A Functional Proteomic Method for Biomarker Discovery

The sequencing of the human genome holds out the hope for personalized medicine, but it is clear that analysis of DNA or RNA content alone is not sufficient to understand most disease processes. Proteomic strategies that allow unbiased identification of proteins and their post-transcriptional and -translation modifications are an essential complement to genomic strategies. However, the enormity of the proteome and limitations in proteomic methods make it difficult to determine the targets that are particularly relevant to human disease. Methods are therefore needed that allow rational identification of targets based on function and relevance to disease. Screening methodologies such as phage display, SELEX, and small-molecule combinatorial chemistry have been widely used to discover specific ligands for cells or tissues of interest, such as tumors. Those ligands can be used in turn as affinity probes to identify their cognate molecular targets when they are not known in advance. Here we report an easy, robust and generally applicable approach in which phage particles bearing cell- or tissue-specific peptides serve directly as the affinity probes for their molecular targets. For proof of principle, the method successfully identified molecular binding partners, three of them novel, for 15 peptides specific for pancreatic cancer

Sequence-selective assembly of tweezer-molecules on linear templates enables frameshift-reading of sequence information

Monomer-sequence information in synthetic copolyimides can be recognised by tweezer-type molecules binding to adjacent triplet-sequences on the polymer chains. In the present paper different tweezer-molecules are found to have different sequence-selectivities, as demonstrated in solution by 1H NMR spectroscopy and in the solid state by single crystal X-ray analyses of tweezer-complexes with linear and macrocyclic oligo-imides. This work provides clear-cut confirmation of polyimide chain-folding and adjacent-tweezer-binding. It also reveals a new and entirely unexpected mechanism for sequence-recognition which, by analogy with a related process in biomolecular information processing, may be termed "frameshift-reading". The ability of one particular tweezer-molecule to detect, with exceptionally high sensitivity, long-range sequence-information in chain-folding aromatic copolyimides, is readily explained by this novel process

Reproducible isolation of distinct, overlapping segments of the phosphoproteome

The ability to routinely analyze and quantitatively measure changes in protein phosphorylation on a proteome-wide scale is essential for biological and clinical research. We assessed the ability of three common phosphopeptide isolation methods (phosphoramidate chemistry (PAC), immobilized metal affinity chromatography (IMAC) and titanium dioxide) to reproducibly, specifically and comprehensively isolate phosphopeptides from complex mixtures. Phosphopeptides were isolated from aliquots of a tryptic digest of the cytosolic fraction of Drosophila melanogaster Kc167 cells and analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry. Each method reproducibly isolated phosphopeptides. The methods, however, differed in their specificity of isolation and, notably, in the set of phosphopeptides isolated. The results suggest that the three methods detect different, partially overlapping segments of the phosphoproteome and that, at present, no single method is sufficient for a comprehensive phosphoproteome analysis

Factors Associated with Amplified HIV Transmission Behavior Among American Men Who Have Sex with Men Engaged in Care: Implications for Clinical Providers

BACKGROUND: The HIV epidemic continues unabated in the United States, with men who have sex with men (MSM) being most frequently infected. PURPOSE: To understand the biological and behavioral risk factors associated with increased HIV transmission efficiency, that is HIV transmission risk behavior in the context of uncontrolled HIV replication or intercurrent sexually transmitted infections. METHODS: Participants were 201 HIV-infected MSM who received their primary care at an HIV ambulatory care center in Boston. Logistic regression models were conducted to determine factors associated with engaging in behavior associated with potentially amplified transmission. RESULTS: In the final model, heavy alcohol use (AOR: 3.27; 95% CI 1.37–7.79), as well as stimulant drug use (crystal meth, crack, or other cocaine; AOR: 3.00; CI 1.32–6.84), having at least a college degree (OR: 2.74; CI: 1.15–6.54), and decreased duration of HIV infection (OR: 0.91; CI: 0.85–0.97) were each uniquely associated with enhanced HIV transmission behavior. CONCLUSIONS: HIV primary care providers should routinely assess patients for potential HIV transmission behaviors, particularly those who are younger and more recently diagnosed with HIV, who drink alcohol heavily, and who use any nonprescription drugs, particularly stimulants, in order to decrease the spread of HIV