Characterization of Major Zinc Containing Myonecrotic and Procoagulant Metalloprotease `Malabarin' from Non Lethal Trimeresurus malabaricus Snake Venom with Thrombin Like Activity: Its Neutralization by Chelating Agents

A major myonecrotic zinc containing metalloprotease `malabarin' with thrombin like activity was purified by the combination of gel permeation and anion exchange chromatography from T. malabaricus snake venom. MALDI-TOF analysis of malabarin indicated a molecular mass of 45.76 kDa and its N-terminal sequence was found to be Ile-Ile-Leu-Pro(Leu)-Ile-Gly-Val-Ile-Leu(Glu)-Thr-Thr. Atomic absorption spectral analysis of malabarin raveled the association of zinc metal ion. Malabarin is not lethal when injected i.p. or i.m. but causes extensive hemorrhage and degradation of muscle tissue within 24 hours. Sections of muscle tissue under light microscope revealed hemorrhage and congestion of blood vessel during initial stage followed by extensive muscle fiber necrosis with elevated levels of serum creatine kinase and lactate dehydrogenase activity. Malabarin also exhibited strong procoagulant action and its procoagulant action is due to thrombin like activity; it hydrolyzes fibrinogen to form fibrin clot. The enzyme preferentially hydrolyzes A alpha followed by B beta subunits of fibrinogen from the N-terminal region and the released products were identified as fibrinopeptide A and fibrinopeptide B by MALDI. The myonecrotic, fibrinogenolytic and subsequent procoagulant activities of malabarin was neutralized by specific metalloprotease inhibitors such as EDTA, EGTA and 1, 10-phenanthroline but not by PMSF a specific serine protease inhibitor. Since there is no antivenom available to neutralize local toxicity caused by T. malabaricus snakebite, EDTA chelation therapy may have more clinical relevance over conventional treatment.

Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR

Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1 alpha (ck1 alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1 alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1 alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1 alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1 alpha - substrate peptide complex has also been used to understand the structural basis of association between ck1 alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available. Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1 alpha have been identified using the structural model of kinase substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

Small molecule inhibitors of HCV replication from Pomegranate

Hepatitis C virus (HCV) is the causative agent of end-stage liver disease. Recent advances in the last decade in anti HCV treatment strategies have dramatically increased the viral clearance rate. However, several limitations are still associated, which warrant a great need of novel, safe and selective drugs against HCV infection. Towards this objective, we explored highly potent and selective small molecule inhibitors, the ellagitannins, from the crude extract of Pomegranate (Punica granatum) fruit peel. The pure compounds, punicalagin, punicalin, and ellagic acid isolated from the extract specifically blocked the HCV NS3/4A protease activity in vitro. Structural analysis using computational approach also showed that ligand molecules interact with the catalytic and substrate binding residues of NS3/4A protease, leading to inhibition of the enzyme activity. Further, punicalagin and punicalin significantly reduced the HCV replication in cell culture system. More importantly, these compounds are well tolerated ex vivo and `no observed adverse effect level' (NOAEL) was established upto an acute dose of 5000 mg/kg in BALB/c mice. Additionally, pharmacokinetics study showed that the compounds are bioavailable. Taken together, our study provides a proof-of-concept approach for the potential use of antiviral and non-toxic principle ellagitannins from pomegranate in prevention and control of HCV induced complications.

Enhanced non-homologous end joining contributes toward synthetic lethality of pathological RAD51C mutants with poly (ADP-ribose) polymerase

Here, we show that PARP inhibitor-mediated cell death of RAD51C-deficient cells occur by NHEJ-driven illegitimate repair of one-ended double-strand breaks, and the hypomorphic RAD51C pathological mutant cells can be targeted by `synergistic toxicity' induced by low-dose PARP inhibitor and IR.Poly (ADP-ribose) polymerase 1 (PARP1) inhibitors are actively under clinical trials for the treatment of breast and ovarian cancers that arise due to mutations in BRCA1 and BRCA2. The RAD51 paralog RAD51C has been identified as a breast and ovarian cancer susceptibility gene. The pathological RAD51C mutants that were identified in cancer patients are hypomorphic with partial repair function. However, targeting cancer cells that express hypomorphic mutants of RAD51C is highly challenging. Here, we report that RAD51C-deficient cells can be targeted by a `synthetic lethal' approach using PARP inhibitor and this sensitivity was attributed to accumulation of cells in the G(2)/M and chromosomal aberrations. In addition, spontaneous hyperactivation of PARP1 was evident in RAD51C-deficient cells. Interestingly, RAD51C-negative cells exhibited enhanced recruitment of non-homologous end joining (NHEJ) proteins onto chromatin and this accumulation correlated with increased activity of error-prone NHEJ as well as genome instability leading to cell death. Notably, inhibition of DNA-PKcs or depletion of KU70 or Ligase IV rescued this phenotype. Strikingly, stimulation of NHEJ by low dose of ionizing radiation (IR) in the PARP inhibitor-treated RAD51C-deficient cells and cells expressing pathological RAD51C mutants induced enhanced toxicity `synergistically'. These results demonstrate that cancer cells arising due to hypomorphic mutations in RAD51C can be specifically targeted by a `synergistic approach' and imply that this strategy can be potentially applied to cancers with hypomorphic mutations in other homologous recombination pathway genes.

Instabilities in unsteady boundary layers with reverse flow

Instabilities arising in unsteady boundary layers with reverse flow have been investigated experimentally. Experiments are conducted in a piston driven unsteady water tunnel with a shallow angle diffuser placed in the test section. The ratio of temporal (Pi(t)) to spatial (Pi(x)) component of the pressure gradient can be varied by a controlled motion of the piston. In all the experiments, the piston velocity variation with time is trapezoidal consisting of three phases: constant acceleration from rest, constant velocity and constant deceleration to rest. The adverse pressure gradient (and reverse flow) are due to a combination of spatial deceleration of the free stream in the diffuser and temporal deceleration of the free stream caused by the piston deceleration. The instability is usually initiated with the formation of one or more vortices. The onset of reverse flow in the boundary layer, location and time of formation of the first vortex and the subsequent flow evolution are studied for various values of the ratio Pi(x) (Pi(x) + Pi(t)) for the bottom and the top walls. Instability is due to the inflectional velocity profiles of the unsteady boundary layer. The instability is localized and spreads to the other regions at later times. At higher Reynolds numbers growth rate of instability is higher and localized transition to turbulence is observed. Scalings have been proposed for initial vortex formation time and wavelength of the instability vortices. Initial vortex formation time scales with convective time, delta/Delta U, where S is the boundary layer thickness and Delta U is the difference of maximum and minimum velocities in the boundary layer. Non-dimensional vortex formation time based on convective time scale for the bottom and the top walls are found to be 23 and 30 respectively. Wavelength of instability vortices scales with the time averaged boundary layer thickness. (C) 2015 Elsevier Masson SAS. All rights reserved.

A thermal-elastic analysis on laser-induced reverse bulging and plugging in circular brass foil

A new failure mode is observed in circular brass foils induced by laser beam. The new failure is based on the following experimental facts : (1) the peripheries of the circular brass foils are fixed and the surfaces of the foils are radiated by laser beam ; (2) the laser beam used is considered to be non-Gaussian spatially, actually an approximately uniform distribution limited in a certain size spot ; (3) the pulse on time of laser beam should be 250 μs, i.e. so called long duration pulse laser. The failure process consists of three stages ; i.e. thermal bulging, localized shear deformation and perforation by plugging. The word reverse in reverse bulging and plugging mode means that bulging and plugging occur in the direction of incident laser beam. To study the newly-discovered type of failure quantitatively, analytical solutions for the axisymmetric temperature field and deflection curve are derived. The calculated results show that the newly discovered failure mode is attributed to the spatial structure effect of laser beam indeed.

Shear deformation analysis on laser-induced reverse bulging and plugging

A new kind of failure mode is observed in circular brass foils in which their peripheries are fixed and their surfaces are subjected to a long pulsed laser over a central region. The failure is classified into three stages; they are referred to as thermal bulging, localized shear deformation and perforation by plugging. A distinct feature of the failure mode is that bulging and plugging occurred in the direction opposite to the incident laser beam. To study the failure mode, we investigate the non-linear response of heated, non-homogeneous circular plates. Based on the large deflection equations of Berger [J. Appl. Mech. 22 (3), 465-472 (1965)], Ohnabe and Mizuguchi [Int. J. Non-Linear Mech. 28 (4), 365-372 (1993)] and the parabolic shear deformation theory of Bhimaraddi and Stevens [J. Appl. Mech. 51 (1), 195-198 (1984)], we have derived new coupled governing equations of shear deformation and deflection. The new equations are solved, for the plate with a clamped edge, by the Galerkin and iterative methods. The numerical results for the shear deformation distribution are in good agreement with the experimental observation.

Inibição do receptor de glutamato do tipo NMDA em um modelo de hipóxia-isquemia prenatal: avaliação morfofuncional do cerebelo

Lesões sistêmicas peri e pré-natais alteram o desenvolvimento do SNC, levando a problemas cognitivos e motores em crianças que podem perdurar por toda a vida. Um tipo particular de lesão é a hipóxia-isquemia (HI), caracterizada pela interrupção momentânea ou permanente do fluxo sanguíneo. Um dos mecanismos propostos para as lesões decorrentes da HI é a excitotoxicidade glutamatérgica. O uso de inibidores da neurotransmissão glutamatérgica tem sido estudados em diversos modelos de HI. Neste trabalho, avaliamos os efeitos morfofuncionais da administração de um antagonista não-competitivo do receptor de glutamato NMDA sobre o desenvolvimento do cerebelo. Ratas no 18 dia de gestação foram anestesiadas, os cornos uterinos expostos e as 4 artérias uterinas obstruídas por 45 minutos (Grupo H). Animais controle tiveram os úteros expostos, sem a obstrução (Grupo S). Após a cirurgia a gestação prosseguiu. Somente animais nascidos a termo foram utilizados. Um dia após o nascimento, metade de cada ninhada foi designada para receber MK801, 0,3mg/kg/dia, (grupos SM e HM) e a outra metade recebeu solução salina (grupos SS e HS), por 5 dias. Após anestesia e perfusão-fixação com paraformaldeído 4% aos 9, 23, 30 e 60 dias pós-natais, cortes parassagitais do cerebelo foram obtidos em criótomo e submetidos à imunohistoquímica para calbindina, GFAP, GLAST, PDGFRα e MBP. A partir de 45 dias de vida, os animais foram testados em vários de testes comportamentais: labirinto em cruz elevado (LCE), campo vazado (CV), ROTAROD, teste de caminhada sobre barras (ladder test) e teste do comprimento da passada (stride length). Aos 9 dias, a espessura da árvore dendrítica era menor nos animais SM, HS/HM, demonstrando efeitos deletérios tanto do MK801 quanto da HI. Menor número de células PDGFRα+ foi observado nos animais HS/HM, sem efeitos da administração de MK801. Aos 23 dias, maior número de células PDGFRα+ foi observado nos animais HM comparado aos outros 3 grupos, indicando efeito neuroprotetor do MK801. Nessa idade, menor número de fibras mielinizadas (MBP+) foi observada nos animais HS, e a administração de MK801 parece reverter estes efeitos. Aos 9 dias a distribuição de GLAST estava alterada nos animais HS, com os efeitos da HI parcialmente revertidos pelo MK801. Não foram observados efeitos da HI ou do MK801 sobre comportamentos relacionados a ansiedade pelo LCE, assim como na latência de queda no ROTAROD. HI piora a performance motora no ladder test. No teste do CV, não observamos efeitos da HI sobre a busca por novidade assim como sobre a atividade locomotora espontânea. No entanto, MK801 diminui comportamentos de autolimpeza e a atividade locomotora espontânea. Menor variação das passadas foi observada em decorrência da administração de MK801 no stride length, com nenhum efeito da HI. Nossos resultados demonstram que a inibição do receptor NMDA tem um efeito neuroprotetor sobre os progenitores de oligodendrócitos e mielinização, provavelmente pela manutenção da capacidade proliferativa por um período maior. A atividade do receptor NMDA exerce importante papel na diferenciação das células de Purkinje, assim como na distribuição do transportador GLAST, corroborando a importância deste receptor na gênese das lesões causadas pela HI.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

Avaliação da resposta imune de neonatos não infectados pelo HIV-1 nascidos de gestantes soropositivas

A síndrome da imunodeficiência adquirida (AIDS), causada pelo vírus da imunodeficiência humana (HIV), é uma das mais destrutivas epidemias do mundo, e a infecção pelo HIV em mulheres jovens vem aumentando rapidamente nos dias atuais. Esse fato tem um impacto importante na transmissão vertical do vírus. Apesar da grande maioria dos casos de aids pediátrica em todo mundo resultar da transmissão vertical, aproximadamente dois terços das crianças expostas ao HIV durante a vida fetal não são infectadas pelo vírus. Muitos trabalhos sugerem que durante a gestação doenças infecciosas maternas podem ter consequências complexas para o desenvolvimento do feto, e poucos trabalhos têm explorado o impacto da exposição ao HIV sobre a responsividade imunológica de crianças não infectadas a diferentes estímulos, particularmente na era das drogas antirretrovirais. Portanto, esse trabalho teve como objetivo avaliar eventos imunes em neonatos não-infectados expostos ao HIV-1 nascidos de gestantes que controlam (G1) ou não (G2) a carga viral plasmática, usando neonatos não expostos como controle. Para tanto, sangue do cordão umbilical de cada neonato foi coletado, plasma e células mononucleares foram separados e a linfoproliferação e o perfil de citocinas foram avaliados. Os resultados demonstraram que a linfoproliferação in vitro induzido por ativadores policlonais foi maior nos neonatos do G2. Entretanto, nenhuma cultura de célula respondeu a um conjunto de peptídeos sintéticos do envelope do HIV-1. A dosagem de citocinas no plasma e nos sobrenadantes das culturas ativadas policlonalmente demonstrou que, enquanto a IL-4 e IL-10 foram as citocinas dominantes produzidas nos grupos G1 e controle, a secreção de IFN-γ, IL-1, Il-6, IL-17 e TNF-α foi significativamente superior nos neonatos G2. Níveis sistêmicos de IL-10 observados dentre os neonatos G1 foram maiores naqueles nascidos de mães tratadas com drogas inibidoras da transcriptase reversa do vírus. Por outro lado, níveis superiores de citocinas inflamatórias foram observados dentre estes nascidos de gestantes tratadas com terapia antirretroviral de alta eficácia. Em resumo, nossos resultados indicam uma responsividade imune alterada em neonatos expostos in utero ao HIV-1 e reforça o papel do tratamento materno anti-viral com drogas menos potentes em atenuar tais distúrbios.

Characterization of vertical Mo/diamond Schottky barrier diode from non-ideal I-V and C-V measurements based on MIS model

In this study, we investigated non-ideal characteristics of a diamond Schottky barrier diode with Molybdenum (Mo) Schottky metal fabricated by Microwave Plasma Chemical Vapour Deposition (MPCVD) technique. Extraction from forward bias I-V and reverse bias C- 2-V measurements yields ideality factor of 1.3, Schottky barrier height of 1.872 eV, and on-resistance of 32.63 mö·cm2. The deviation of extracted Schottky barrier height from an ideal value of 2.24 eV (considering Mo workfunction of 4.53 eV) indicates Fermi level pinning at the interface. We attributed such non-ideal behavior to the existence of thin interfacial layer and interface states between metal and diamond which forms Metal-Interfacial layer-Semiconductor (MIS) structure. Oxygen surface treatment during fabrication process might have induced them. From forward bias C-V characteristics, the minimum thickness of the interfacial layer is approximately 0.248 nm. Energy distribution profile of the interface state density is then evaluated from the forward bias I-V characteristics based on the MIS model. The interface state density is found to be uniformly distributed with values around 1013 eV - 1·cm- 2. © 2013 Elsevier B.V.

Designing output-feedback predictive controllers by reverse-engineering existing LTI controllers

An approach to designing a constrained output-feedback predictive controller that has the same small-signal properties as a pre-existing output-feedback linear time invariant controller is proposed. Systematic guidelines are proposed to select an appropriate (non-unique) realization of the resulting state observer. A method is proposed to transform a class of offset-free reference tracking controllers into the combination of an observer, steady-state target calculator and predictive controller. The procedure is demonstrated with a numerical example. © 2013 IEEE.

Six-wave mixing phase-dispersion by optical heterodyne detection in dressed reverse N-type four-level system

We have investigated the dressed effects of non-degenerate four-wave mixing (NDFWM) and demonstrated a phase-sensitive method of studying the fifth-order nonlinear susceptibility due to atomic coherence in RN-type four-level system. In the presence of a strong coupling field, NDFWM spectrum exhibits Autler-Townes splitting, accompanied by either suppression or enhancement of the NDFWM signal, which is directly related to the competition between the absorption and dispersion contributions. The heterodyne-detected nonlinear absorption and dispersion of six-wave mixing signal in the RN-type system show that the hybrid radiation-matter detuning damping oscillation is in the THz range and can be controlled and modified through the colour-locked correlation of twin noisy fields.

Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis

Steroid derivatives show a complex interaction with P-glycoprotein (Pgp). To determine the essential structural requirements of a series of structurally related and functionally diverse steroids for Pgp-mediated transport or inhibition, a three-dimensional quantitative structure activity relationship study was performed by comparative similarity index analysis modeling. Twelve models have been explored to well correlate the physiochemical features with their biological functions with Pgp on basis of substrate and inhibitor datasets, in which the best predictive model for substrate gave cross-validated q(2) = 0.720, non-cross-validated r(2) = 0.998, standard error of estimate SEE = 0.012, F = 257.955, and the best predictive model for inhibitor gave q(2) = 0.536, r(2) = 0.950, SEE = 1.761 and F = 45.800. The predictive ability of all models was validated by a set of compounds that were not included in the training set. The physiochemical similarities and differences of steroids as Pgp substrate and inhibitor, respectively, were analyzed to be helpful in developing new steroid-like compounds. (C) 2004 Elsevier B.V. All rights reserved.

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

BACKGROUND: Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyperacetylation of cellular proteins. Therefore, elucidating the mechanisms by which HDACi trigger differentiation, cell cycle arrest, or apoptosis of cancer cells could inform development of more targeted therapies. We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. RESULTS: We identified several thousand specific regulatory elements [~10 % of total DNase I-hypersensitive (DHS) sites] that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid treatment. Most of the differential DHS sites display hallmarks of enhancers, including being enriched for non-promoter regions, associating with nearby gene expression changes, and increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 increases binding at opened DHS sites with HDACi treatment by ChIP-seq, but PU.1 knockdown by shRNA fails to block the chromatin accessibility and expression changes. A machine-learning approach indicates H3K27me3 initially marks PU.1-bound sites that open with HDACi treatment, suggesting these sites are epigenetically poised. CONCLUSIONS: We find HDACi treatment of K562 cells results in site-specific chromatin remodeling at epigenetically poised regulatory elements. PU.1 shows evidence of a pioneer role in this process by marking poised enhancers but is not required for transcriptional activation.