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Recent Research Papers of Note: Sep 16, 2011

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Proteomics Research Papers of Note, August 2011

Journal: Journal of the Science of Food and Agriculture, Aug. 4 [Epub ahead of print]

Title: Comparative proteome analysis of glutenin synthesis and accumulation in developing grains between superior and poor quality bread wheat cultivars.

Authors: Liu W; Zhang Y; Gao X; Wang K; Wang S; Zhang Y; He Z; Ma W; Yan Y.

The scientists studied wheat glutenin accumulation patterns and their relationship to wheat quality by examining the proteomes of grains from three wheat cultivars, identifying glutenin subunits that had positive and negative effects on dough quality.


Journal: Cancer Letters, Aug. 6 [Epub ahead of print]

Title: Reverse phase protein microarrays quantify and validate the bioenergetic signature as biomarker in colorectal cancer.

Authors: Aldea M; Clofent J; Núñez de Arenas C; Chamorro M; Velasco M; Berrendero JR; Navarro C; Cuezva JM.

Using reverse phase protein microarrays, the researchers quantified proteins of energy metabolism in normal and tumor biopsies of colorectal cancer patients, finding a significant shift in cancer samples towards an enhanced glycotic phenotype and concurrent mitochondrial alteration.


Journal: PLoS One, Aug. 8

Title: Integrated proteomic and transcriptomic investigation of the acetaminophen toxicity in liver microfluidic biochip.

Authors: Prot JM; Briffaut AS; Letourneur F; Chafey P; Merlier F; Grandvalet Y; Legallais C; Leclerc E.

The researchers developed a method and protocol for studying acetaminophen toxicity in liver cells cultivated in a biochip by transcriptomic and proteomic analysis.


Journal: Vaccine, Aug 22. [Epub ahead of print]

Title: Improving reverse vaccinology with a machine learning approach.

Authors: Bowman BN; McAdam PR; Vivona S; Zhang JX; Luong T; Belew RK; Sahota H; Guiney D; Valafar F; Fierer J; Woelk CH.

The researchers used support vector machine classification for reverse vaccinology work, pairing a training dataset of 136 bacterial protective antigens with 136 non-antigens to develop a method for predicting which proteins in a bacterial proteome are protective antigens.


Journal: Protein Science, Aug. 24 [Epub ahead of print]

Title: Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.

Authors: Hjelm B; Forsström B; Igel U; Johannesson H; Stadler C; Lundberg E; Ponten F; Sjöberg A; Rockberg J; Schwenk JM; Nilsson P; Johansson C; Uhlén M.

The authors describe a method to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody and then using synthetic peptides for sequential epitope-specific capture. They selected polyclonal antibodies to four cancer-related proteins and then generated and validated antibodies to several non-overlapping epitopes.


Journal: BMC Cancer, Aug. 26 [Epub ahead of print]

Title:Searching for early breast cancer biomarkers by serum protein profiling of pre-diagnostic serum; a nested case-control study.

Authors:Opstal-van Winden AW; Krop EJ; Karedal MH; Gast MC; Lindh CH; Jeppsson MC; Jonsson BA; Grobbee DE; Peeters PH; Beijnen JH; van Gils CH; Vermeulen RC.

Using the Prospect-EPIC cohort, the researchers developed what they claim is the first pre-diagnostic serum protein profile in relation to breast cancer with the aim of discovering early biomarkers for the disease. They demonstrated that serum profiles are altered up to three years before breast cancer detection.


Journal: Molecular & Cellular Proteomics, Aug. 29 [Epub ahead of print]

Title: A tool for biomarker discovery in the urinary proteome: a manually-curated human and animal urine protein biomarker database.

Authors: Shao C; Li M; Li X; Wei L; Zhu L; Yang F; Jia L; Mu Y; Wang J; Guo Z; Zhang D; Yin J; Wang Z; Sun W; Zhang Z; Gao Y.

The researchers manually compiled a database of urinary protein biomarkers to allow the accurate and convenient comparison of studies in this area. Currently the database contains 553 and 275 records complied from 174 and 31 publications of human and animal urine biomarker studies, respectively. The researchers also found that biomarkers identified by different proteomic methods had poor overlap.


Journal: Proteomics, Aug. 29 [Epub ahead of print]

Title: An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates.

Authors: Ahrné E; Ohta Y; Nikitin F; Scherl A; Lisacek F; Müller M.

The authors present a method for decoy library creation using new techniques to prevent decoy spectra from being too similar to original library spectra while retaining important features of real MS/MS spectra to improve estimation of false discovery rates in mass spec experiments.


Journal: Molecular & Cellular Proteomics, Aug. 29 [Epub ahead of print]

Title: iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Authors: Shteynberg D; Deutsch EW; Lam H; Eng JK; Sun Z; Tasman N; Mendoza L; Moritz RL; Aebersold R; Nesvizhskii AI.

The researchers detail iProphet, a new addition to the open source Trans-Proteomic Pipeline suite of proteomics informatics tools that, they claim, will provide a more accurate representation of the multi-level nature of shotgun proteomic data when applied in tandem with the PeptideProphet software.

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.