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Recent Research Papers of Note: May 28, 2010


Proteomics research papers of note, May 2010

Journal: Journal of Proteome Research, May 7

Title: Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems

Authors: Jayapal KP; Sui S; Philp RJ; Kok YJ; Yap MG; Griffin TJ; Hu WS

Currently quantitative proteomics focuses mainly on measuring overall protein dynamics – the net result of protein synthesis and degradation – which is vital to understanding cellular dynamics and moving from transcriptome to proteome analysis. Protein dynamics are typically estimated through "label-chase" experiments using isotope-labeled precursors. However, the authors note, this technique assumes a steady state that may not apply to many intrinsically dynamic systems. The authors present a novel extension of the "label-chase" concept using SILAC and iTRAQ reagents to estimate protein turnover rates in Streptomyces coelicolor cultures.

Journal: Journal of Proteomics, May 12 [Epub ahead of print]

Title: Quantitative proteome profiling of respiratory virus-infected lung epithelial cells

Authors: van Diepen A; Brand HK; Sama I; Lambooy LH; van den Heuvel LP; van der Well L; Huynen M; Osterhaus AD; Andeweg AC; Hermans PW.

Respiratory virus infections are a significant cause of mortality in humans. To better understand the molecular pathogenesis of these infections, the authors undertook a study of the protein profiles of infected lung epithelial cells, comparing infected and mock-infected cells via 2D gel electrophoresis to identify proteins that were differentially expressed due to infection. The differences in expression discovered point toward an induction of apoptosis upon infection.

Journal: Journal of Psychiatric Research, May 12 [Epub ahead of print]

Title: Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia

Authors: Martins-de-Souza D; Maccarrone G; Wobrock T; Zerr I; Gormanns P; Reckow S; Falkai P; Schmitt A; Turck CW

The DNA changes and environmental factors that lead to schizophrenia lead to differential protein expression. The authors compared the proteome of thalamus samples from schizophrenic and non-schizophrenic subjects, identifying 551 total proteins, 50 of which showed significant differential expression. The protein differences corroborated the importance of myelin/oligodendrocyte and energy metabolism in schizophrenia and suggested potential biomarkers that could enhance understanding of the disease.

Journal: Proteomics, May 17 [Epub ahead of print]

Title: Proteome profiling reveals gender differences in the composition of human serum

Authors: Miike K; Aoki M; Yamashita R; Takegawa Y; Saya H; Miike T; Yamamura KI

Proteome analysis using serum has potential for the discovery of new biomarkers enabling advances in disease prevention and treatment. The technology, however, is still in its early stages. The authors developed a semi-comprehensive technique using iTRAQ labeling and HPLC and nano-LC mass spectrometry to compare the composition of the serum proteome in males and females and detect gender-based differences.

Journal: Proteomics, May 18 [Epub ahead of print]

Title: Quantitative proteome analysis of detergent-resistant membranes identifies the differential regulation of protein kinase C isoforms in apoptotic T cells

Authors: Solstad T; Bjorgo E; Koehler CJ; Strozynsky M; Torgersen KM; Tasken K; Thiede B

Evidence suggests that detergent-resistant membranes have a role in signaling pathways of apoptosis. To investigate this role, the authors developed a method combining DRMs isolation and methanol/chloroform extraction with SILAC-based quantitative proteome analysis of DRMs from control and cisplatin-induced apoptotic Jurkat T cells. They were able to show three isoforms of protein kinase C that are regulated differentially upon induction of apoptosis, demonstrating the usefulness of proteomic analysis of DRMs as a tool to study differential localization and regulation of important signaling molecules.

Journal: Journal of Proteome Research, May 20 [Epub ahead of print]

Title: Quantitative proteomic profiling studies of pancreatic cancer stem cells

Authors: Dai L; Li C; Shedden K; Lee CJ; Li C; Quoc HV; Simeone DM; Lubman DM

Proteomic study of tumor cell subpopulations is a promising way of researching the molecular machinery underlying cancer signaling pathways but is challenged by the small amount of sample typically available for study. The authors describe a capillary scale shotgun technique for profiling the proteome of pancreatic cancer stem cells that identified 169 differentially expressed proteins.

Journal: Analytical Biochemistry, May 20 [Epub ahead of print]

Title: Gel-absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry

Authors: Zhou J; Xiong J; Li J; Huang S; Zhang H; He Q; Lin Y; Chen P; Wang X; Liang S

The authors developed a sample-preparation method for shotgun analysis of membrane proteome based on gel absorption. The new method avoided protein loss and adverse protein modifications during gel-embedment and improved the in-gel digestion and recovery of tryptic peptides – particularly hydrophobic peptides. Compared to conventional tube-gel digestion, the new method increased the numbers of identified membrane proteins by 25 percent and integral membrane proteins by 30.2 percent, the authors said.

Journal: Science, May 21

Title: A global protein kinase and phosphatase interaction network in yeast

Authors: Breitkreutz A; Choi H; Sharom JR; Boucher L; Neduva V; Larsen B; Lin ZY; Breitkreutz BJ; Stark C; Liu G; Ahn J; Dewar-Darch D; Reguly T; Tang X; Almeida R; Qin ZS; Pawson T; Gingras AC; Nesvizhskii AI; Tyers M.

The interaction of protein kinases and phosphatases with regulatory subunits and substrates is key to cellular regulation. Using mass spectrometry analysis of protein complexes, the authors identified a kinase and phosphatase interaction network in budding yeast of 1,844 interactions, including many dense local regions of interactions that suggested new functions.

Journal: Journal of Proteome Research, May 26 [Epub ahead of print]

Title: Quantitative Analysis of mTRAQ-Labeled Proteome Using Full MS Scans

Authors: Kang UB; Yeom J; Kim H; Lee C

Quantification of proteome differences between different physiological conditions is a challenging task in proteomics. One method for quantification is using mass tags to introduce stable isotopes into peptides or proteins for quantification via mass spectrometry. The authors used mTRAQ labeling to analyze colon cancer tissues, identifying and quantifying a total of 3,320 proteins.

Journal: Bioinformatics, May 26 [Epub ahead of print]

Title: Prediction of protease substrates using sequence and structure features

Authors: Barkan DT; Hostetter DR; Mahrus S; Pieper U; Wells JA; Craik CS; Sali A

Granzyme B and caspases induce apoptosis in virally infected and neoplastic cells by cleaving specific protein substrates. Substrates for these proteases have been determined experimentally, but many have yet to be discovered. The authors present a bioinformatics approach to predicting novel substrates based on support vector machine learning, applying the methodology to the roughly 25,000 proteins in the human proteome to generate a ranked list of predicted substrates.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.