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Recent Research Papers of Note: Apr 8, 2011


Proteomics research papers of note, March 2011

Journal: Proteomics, Mar 10 [Epub ahead of print]

Title: Dynamics of post-translational modifications and protein stability in the stroma of Chlamydomonas reinhardtii chloroplasts.

Authors: Bienvenut WV; Espagne C; Martinez A; Majeran W; Valot B; Zivy M; Vallon O; Adam Z; Meinnel T; Giglione C.

Using 2DE profiling coupled with MS analysis, the researchers investigated the dynamics of the stromal proteome in Chlamydomonas reinhardtii by characterizing the half-life of these proteins. With the results, they put together an interactive map of the stromal proteome, which currently features 274 distinct protein variants. Their findings also suggested that N-α-terminal-acetylation could contribute to protein stabilization.

Journal: Molecular & Cellular Proteomics, Mar. 15 [Epub ahead of print]

Title: Redox proteomics of protein-bound methionine oxidation.

Authors: Ghesquiere B; Jonckheere V; Colaert N; Van Durme J; Timmerman E; Goethals M; Schymkowitz J; Rousseau F; Vandekerckhove J; Gevaert K.

The authors describe a new method to measure the degree of protein-bound methionine-sulfoxide formation on a proteome-wide scale, mapping more than 2,000 oxidation-sensitive methionines in more than 1,600 proteins and quantifying the extent of their oxidation.

Journal: Journal of Proteome Research, Mar. 16 [Epub ahead of print]

Title: Toward protein biomarkers for allergy: CD4+ T cell proteomics in allergic and nonallergic subjects sampled in and out of pollen season.

Authors: Blüggel M; Spertini F; Lutter P; Wassenberg J; Audran R; Corthésy B; Müllner S; Blum S; Wattenberg A; Mercenier A; Affolter M; Kussmann M.

The researchers studied CD+4 cells from 20 adult volunteers, quantitatively analyzing their proteomes in and out of pollen season using 2D gel electrophoresis to identify predictive markers of progression from genetic predisposition to allergy to allergy itself. They found three proteins that were differentially expressed in allergic and non-allergic subjects during pollen season and three others that were differentially expressed outside of pollen season.

Journal: Astrobiology, Mar. 18 [Epub ahead of print]

Title: Responses of haloarchaea to simulated microgravity.

Authors: Dornmayr-Pfaffenhuemer M; Legat A; Schwimbersky K; Fendrihan S; Stan-Lotter H.

The authors grew two haloarchaeal strains in simulated microgravity and investigated the changes in their proteomes in order to better understand the potential survival of microbes during interplanetary travel inside meteorites.

Journal: Journal of Computational Biology, Mar. 18

Title: Proteome coverage prediction for integrated proteomics datasets.

Authors: Claassen M; Aebersold R; Buhmann JM.

The authors describe a generalized hierarchical Pitman-Yor process model that captures redundancy within integrated datasets that they propose will improve prediction of proteome coverage from large, heterogeneous proteomic datasets.

Journal: Journal of the American Society for Mass Spectrometry, Mar 22 [Epub ahead of print]

Title: Mass spectrometric characterization of protein structure details refines the proteome signature for invasive ductal breast carcinoma.

Authors: Röwer C; Koy C; Hecker M; Reimer T; Gerber B; Thiesen HJ; Glocker MO.

The authors applied 2D gel analysis to six breast cancer patients, examining protein expression differences between invasive ductal breast carcinoma from controls. Using MS/MS analysis of protein spots, they found 38 differentially expressed spots, including several post-translationally modified isoforms, that enabled accurate separation of tumor from control samples.

Journal: Cellular Signaling, Mar 26 [Epub ahead of print]

Title: Towards a comprehensive characterization of the phosphotyrosine proteome.

Authors: Lind SB; Artemenko KA; Elfineh L; Mayrhofer C; Zubarev RA; Bergquist J; Pettersson U.

The authors immunoaffinity-enriched pTyr proteins and peptides from K562 leukemia cells and analyzed them using high-resolution LC-MS. They identified 294 pTyr peptides belonging to 217 pTyr proteins, including many involved in RNA processing and three transcription factors.

Journal: BMC Research Notes, Mar. 28 [Epub ahead of print]

Title: A DIGE study on the effects of salbutamol on the rat muscle proteome — an exemplar of best practice for data sharing in proteomics.

Authors: Kenyani J; Medina-Aunon JA; Martinez-Bartolome S; Albar JP; Wastling JM; Jones AR.

The researchers performed a study of the effects of salbutamol at two time points on the protein complement of rat skeletal muscle cells using DIGE, identifying 110 proteins that were potentially modified. They also described how this data could be added to the PRIDE database using the PRIDESpotMapper software tool and demonstrated how to use the ProteoRed MIAPE tool to create and share MIAPE reports for their work.

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

Title: Protein alterations associated with pancreatic cancer and chronic pancreatitis found in human plasma using global quantitative proteomics profiling.

Authors: Pan S; Chen R; Crispin DA; May D; Stevens T; McIntosh MW; Bronner MP; Ziogas A; Anton-Culver H; Brentnall TA.

The researchers conducted a quantitative proteomics study using multidimensional fractionation at the protein and peptide level to look for biomarkers for pancreatic cancer, finding more than 1,300 proteins in plasma across eight orders of magnitude, and identifying several potential biomarkers including the proteins TIMP1, ICAM1, and AZGP1.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.