Protein Expression, Characterization and Activity Comparisons of Wild Type and Mutant DUSP5 Proteins

Background The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function. Results In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function. We demonstrate that both proteins are active and, interestingly, the S147P protein is hypoactive as compared to the DUSP5 WT protein in two distinct biochemical substrate assays. Furthermore, due to the novel positioning of the S147P mutation, we utilize computational modeling to reconstruct full-length DUSP5 and S147P to predict a possible mechanism for the reduced activity of S147P. Conclusion Taken together, this is the first evidence of the generation and characterization of an active, full-length, mutant DUSP5 protein which will facilitate future structure-function and drug development-based studies

Scaling relation for determining the critical threshold for continuum percolation of overlapping discs of two sizes

We study continuum percolation of overlapping circular discs of two sizes. We propose a phenomenological scaling equation for the increase in the effective size of the larger discs due to the presence of the smaller discs. The critical percolation threshold as a function of the ratio of sizes of discs, for different values of the relative areal densities of two discs, can be described in terms of a scaling function of only one variable. The recent accurate Monte Carlo estimates of critical threshold by Quintanilla and Ziff [Phys. Rev. E, 76 051115 (2007)] are in very good agreement with the proposed scaling relation.Comment: 4 pages, 3 figure

Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens

PD/00193/2012 UID/FIS/00068/2019 PTDC/BBBBQB/3554/2014 PTDC/BIA-BQM/31981/2017 PD/BD/114445/2016 UID/Multi/04378/2019 ROTEIRO/0031/2013 -PINFRA/22161/2016The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His47), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His47 is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His47 with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were 15N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His47 on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P13 also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.publishersversionpublishe

An Efficient Block Circulant Preconditioner For Simulating Fracture Using Large Fuse Networks

{\it Critical slowing down} associated with the iterative solvers close to the critical point often hinders large-scale numerical simulation of fracture using discrete lattice networks. This paper presents a block circlant preconditioner for iterative solvers for the simulation of progressive fracture in disordered, quasi-brittle materials using large discrete lattice networks. The average computational cost of the present alorithm per iteration is $O(rs log s) + delops$, where the stiffness matrix ${\bf A}$ is partioned into $r$-by-$r$ blocks such that each block is an $s$-by-$s$ matrix, and $delops$ represents the operational count associated with solving a block-diagonal matrix with $r$-by-$r$ dense matrix blocks. This algorithm using the block circulant preconditioner is faster than the Fourier accelerated preconditioned conjugate gradient (PCG) algorithm, and alleviates the {\it critical slowing down} that is especially severe close to the critical point. Numerical results using random resistor networks substantiate the efficiency of the present algorithm.Comment: 16 pages including 2 figure

Mechanical characterization of microwave sintered zinc oxide

The mechanical characterization of microwave sintered zinc oxide disks is reported. The microwave sintering was done with a specially designed applicator placed in a domestic microwave oven operating at a frequency of 2.45 GHz to a maximum power output of 800 Watt, These samples with a wide variation of density and hence, of open pore volume percentage, were characterized in terms of its elastic modulus determination by ultrasonic time of flight measurement using a 15 MHz transducer, In addition, the load dependence of the microhardness was examined for the range of loads 0.1-20 N, Finally, the fracture toughness data (K-IC) was obtained using the indentation techniqu

Preparation, Characterization and In Vitro Drug Release Studies of 6-mercaptopurine Thin Film

Oral thin films of 6-mercaptopurine were fabricated from mucoadhesive polymer, chitosan and polyvinylpyrrolidone for the purpose of prolonging drug release and improving its bioavailability. All fabricated film formulations prepared were smooth and translucent, with good flexibility. The weight and thickness of all the formulations were found to be uniform. These films were also evaluated for surface pH, folding endurance, swelling percentage (% S) and in vitro disintegration time. Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) were used to evaluate the physico-chemical nature of the films. In-vitro drug release have shown enhanced release profiles for thin films compared to pure drug and the release patterns have been found to be pH dependant. The results of the study reveals that fabrication of 6-MP oral thin film by using solvent cast technology is a simple and an efficient method for drug delivery to achieve desired therapeutic compliance.Keywords: 6-mercaptopurine; In Vitro Drug Release; SEM; FTI

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio

Functionalization of Hydrogen-free Diamond-like Carbon Films using Open-air Dielectric Barrier Discharge Atmospheric Plasma Treatments

A dielectric barrier discharge (DBD) technique has been employed to produce uniform atmospheric plasmas of He and N2 gas mixtures in open air in order to functionalize the surface of filtered-arc deposited hydrogen-free diamond-like carbon (DLC) films. XPS measurements were carried out on both untreated and He/N2 DBD plasma treated DLC surfaces. Chemical states of the C 1s and N 1s peaks were collected and used to characterize the surface bonds. Contact angle measurements were also used to record the short- and long-term variations in wettability of treated and untreated DLC. In addition, cell viability tests were performed to determine the influence of various He/N2 atmospheric plasma treatments on the attachment of osteoblast MC3T3 cells. Current evidence shows the feasibility of atmospheric plasmas in producing long-lasting variations in the surface bonding and surface energy of hydrogen-free DLC and consequently the potential for this technique in the functionalization of DLC coated devices

Dynamics of Ordering in Alloys with Modulated Phases

This paper presents a theoretical model for studying the dynamics of ordering in alloys which exhibit modulated phases. The model is different from the standard time-dependent Ginzburg-Landau description of the evolution of a non-conserved order parameter and resembles the Swift-Hohenberg model. The early-stage growth kinetics is analyzed and compared to the Cahn-Hilliard theory of continuous ordering. The effects of non-linearities on the growth kinetics are discussed qualitatively and it is shown that the presence of an underlying elastic lattice introduces qualitatively new effects. A lattice Hamiltonian capable of describing these effects and suitable for carrying out simulations of the growth kinetics is also constructed.Comment: 18 pages, 3 figures (postscript files appended), Brandeis-BC9

Influence of Al Content on the Corrosion Behavior of Biodegradable Magnesium Alloys in Simulated Physiological Solution

Magnesium (Mg) and its alloys have gained wide popularity in the biomedical field as promising candidates for degradable implant applications. Among Mg alloys, AZ (aluminum and zinc) series alloys are the most widely investigated for implant applications and reported in the literature. In all AZ series Mg alloys, aluminium content is the influencing factor that imparts different properties to the Mg alloys. In the present study, pure Mg, AZ31 and AZ91 Mg alloys were selected and the effect of aluminium content on the biocorrosion has been investigated in Ringer’s solution. It was a clear observation that the increased aluminum content has a severe effect on the degradation behavior of magnesium. From the weight loss measurements, AZ31 has shown lower corrosion rate compared with pure Mg and AZ91. The surface morphologies also showed the formation of more pits on pure Mg and AZ91 Mg alloy compared with AZ31 Mg alloy. By correlating the degradation behavior with the microstructure, galvanic corrosion was found to be the main reason behind the accelerated corrosion rate in AZ91 Mg alloy compared with AZ31 alloy. The phases on the corroded sample surfaces were examined by X-ray diffraction (XRD) method and scanning electron microscopy (SEM) and found that the corrosion products which were deposited on the surfaces provided protection against the chloride ions which was indicated by the decreased corrosion rates as immersion time was increased