors submitted the flow-through fraction from strong ion exchange separation to TiO2 enrichment, finding that the process allowed for the identification of more phosphopeptides with less time needed for mass spec analysis.


Journal: Journal of Proteome Research, Aug. 19 [Epub ahead of print]

Title: Les maîtres de l'orge: the proteome content of your beer mug

Authors: Righetti PG; Fasoli E; Aldini G; Regazzoni L; Kravchuk A; Citterio A.

The researchers used mass spectrometry to analyze the residual proteome of beer, identifying 17 different barley proteins, 2 maize proteins, and 35 gene products from Saccharomyces cerevisiae. Understanding of the beer proteome could help brewers improve beer texture and flavor, the authors said.


Journal: Environmental Microbiology, Aug. 20 [Epub ahead of print]

Title: Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland

Authors: Habicht KS; Miller M; Cox RP; Frigaard NU; Tonolla M; Peduzzi S; Falkenby LG; Andersen JS.

The authors submitted Chlorobium clathratiforme specimens from four different positions in the water column in Lake Cadagno, Switzerland, to comparative proteomic analysis to investigate changes in protein expression in response to varying levels of light exposure and constructed possible pathways for carbon, nitrogen, and sulfur metabolism based on the protein expression levels.


Journal: BMC Bioinformatics, Aug. 23 [Epub ahead of print]

Title: A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra

Authors: Xu H; Freitas MA.

High-throughput shotgun proteomics data typically contains a number of spectra from non-peptide ions, complicating database searches and increasing computational expenses. The authors put forth a new algorithm they claim removes significant amounts of extraneous spectra, allowing for more efficient database searches.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.