Directed evolution of cyclic peptides for inhibition of autophagy

In recent decades it has become increasingly clear that induction of autophagy plays an important role in the development of treatment resistance and dormancy in many cancer types. Unfortunately, chloroquine (CQ) and hydroxychloroquine (HCQ), two autophagy inhibitors in clinical trials, suffer from poor pharmacokinetics and high toxicity at therapeutic dosages. This has prompted intense interest in the development of targeted autophagy inhibitors to re-sensitize disease to treatment with minimal impact on normal tissue. We utilized Scanning Unnatural Protease Resistant (SUPR) mRNA display to develop macrocyclic peptides targeting the autophagy protein LC3. The resulting peptides bound LC3A and LC3B—two essential components of the autophagosome maturation machinery—with mid-nanomolar affinities and disrupted protein–protein interactions (PPIs) between LC3 and its binding partners in vitro. The most promising LC3-binding SUPR peptide accessed the cytosol at low micromolar concentrations as measured by chloroalkane penetration assay (CAPA) and inhibited starvation-mediated GFP-LC3 puncta formation in a concentration-dependent manner. LC3-binding SUPR peptides re-sensitized platinum-resistant ovarian cancer cells to cisplatin treatment and triggered accumulation of the adapter protein p62 suggesting decreased autophagic flux through successful disruption of LC3 PPIs in cell culture. In mouse models of metastatic ovarian cancer, treatment with LC3-binding SUPR peptides and carboplatin resulted in almost complete inhibition of tumor growth after four weeks of treatment. These results indicate that SUPR peptide mRNA display can be used to develop cell-penetrating macrocyclic peptides that target and disrupt the autophagic machinery in vitro and in vivo.

SUPR peptide mRNA display was used to evolve a cell-permeable, macrocyclic peptide for autophagy inhibition.     

Preparation and characterization of some unusually transparent poly(dimethylsiloxane) nanocomposites

A technique was developed for preparing poly(dimethylsiloxane) nanocomposites having unusually high transparencies as quantitatively judged by ultraviolet–visible spectroscopy. The method was the in situ generation of silica particles by a two‐step sol–gel procedure in which the required water of hydrolysis was simply absorbed from the air, and the catalyst was generated in situ from a tin salt. Electron microscopy showed that the phase‐separated silica domains were very small (30–50 nm in diameter) and well dispersed, as expected from the transparency of the composites. Stress‐strain measurements in tension indicated that the particles provide very good reinforcement. Ultra‐small‐angle X‐ray scattering data showed that the domain morphology depends strongly on catalyst, but weakly on loading level. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1897–1901, 2003     

Identification of regions of fastest mixing in a system of point vortices

This paper describes a numerical method for efficiently identifying the regions of fastest mixing of a passive dye in a flow due to a system of point vortices. Results obtained from computations are presented for systems of three and four point vortices, both in the unbounded domain and inside a circular cylinder. The flow is two‐dimensional and the fluid is incompressible. The regions where mixing is possible are found by studying the largest Lagrangian Lyapunov exponent distribution with respect to various initial positions of tracer particles. The regions of fastest mixing are then identified from the Lyapunov exponent distribution at small times. The results of the method are verified by quantifying the mixing by using a traditional box counting technique. The technique is then applied to several different initial configurations of vortices and some interesting results are obtained. Some numerical findings about the nature of the exponents computed are also discussed. Copyright © 2002 John Wiley Sons, Ltd.     

Alum-Catalyzed Domino Synthesis of 12-Substituted-8,9,10,12-tetrahydrobenzoxanthen-11-ones Under Solvent-Free Conditions

Alum is found to catalyze efficiently the one-pot, three-component condensation of aldehydes, α/β-naphthol, and dimedone to afford various 12-substituted-8,9,10,12-tetrahydrobenzoxanthen-11-ones in excellent yields. The use of alum catalyst and the solvent-free conditions make this method simple, convenient, eco-friendly, and cost-effective.     

Total synthesis of the Bacteroides fragilis zwitterionic polysaccharide A1 repeating unit

Nearly all bacteria capsular polysaccharides are T-cell-independent antigens that do not promote immunoglobulin class switching from IgM to IgG nor memory responses. In contrast, zwitterionic polysaccharides activate T-cell-dependent immune responses by major histocompatability complex class II presentation, a mechanism previously believed to be reserved for peptidic antigens. The best studied zwitterionic polysaccharide, polysaccharide A1 (PS A1) is found on the capsule of the commensal bacteria Bacteroides fragilis . Its potent immunomodulatory properties have been linked to postoperative intra-abdominal abscess formation. Here, we report the synthesis of the PS A1 tetrasaccharide repeating unit (2) as a tool to investigate the biological role of this polysaccharide. A modular synthetic strategy originating from the reducing end of the PS A1 repeating unit was unsuccessful and illustrated the limitations of glycosylation reactions between highly armed glycosylating agents and poor nucleophiles. Thus, a [3 + 1] glycosylation relying on trisaccharide 5 and pyruvalated galactose 6 was used to complete the first total synthesis of the PS A1 repeating unit (2).     

Modal Analysis of a Servo-Hydraulic High Speed Machine and its Application to Dynamic Tensile Testing at an Intermediate Strain Rate

This paper describes the experimental procedure to identify the predominant frequencies of the high speed testing machine by conducting modal analysis. The effects due to the predominant frequencies of the system and loading rate on the magnitude of system ringing and the flow stress were analyzed by using a single degree-of-freedom (SDOF) spring-mass-damper model. The system was then used to study the dynamic tensile behavior of two engineering materials, i.e., polyethylene (PE) fabric-cement composite and Alkaline Resistant (AR) glass fabrics at an intermediate strain rate. The stress oscillations in the response of these materials due to system ringing were addressed. The failure behavior of each material was studied by examining high speed digital camera images of specimens during the test. The validity of the dynamic tensile tests was investigated by examining the condition of dynamic stress equilibrium—a criterion used in split Hopkinson pressure bar (SHPB) tests. The results show that the quantitative criterion for a valid SHPB test is also applicable to dynamic tensile tests of these materials at the intermediate strain rate.     

A new complexity measure for time series analysis and classification

Complexity measures are used in a number of applications including extraction of information from data such as ecological time series, detection of non-random structure in biomedical signals, testing of random number generators, language recognition and authorship attribution etc. Different complexity measures proposed in the literature like Shannon entropy, Relative entropy, Lempel-Ziv, Kolmogrov and Algorithmic complexity are mostly ineffective in analyzing short sequences that are further corrupted with noise. To address this problem, we propose a new complexity measure ETC and define it as the “Effort To Compress” the input sequence by a lossless compression algorithm. Here, we employ the lossless compression algorithm known as Non-Sequential Recursive Pair Substitution (NSRPS) and define ETC as the number of iterations needed for NSRPS to transform the input sequence to a constant sequence. We demonstrate the utility of ETC in two applications. ETC is shown to have better correlation with Lyapunov exponent than Shannon entropy even with relatively short and noisy time series. The measure also has a greater rate of success in automatic identification and classification of short noisy sequences, compared to entropy and a popular measure based on Lempel-Ziv compression (implemented by Gzip).     

Performance analysis of single stage kanban controlled production systems using parametric decomposition

We present a new approach that permits efficient performance analysis of kanban systems with general demand processes, material arrival processes, and service times. The approach is based on parametric characterization of the traffic processes (arrival and departure) in the network and uses two-moment approximations to estimate performance measures at individual stations. We derive traffic flow constraints that are particular to closed queuing networks with synchronization stations and use these to establish relationships between the parameters characterizing arrival and departure processes at the stations in the network. The resultant set of non-linear equations is solved to estimate network performance measures. Numerical studies show that the approach is not only fast but also reasonably accurate when compared to simulation. These studies also provide insights with respect to the impact of different types of variability on the performance of a kanban system. This work also provides a fundamental building block that can be used in the analysis of multi-stage kanban systems. AMS Subject Classifications 68M20, 60K20, 90B05, 90B30     

Multi-channel gain and noise figure evaluation of Raman/EDFA hybrid amplifiers

We present detailed multi-channel experimental characterization of different configurations of single pump hybrid Raman-erbium doped fiber (EDF) amplifiers. The incorporation of an EDF section in a dispersion compensating Raman amplifier is demonstrated to provide superior performance than Raman only system. It is shown that the multi-channel gain spectrum is quite different form the single-channel case. We have also measured the polarization dependent gain (PDG) of the hybrid amplifier configurations and results show that different configurations of hybrid amplifiers have different PDG effects on long-haul optically amplified link.     

String tension,gluebal masses and finite size effects in lattice SU(3)

We estimate the string tension by looking at Wilson loops and measuring the correlation between Wilson lines at g² = 1.0 for lattice SU(3). The bound $\text{Λ}{}_{\mathrm{<mtext>L</mtext>}}\text{σ}\text{?0.0087 ± 0.0011}$ is larger than the previous results. The mass of the 0⁺⁺ glueball is also estimated. The finite size effects on these quantities are shown to be large by comparing results on a 6³ × 10 lattice with those on 9⁴ lattice.