A Chemical Proteomic Probe for Detecting Dehydrogenases: \u3cem\u3eCatechol Rhodanine\u3c/em\u3e

The inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (ex. a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand probe, such as a fluorescent common ligand that can be used to stain members of the subproteome in a native gel. Here, we describe such a fluorescent probe, based on a catechol rhodanine acetic acid (CRAA) ligand that binds to dehydrogenases. The CRAA ligand is fluorescent and binds to dehydrogenases at pH \u3e 7, and hence can be used effectively to stain dehydrogenases in native gels to identify what subset of proteins in a mixture are dehydrogenases. Furthermore, if one is designing inhibitors to target one or more of these dehydrogenases, the CRAA staining can be performed in a competitive assay format, with or without inhibitor, to assess the selectivity of the inhibitor for the targeted dehydrogenase. Finally, the CRAA probe is a privileged scaffold for dehydrogenases, and hence can easily be modified to increase affinity for a given dehydrogenase

An \u3cem\u3eIn Vitro\u3c/em\u3e Spectroscopic Analysis to Determine Whether Para-Chloroaniline Is Produced from Mixing Sodium Hypochlorite and Chlorhexidine

Introduction: The purpose of this in vitro study was to determine whether para-chloroaniline (PCA) is formed through the reaction of mixing sodium hypochlorite (NaOCl) and chlorhexidine (CHX). Methods: Initially, commercially available samples of chlorhexidine acetate (CHXa) and PCA were analyzed with 1H nuclear magnetic resonance (NMR) spectroscopy. Two solutions, NaOCl and CHXa, were warmed to 37ºC, and when mixed they produced a brown precipitate. This precipitate was separated in half, and pure PCA was added to 1 of the samples for comparison before they were each analyzed with 1H NMR spectroscopy. Results: The peaks in the 1H NMR spectra of CHXa and PCA were assigned to specific protons of the molecules, and the location of the aromatic peaks in the PCA spectrum defined the PCA doublet region. Although the spectrum of the precipitate alone resulted in a complex combination of peaks, on magnification there were no peaks in the PCA doublet region that were intense enough to be quantified. In the spectrum of the precipitate to which PCA was added, 2 peaks do appear in the PCA doublet region. Comparing this spectrum with that of precipitate alone, the peaks in the PCA doublet region are not visible before the addition of PCA. Conclusions: On the basis of this in vitro study, the reaction mixture of NaOCl and CHXa does not produce PCA at any measurable quantity, and further investigation is needed to determine the chemical composition of the brown precipitate

An \u3cem\u3eIn Vitro\u3c/em\u3e Spectroscopic Analysis to Determine the Chemical Composition of the Precipitate Formed by Mixing Sodium Hypochlorite and Chlorhexidine

Introduction—The purpose of this in vitro study was to determine the chemical composition of the precipitate formed by mixing sodium hypochlorite (NaOCl) and Chlorhexidine (CHX), and relative molecular weight of the components. Methods—Using commercially available chlorhexidine gluconate (CHXg), a 2% solution was formed and mixed in a 1:1 ratio with commercially available NaOCl producing a brown precipitate. The precipitate as well as a mixture of precipitate and pure chlorhexidine diacetate (CHXa) was then analyzed using 1D and 2D NMR spectroscopy. Results—The 1D and 2D NMR spectra were fully assigned, in terms of chemical shifts of all proton and carbon atoms in intact CHX. This permitted identification of CHX breakdown products with and without the aliphatic linker present, including lower molecular weight components of CHX that contained a para-substituted benzene that was not para-chloroaniline (PCA). Conclusions—Based on this in vitro study, the precipitate formed by NaOCl and CHX is composed of at least two separate molecules, all of which are smaller in size than CHX. Along with native CHX, the precipitate contains two chemical fragments derived from CHX, neither of which are PCA

Redundancy Scheduling with Locally Stable Compatibility Graphs

Redundancy scheduling is a popular concept to improve performance in parallel-server systems. In the baseline scenario any job can be handled equally well by any server, and is replicated to a fixed number of servers selected uniformly at random. Quite often however, there may be heterogeneity in job characteristics or server capabilities, and jobs can only be replicated to specific servers because of affinity relations or compatibility constraints. In order to capture such situations, we consider a scenario where jobs of various types are replicated to different subsets of servers as prescribed by a general compatibility graph. We exploit a product-form stationary distribution and weak local stability conditions to establish a state space collapse in heavy traffic. In this limiting regime, the parallel-server system with graph-based redundancy scheduling operates as a multi-class single-server system, achieving full resource pooling and exhibiting strong insensitivity to the underlying compatibility constraints.Comment: 28 pages, 4 figure

Solution Structures of \u3cem\u3eMycobacterium tuberculosis\u3c/em\u3e Thioredoxin C and Models of Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function

Co-Developing Drugs with Indigenous Communities: Lessons from Peruvian Law and the Ayahuasca Patent Dispute

This paper will examine the issues surrounding the codevelopment of drugs derived from traditional medicines used by indigenous peoples in Amazonia, with a focus on Peru. In particular, this paper will explore what national, regional and international legal structures are in place to protect the interests of indigenous peoples, while at the same time providing medical benefit to the world. This issue is explored in the context of Peruvian, U.S., and international treaties – especially the TRIPS agreement, the Andean Community, sui generis protections, and the US-Peru Trade Promotion Agreement

Repurposing - Finding New Uses for Old (and Patented) Drugs: Bridging the Valley of Death, to Translate Academic Research Into New Medicines

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Asymptotically Optimal Load Balancing Topologies

We consider a system of $N$ servers inter-connected by some underlying graph topology $G_N$. Tasks arrive at the various servers as independent Poisson processes of rate $\lambda$. Each incoming task is irrevocably assigned to whichever server has the smallest number of tasks among the one where it appears and its neighbors in $G_N$. Tasks have unit-mean exponential service times and leave the system upon service completion. The above model has been extensively investigated in the case $G_N$ is a clique. Since the servers are exchangeable in that case, the queue length process is quite tractable, and it has been proved that for any $\lambda < 1$, the fraction of servers with two or more tasks vanishes in the limit as $N \to \infty$. For an arbitrary graph $G_N$, the lack of exchangeability severely complicates the analysis, and the queue length process tends to be worse than for a clique. Accordingly, a graph $G_N$ is said to be $N$-optimal or $\sqrt{N}$-optimal when the occupancy process on $G_N$ is equivalent to that on a clique on an $N$-scale or $\sqrt{N}$-scale, respectively. We prove that if $G_N$ is an Erd\H{o}s-R\'enyi random graph with average degree $d(N)$, then it is with high probability $N$-optimal and $\sqrt{N}$-optimal if $d(N) \to \infty$ and $d(N) / (\sqrt{N} \log(N)) \to \infty$ as $N \to \infty$, respectively. This demonstrates that optimality can be maintained at $N$-scale and $\sqrt{N}$-scale while reducing the number of connections by nearly a factor $N$ and $\sqrt{N} / \log(N)$ compared to a clique, provided the topology is suitably random. It is further shown that if $G_N$ contains $\Theta(N)$ bounded-degree nodes, then it cannot be $N$-optimal. In addition, we establish that an arbitrary graph $G_N$ is $N$-optimal when its minimum degree is $N - o(N)$, and may not be $N$-optimal even when its minimum degree is $c N + o(N)$ for any $0 < c < 1/2$.Comment: A few relevant results from arXiv:1612.00723 are included for convenienc

Achievable Performance in Product-Form Networks

We characterize the achievable range of performance measures in product-form networks where one or more system parameters can be freely set by a network operator. Given a product-form network and a set of configurable parameters, we identify which performance measures can be controlled and which target values can be attained. We also discuss an online optimization algorithm, which allows a network operator to set the system parameters so as to achieve target performance metrics. In some cases, the algorithm can be implemented in a distributed fashion, of which we give several examples. Finally, we give conditions that guarantee convergence of the algorithm, under the assumption that the target performance metrics are within the achievable range.Comment: 50th Annual Allerton Conference on Communication, Control and Computing - 201

Mixing Properties of CSMA Networks on Partite Graphs

We consider a stylized stochastic model for a wireless CSMA network. Experimental results in prior studies indicate that the model provides remarkably accurate throughput estimates for IEEE 802.11 systems. In particular, the model offers an explanation for the severe spatial unfairness in throughputs observed in such networks with asymmetric interference conditions. Even in symmetric scenarios, however, it may take a long time for the activity process to move between dominant states, giving rise to potential starvation issues. In order to gain insight in the transient throughput characteristics and associated starvation effects, we examine in the present paper the behavior of the transition time between dominant activity states. We focus on partite interference graphs, and establish how the magnitude of the transition time scales with the activation rate and the sizes of the various network components. We also prove that in several cases the scaled transition time has an asymptotically exponential distribution as the activation rate grows large, and point out interesting connections with related exponentiality results for rare events and meta-stability phenomena in statistical physics. In addition, we investigate the convergence rate to equilibrium of the activity process in terms of mixing times.Comment: Valuetools, 6th International Conference on Performance Evaluation Methodologies and Tools, October 9-12, 2012, Carg\`ese, Franc