Combinatorial discovery of polymers resistant to bacterial attachment

Bacterial attachment and subsequent biofilm formation are key challenges to the long term performance of many medical devices. Here, a high throughput approach coupled with the analysis of surface structure-property relationships using a chemometics approach has been developed to simultaneously investigate the interaction of bacteria with hundreds of polymeric materials on a microarray format. Using this system, a new group of materials comprising ester and hydrophobic moieties are identified that dramatically reduce the attachment of clinically relevant, pathogenic bacteria (Pseudomonas aeruginosa, Staphylococcus aureus and uropathogenic Escherichia coli). Hit materials coated on silicone catheters resulted in up to a 30 fold reduction in coverage compared to a commercial silver embedded catheter, which has been proven to half the incidence of clinically acquired infection. These polymers represent a new class of materials resistant to bacterial attachment that could not have been predicted from the current understanding of bacteria-surface interactions

Engineered Toxins “Zymoxins” Are Activated by the HCV NS3 Protease by Removal of an Inhibitory Protein Domain

The synthesis of inactive enzyme precursors, also known as “zymogens,” serves as a mechanism for regulating the execution of selected catalytic activities in a desirable time and/or site. Zymogens are usually activated by proteolytic cleavage. Many viruses encode proteases that execute key proteolytic steps of the viral life cycle. Here, we describe a proof of concept for a therapeutic approach to fighting viral infections through eradication of virally infected cells exclusively, thus limiting virus production and spread. Using the hepatitis C virus (HCV) as a model, we designed two HCV NS3 protease-activated “zymogenized” chimeric toxins (which we denote “zymoxins”). In these recombinant constructs, the bacterial and plant toxins diphtheria toxin A (DTA) and Ricin A chain (RTA), respectively, were fused to rationally designed inhibitor peptides/domains via an HCV NS3 protease-cleavable linker. The above toxins were then fused to the binding and translocation domains of Pseudomonas exotoxin A in order to enable translocation into the mammalian cells cytoplasm. We show that these toxins exhibit NS3 cleavage dependent increase in enzymatic activity upon NS3 protease cleavage in vitro. Moreover, a higher level of cytotoxicity was observed when zymoxins were applied to NS3 expressing cells or to HCV infected cells, demonstrating a potential therapeutic window. The increase in toxin activity correlated with NS3 protease activity in the treated cells, thus the therapeutic window was larger in cells expressing recombinant NS3 than in HCV infected cells. This suggests that the “zymoxin” approach may be most appropriate for application to life-threatening acute infections where much higher levels of the activating protease would be expected

GeNets: a unified web platform for network-based genomic analyses

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets