Efficacious Anticancer Drug Delivery Mediated by a pH-Sensitive Self-Assembly of a Conserved Tripeptide Derived from Tyrosine Kinase NGF Receptor

We present herein a short tripeptide sequence (Lys-Phe-Gly or KFG) that is situated in the juxtamembrane region of the tyrosine kinase nerve growth factor (Trk NGF) receptors. KFG self-assembles in water and shows a reversible and concentration-dependent switching of nanostructures from nanospheres (vesicles) to nanotubes, as evidenced by dynamic light scattering, transmission electron microscopy, and atomic force microscopy. The morphology change was associated with a transition in the secondary structure. The tripeptide vesicles have inner aqueous compartments and are stable at pH7.4 but rupture rapidly at pH approximate to 6. The pH-sensitive response of the vesicles was exploited for the delivery of a chemotherapeutic anticancer drug, doxorubicin, which resulted in enhanced cytotoxicity for both drug-sensitive and drug-resistant cells. Efficient intracellular release of the drug was confirmed by fluorescence-activated cell sorting analysis, fluorescence microscopy, and confocal microscopy.

Parallel Flow-Sensitive Pointer Analysis by Graph-Rewriting

Precise pointer analysis is a problem of interest to both the compiler and the program verification community. Flow-sensitivity is an important dimension of pointer analysis that affects the precision of the final result computed. Scaling flow-sensitive pointer analysis to millions of lines of code is a major challenge. Recently, staged flow-sensitive pointer analysis has been proposed, which exploits a sparse representation of program code created by staged analysis. In this paper we formulate the staged flow-sensitive pointer analysis as a graph-rewriting problem. Graph-rewriting has already been used for flow-insensitive analysis. However, formulating flow-sensitive pointer analysis as a graph-rewriting problem adds additional challenges due to the nature of flow-sensitivity. We implement our parallel algorithm using Intel Threading Building Blocks and demonstrate considerable scaling (upto 2.6x) for 8 threads on a set of 10 benchmarks. Compared to the sequential implementation of staged flow-sensitive analysis, a single threaded execution of our implementation performs better in 8 of the benchmarks.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Risk-sensitive control of continuous time Markov chains

We study risk-sensitive control of continuous time Markov chains taking values in discrete state space. We study both finite and infinite horizon problems. In the finite horizon problem we characterize the value function via Hamilton Jacobi Bellman equation and obtain an optimal Markov control. We do the same for infinite horizon discounted cost case. In the infinite horizon average cost case we establish the existence of an optimal stationary control under certain Lyapunov condition. We also develop a policy iteration algorithm for finding an optimal control.

Selective and Sensitive Turn-on Chemosensor for Arsenite Ion at the ppb Level in Aqueous Media Applicable in Cell Staining

A newly designed and structurally characterized cell permeable diformyl-p-cresol based receptor (HL) selectively senses the AsO33- ion up to ca. 4.1 ppb in aqueous media over the other competitive ions at biological pH through an intermolecular H-bonding induced CHEF (chelationenhanced fluorescence) process, established by detailed experimental and theoretical studies. This biofriendly probe is highly competent in recognizing the existence of AsO33- ions in a living organism by developing an image under a fluorescence microscope and useful to estimate the amount of arsenite ions in various water samples.

Highly Sensitive Carbon Nanotubes Coated Etched Fiber Bragg Grating Sensor for Humidity Sensing

The sensing of relative humidity (RH) at room temperature has potential applications in several areas ranging from biomedical to horticulture, paper, and textile industries. In this paper, a highly sensitive humidity sensor based on carbon nanotubes (CNTs) coated on the surface of an etched fiber Bragg grating (EFBG) sensor has been demonstrated, for detecting RH over a wide range of 20%-90% at room temperature. When water molecules interact with the CNT coated EFBG, the effective refractive index of the fiber core changes, resulting in a shift in the Bragg wavelength. It has been possible to achieve a high sensitivity of similar to 31 pm/% RH, which is the highest compared with many of the existing FBG-based humidity sensors. The limit of detection in the CNT coated EFBG has been found to be similar to 0.03 RH. The experimental data shows a linear response of Bragg wavelength shift with increase in humidity. This novel method of incorporating CNTs on to the FBG sensor for humidity sensing has not been reported before.

Nanocomposite Based Organic-Inorganic Cu3BiS3 High Sensitive Hybrid Photonic Devices

We report the synthesis and application Cu3BiS3 nanorods in infrared photodectection. Cu3BiS3 nano rods were characterized structurally, optically and electrically. The detailed IR photodectection properties in terms of photo response were demonstrated with IA lamp and 1064 nm laser illuminations. The rapid photocurrent time constants followed by the slower components, resulting due to the defect states. The photo detecting properties for different concentrations of nanorods blended with the conjugate polymer devices were demonstrated. Further the photocurrent was enhanced to threefold increase from 3.47 x 10(-7) A to 2.37 x 10(-3) A at 1 V for 10 mg nanorods embedded in the polymer device. Responsivity of hybrid device was enhanced from 0.0158 NW to 102 NW. The detailed trap assisted space charge transport properties were studied considering the different regimes. Hence Cu3BiS3 can be a promising candidate in the nano switchable near IA photodetectors.

Sensitive detection of C-reactive protein using optical fiber Bragg gratings

An accurate and highly sensitive sensor platform has been demonstrated for the detection of C-reactive protein (CRP) using optical fiber Bragg gratings (FBGs). The CRP detection has been carried out by monitoring the shift in Bragg wavelength (Delta lambda(B)) of an etched FBG (eFBG) coated with an anti-CRP antibody (aCRP)-graphene oxide (GO) complex. The complex is characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and atomic force microscopy. A limit of detection of 0.01 mg/L has been achieved with a linear range of detection from 0.01 mg/L to 100 mg/L which includes clinical range of CRP. The eFBG sensor coated with only aCRP (without GO) show much less sensitivity than that of aCRP-GO complex coated eFBG. The eFBG sensors show high specificity to CRP even in the presence of other interfering factors such as urea, creatinine and glucose. The affinity constant of similar to 1.1 x 10(10) M-1 has been extracted from the data of normalized shift (Delta lambda(B)/lambda(B)) as a function of CRP concentration. (C) 2014 Elsevier B.V. All rights reserved.

Highly sensitive and rapid detection of acetylcholine using an ITO plate modified with platinum-graphene nanoparticles

Determining the concentrations of acetylcholine (ACh) and choline (Ch) is clinically important. ACh is a neurotransmitter that acts as a key link in the communication between neurons in the spinal cord and in nerve skeletal junctions in vertebrates, and plays an important role in transmitting signals in the brain. A bienzymatic sensor for the detection of ACh was prepared by co-immobilizing choline oxidase (ChO) and acetylcholinesterase (AChE) on graphene matrix/platinum nanoparticles, and then electrodepositing them on an ITO-coated glass plate. Graphene nanoparticles were decorated with platinum nanoparticles and were electrodeposited on a modified ITO-coated glass plate to form a modified electrode. The modified electrode was characterized by scanning electron microscopy (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) studies. The optimum response of the enzyme electrode was obtained at pH 7.0 and 35 degrees C. The response time of this ACh-sensing system was shown to be 4 s. The linear range of responses to ACh was 0.005-700 mu M. This biosensor exhibits excellent anti-interferential abilities and good stability, retaining 50% of its original current even after 4 months. It has been applied for the detection of ACh levels in human serum samples.

Path Sensitive Cache Analysis Using Cache Miss Paths

Cache analysis plays a very important role in obtaining precise Worst Case Execution Time (WCET) estimates of programs for real-time systems. While Abstract Interpretation based approaches are almost universally used for cache analysis, they fail to take advantage of its unique requirement: it is not necessary to find the guaranteed cache behavior that holds across all executions of a program. We only need the cache behavior along one particular program path, which is the path with the maximum execution time. In this work, we introduce the concept of cache miss paths, which allows us to use the worst-case path information to improve the precision of AI-based cache analysis. We use Abstract Interpretation to determine the cache miss paths, and then integrate them in the IPET formulation. An added advantage is that this further allows us to use infeasible path information for cache analysis. Experimentally, our approach gives more precise WCETs as compared to AI-based cache analysis, and we also provide techniques to trade-off analysis time with precision to provide scalability.

Simultaneous Determination of Catecholamines in Presence of Uric Acid and Ascorbic Acid at a Highly Sensitive Electrochemically Activated Carbon Paste Electrode

A simple yet remarkable, electrochemically activated carbon paste electrode (EACPE) was prepared by successive potential cycling of carbon paste in a 0.1 M NaOH solution and was effectively used for the simultaneous determination of catecholamines such as dopamine (DA), epinephrine (E) and Norepinephrine (NE) in presence of uric acid (UA) and ascorbic acid (AA). Taking DA as the ideal catecholamine, the electrochemical behaviors of DA, UA and AA such as scan rate and pH variation was studied by cyclic voltammetry (CV) in phosphate buffer solution (PBS, pH 7.1). This electrochemical sensor exhibited strong electrocatalytic activity towards the oxidation of a mixture of catecholamines, UA and AA with apparent reduction of overpotentials. Crider optimum conditions, limit of detection (S/N = 3) of DA, E, NE, UA and AA was found to be 0.08, 0.08, 0.07, 0.1 and 6.0 mu M, respectively by differential pulse voltammetry (DPV). The analytical performance of this modified electrode as a biosensor was also demonstrated for the determination of DA, UA and AA in dopamine injection, human urine and vitamin C tablets, respectively, in presence of other interfering substances. (C) 2015 The Electrochemical Society. All-rights reserved.

Boron and Nitrogen Co-doped Carbon Nanoparticles as Photoluminescent Probes for Selective and Sensitive Detection of Picric Acid

Here, we report the synthesis of boron and nitrogen Co-doped carbon nanoparticles (BN-CNPs) by a hydrothermal method using sucrose, boric acid, and urea as the precursors. The BN-CNPs show excellent photoluminescence with a quantum yield of similar to 14.2% in aqueous solution and can be used as photoluminescent probes for selective and sensitive detection of picric acid (PA). PA quenches the photoluminescence signal remarkably, while other explosives cause a little quenching confirming the high selectivity of BN-CNPs. The sensitivity toward PA sensing is high at pH 7 and increases with temperature. The detection limit as well as the sensitivity are shown to improve by adding NaCl to the PA. The low detection limit can be as low as 10 nM at room temperature and pH 7, which indicates the BN-CNPs are superior as compared to other luminescent probes reported in the literature.

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.

Risk-Sensitive Ergodic Control of Continuous Time Markov Processes With Denumerable State Space

In this article, we study risk-sensitive control problem with controlled continuous time Markov chain state dynamics. Using multiplicative dynamic programming principle along with the atomic structure of the state dynamics, we prove the existence and a characterization of optimal risk-sensitive control under geometric ergodicity of the state dynamics along with a smallness condition on the running cost.