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Recent Research Papers of Note: Aug 5, 2011

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Proteomics research papers of note, July 2011

Journal: Molecular & Cellular Proteomics, July 8

Title: Modeling of pathological traits in Alzheimer's disease based on systemic extracellular signaling proteome.

Authors: Britschgi M; Rufibach K; Bauer Huang SL; et al.

Measuring 91 secreted cellular signaling proteins in cerebrospinal fluid and plasma from Alzheimer's patients, the authors identified signaling proteins that were able to model key pathological markers of Alzheimer's including levels of CSF tau and β-amyloid, suggesting novel signaling pathways involved in the disease.


Journal: Science, July 14 [Epub ahead of print]

Title: The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.

Authors: Eastwood DC; Floudas D; Binder M; et al.

Using genomic, transcriptomic, and proteomic analyses, the authors identified differences in wood decomposition due to different types of fungi and demonstrated that the evolution of ectomycorrhizal biotrophy and brown rot saprotrophy was accompanied by reductions and losses in specific protein families.


Journal: Analytical Chemistry, July 15 [Epub ahead of print]

Title: Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow.

Authors: Liu H; Yang L; Khainovski N; Dong M; Hall SC; Fisher SJ; Biggin MD; Jin J; Witkowska HE.

The authors present an information-dependent, iterative MS/MS acquisition tool that limits MS/MS analyses to subsets of molecular ions likely to identify a maximum number of proteins, thereby improving MS/MS efficiency, improving proteome coverage, and shortening analysis times.


Journal: PLoS One, July 19 [Epub ahead of print]

Title: A functional proteomic method for biomarker discovery.

Authors: Reynolds F; Panneer N; Tutino CM; Wu M; Skrabal WR; Moskaluk C; Kelly KA.

The authors describe a method using phage particles bearing cell- or tissue-specific peptides that serve as affinity probes for molecular targets. Using the method, they identified molecular binding partners for 15 peptides specific to pancreatic cancer.


Journal: Molecular Systems Biology, July 19

Title: Quantification of mRNA and protein and integration with protein turnover in a bacterium.

Authors: Maier T; Schmidt A; Güell M; Kühner S; Gavin AC; Aebersold R; Serrano L.

The authors integrated experimentally determined abundance data for mRNA and proteins as well as individual protein half-lives from Mycoplasma pneumonia in order to perform an integrative analysis of the dynamic interplay between mRNA and proteins.


Journal: Analytical Chemistry, July 20 [Epub ahead of print]

Title: Development of soluble ester-linked aldehyde polymers for proteomics.

Authors: Beaudette P; Rossi NA; Huesgen PF; Yu X; Shenoi RA; Doucet A; Overall CM; Kizhakkedathu JN.

The authors present a method for the targeted selection and release of primary amine-containing peptides from complex mixtures using hyperbranched polyglycerol functionalized with ester-linked aldehyde groups, allowing for isolation of particular classes of peptide for mass spec analysis.


Journal: Journal of Proteomics, July 20 [Epub ahead of print]

Title: Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome.

Authors: Molina L; Salvetat N; Ameur RB; Peres S; Sommerer N; Jarraya F; Ayadi H; Molina F; Granier C.

The authors estimated quantitatively the variability of the normal human proteome using samples from 20 healthy patients, finding that while a portion of the urinary proteome is conserved across individuals, another fraction exists that is more specific to each individual.


Journal: Molecular & Cellular Proteomics, July 25 [Epub ahead of print]

Title:
Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target.

Authors: van Houdt WJ; Emmink BL; Pham TV; et al.

Using 1D gel electrophoresis coupled to nanoLC-MS/MS, the authors investigated proteome differences between three colonsphere cultures derived from resection specimens of liver metastases in patients with colon cancer, identifying the protein BIRC6 as a potential mediator of cancer stem cell drug resistance.


Journal: Proteomics, July 28 [Epub ahead of print]

Title: A reference map of the membrane proteome of Enterococcus faecalis.

Authors: Maddalo G; Chovanec P; Stenberg-Bruzell F; Nielsen HV; Jensen-Seaman MI; Ilag LL; Kline KA; Daley DO.

The authors detail a 102-protein reference map of the E. faecalis membrane proteome, including many proteins with no known function. The map, they said, will enable further research into how the bacterium interacts with its host and the extracellular milieu.

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The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.