THE SYNTHESIS, KINETIC CHARACTERIZATION AND APPLICATION OF A NOVEL BIOTINYLATED AFFINITY LABEL FOR CATHEPSIN-B

In this study we report on the synthesis, kinetic characterization and application of a novel biotinylated and active-site-directed inactivator of cathepsin B. Thus the peptidyliazomethane biotinyl-Phe-Ala-diazomethane has been synthesized by a combination of solid-phase and solution methodologies and has been shown to be a very efficient inactivator of bovine and human cathepsin B. The respective apparent second-order rate constants (k0bs./[I]) for the inactivation of the human and bovine enzymes by this reagent, namely approximately 5.4 x 10(4) M-1 and approximately 7.8 x 10(4) M-1, compare very favourably with those values determined for the urethane-protected analogue benzloxycarbonyl-Phe-Ala-chloromethane first described by Green & Shaw [(1981) J.Biol. Chem. 256, 1923-1928], thus demonstrating that the presence of the biotin moiety at the P3 position is compatible with inhibitor effectiveness. The utilization of this reagent for the detection of cathepsin B in electrophoretic gels, using Western blotting and in combination with a streptavidin/alkaline phosphatase detection system, is also demonstrated. Given that the peptidydiazomethanes exhibit a pronounced reactivity towards cysteine proteinases, we feel that the present label may well constitute the archetypal example of a wide range of reagents for the selective labelling of this class of proteinase, even in a complex biological milieu containing additional classes of proteinases.

Spatial Heterogeneity and Kinetic Regulation of Arsenic Dynamics in Mangrove Sediments: The Sundarbans, Bangladesh

The biogeochemistry of arsenic (As) in sediments is regulated by multiple factors such as particle size, dissolved organic matter (DOM), iron mobilization, and sediment binding characteristics, among others. Understanding the heterogeneity of factors affecting As deposition and the kinetics of mobilization, both horizontally and vertically, across sediment depositional environments was investigated in Sundarban mangrove ecosystems, Bengal Delta, Bangladesh. Sediment cores were collected from 3 different Sundarbans locations and As concentration down the profiles were found to be more associated with elevated Fe and Mn than with organic matter (OM). At one site chosen for field monitoring, sediment cores, pore and surface water, and in situ diffusive gradients in thin films (DGT) measurements (which were used to model As sediment pore-water concentrations and resupply from the solid phase) were sampled from four different subhabitats. Coarse-textured riverbank sediment porewaters were high in As, but with a limited resupply of As from the solid phase compared to fine-textured and high organic matter content forest floor sediments, where porewater As was low, but with much higher As resupply. Depositional environment (overbank verses forest floor) and biological activity (input of OM from forest biomass) considerably affected As dynamics over very short spatial distances in the mosaic of microhabitats that constitute a mangrove ecosystem.

Ecotoxicological screening of Kenyan tannery dust using a luminescent-based bacterial biosensor

Ecotoxicological screening of dust sampled throughout a Kenyan tannery was conducted using a luminescence (lux)-based bacterial biosensor for both solid and liquid assays. This was complemented by chemical analysis in an attempt to identify possible causative toxic components. The biosensor results showed a highly significant (p <0.001) difference in both solid and liquid phase toxicity in samples collected from various identified sampling points in the tannery. A positive correlation was observed between results of the solid and liquid phase techniques, for most of the sampling points indicating that the toxic contaminants were bioavailable both in the solid and liquid state. However, the results generally indicated toxicity associated with liquid phase except certain areas in solid phase such as chemical handling, buffing area and weighing. The most toxic tannery area identified was the weighing area (p <0.001), showing the lowest bioluminescence for both the solid (0.38 +/- 2.21) and liquid phases (0.01 +/- 0.001). Chromium was the metal present in the highest concentration indicating levels higher than the stipulated regulatory requirement of 0.5 mg Cr/m3 for total Cr (highest Cr concentration was at chemical handling at 209.24 mg l(-1)) in all dust samples. The weighing area had the highest Ni concentration (1.87 mg l(-1)) and the chemical handling area showed the highest Zn concentration (31.9 mg l(-1)). These results raise environmental health concerns, as occupational exposure to dust samples from this site has been shown to give rise to elevated concentrations (above the stipulated levels) of chromium in blood, urine and some body tissues, with inhalation being the main route. Health and Safety Executive (HSE), UK, and American Conference of Governmental Industrial Hygienist (ACGIH) and National Institute for Occupational Safety and Health (NIOSH), USA stipulates an occupational exposure limit of 0.5 mg Cr/m3 (8 h TWA) for total chromium. However, schedule 1 of Controls of substances hazardous to health (COSHH) regulations developed by HSE, indicate 0.05 mg m3 (8 h TWA reference periods) to be the limit for Cr (VI) exposure. The exposure limit for individual (e.g., Cr, Zn, Ni etc.) contaminants (homogeneity) was not exceeded, but potential impact of heterogeneity (multi-element synergistic effect) on toxicity requires application of the precautionary principle.

A material model for multiaxial stretching and stress relaxation of polypropylene under process conditions

Polypropylene sheets have been stretched at 160 °C to a state of large biaxial strain of extension ratio 3, and the stresses then allowed to relax at constant strain. The state of strain is reached via a path consisting of two sequential planar extensions, the second perpendicular to the first, under plane stress conditions with zero stress acting normal to the sheet. This strain path is highly relevant to solid phase deformation processes such as stretch blow moulding and thermoforming, and also reveals fundamental aspects of the flow rule required in the constitutive behaviour of the material. The rate of decay of stress is rapid, and such as to be highly significant in the modelling of processes that include stages of constant strain. A constitutive equation is developed that includes Eyring processes to model both the stress relaxation and strain rate dependence of the stress. The axial and transverse stresses observed during loading show that the use of a conventional Levy-Mises flow rule is ineffective, and instead a flow rule is used that takes account of the anisotropic state of the material via a power law function of the principal extension ratios. Finally the constitutive model is demonstrated to give quantitatively useful representation of the stresses both in loading and in stress relaxation.

Hydrobiogeochemical Interactions along “Flow Tubes” Controls: Watershed Scale Contaminant Flow and Transformation at the Oak Ridge IFRC

Geochemical,spectrographic, microbiological and hydrogeologic studies at the ORIFRC site indicate that groundwater transport in structured media may behave as a system of parallel flow tubes. These tubes are preferred flowpaths that enable contaminant transport parallel to bedding planes (strike) over distances of 1000s of meters. A significant flux of groundwater is focused within an interval defined by the interface between the competent bedrock and overlying highly-weathered saprolite, commonly referred to as the"transition zone." Characteristics of this transition zone are dense fractures and the relative absence of weathering products (e.g. clays)results in a significantly higher permeability compared to both the overlying clay-saprolite and underlying bedrock. Several stratabound low seismic velocity zones located below the transition zone were identified during geophysics studies and were also determined to be fractured high permeability preferred contaminant transport pathways during subsequent drilling activities. XANES analysis of precipitates collected from these deeper flow zones indicate 95% or more of the U deposited is U(VI). Linear combination fitting of the EXAFS data shows that precipitates are ~51±5% U(VI)-carbonate-like phase (e.g., liebigite) and ~49±5% U(VI) associated with an iron oxide phase; inclusion of a third component in the fit suggests that up to 15% of the U(VI) may be associated with a phosphate phase or OH- phase (e.g.,schoepite). Although precipitates with similar U(VI)-carbonate and/or phosphate associations were identified in the transition zone pathways,there were also U(VI) complexes adsorbed to mineral surfaces that would tend to be more readily mobilized. Groundwater in the different flow tubes has been determined to consist of different water quality types that vary with the solid phase encountered (e.g., clays, carbonates, clastics) as contaminants migrate along the flow paths. This lateral and vertical variability in geochemistry, particularly pH, has a significant impact on microbiological community composition and activity. Ribosomal RNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter(a diverse population of denitrifiers that are moderately acid tolerant) have a high relative abundance in the acidic source zone at the ORIFRC site.Watershed-scale analysis across different flow paths/tubes revealed strong negative correlation between pH and the absolute and relative abundance of Rhodanobacter. Recent studies also confirmed that the ORIFRC site hosts a diverse fungal community, with significant differences observed between acidic (pH <5) and circumneutral (>5) wells. The lack of nitrous oxide reduction capability in fungi, and the detection of denitrification potential in slurry microcosms suggest that fungi may have aheretofore under appreciated role in biogeochemical transformations, with implications forsite remediation and greenhouse gas emissions. Further research is needed to determine if these organisms can influence U(VI) mobility either directly through immobilization or indirectly through the depletion of nitrate.In conclusion, additional studies are required to quantify the processes (e.g., solid phase reactions, recharge, diffusion, microbial interactions) that are occurring along the groundwater flow tubes identified at the ORIFRC so predictive models can be parameterized and used to assess long-term contaminant fate and transport and remedial options.

Gold Nanoparticles-Coated SU-8 for Sensitive Fluorescence-Based Detections of DNA

SU-8 epoxy-based negative photoresist has been extensively employed as a structural material for fabrication of numerous biological microelectro-mechanical systems (Bio-MEMS) or lab-on-a-chip (LOC) devices. However, SU-8 has a high autofluorescence level that limits sensitivity of microdevices that use fluorescence as the predominant detection workhorse. Here, we show that deposition of a thin gold nanoparticles layer onto the SU-8 surface significantly reduces the autofluorescence of the coated SU-8 surface by as much as 81% compared to bare SU-8. Furthermore, DNA probes can easily be immobilized on the Au surface with high thermal stability. These improvements enabled sensitive DNA detection by simple DNA hybridization down to 1 nM (a two orders of magnitude improvement) or by solid-phase PCR with sub-picomolar sensitivity. The approach is simple and easy to perform, making it suitable for various Bio-MEMs and LOC devices that use SU-8 as a structural material.

Surface Modification of Photoresist SU-8 for Low Autofluorescence and Bioanalytical Applications

This paper reports a surface modification of epoxy-based negative photoresist SU-8 for reducing its autofluorescence while enhancing its biofunctionality. By covalently depositing a thin layer of 20 nm Au nanoparticles (AuNPs) onto the SU-8 surface, we found that the AuNPs-coated SU-8 surface is much less fluorescent than the untreated SU-8. Moreover, DNA probes can easily be immobilized on the Au surface and are thermally stable over a wide range of temperature. These improvements will benefit bioanalytical applications such as DNA hybridization and solid-phase PCR (SP-PCR).

Ranachensinin: A Novel Aliphatic Tachykinin from the Skin Secretion of the Chinese Brown Frog, Rana chensinensis

Amphibian skin secretions contain a plethora of pharmacologically-active substances and represent established sources of bioactive peptides, including tachykinins. Tachykinins are one of the most widely-studied peptide families in animals and are found in neuroendocrine tissues from the lowest vertebrates to mammals. They are characterized by the presence of a highly-conserved C-terminal pentapeptide amide sequence motif (-FXGLM-amide) that also constitutes the bioactive core of the peptide. Amidation of the C-terminal methioninyl residue appears to be mandatory in the expression of biological activity. Here, we describe the isolation, characterization and molecular cloning of a novel tachykinin named ranachensinin, from the skin secretion of the Chinese brown frog, Rana chensinensis. This peptide, DDTSDRSN QFIGLM-amide, contains the classical C-terminal pentapeptide amide motif in its primary structure and an Ile (I) residue in the variable X position. A synthetic replicate of ranachensinin, synthesized by solid-phase Fmoc chemistry, was found to contract the smooth muscle of rat urinary bladder with an EC50 of 20.46 nM. However, in contrast, it was found to be of low potency in contraction of rat ileum smooth muscle with an EC50 of 2.98 µM. These data illustrate that amphibian skin secretions continue to provide novel bioactive peptides with selective effects on functional targets in mammalian tissues.

Use of immunosorbent-purified antigens of Fasciola hepatica in enzyme immunoassays

A monoclonal antibody specific for the T1 tegumental antigen of Fasciola hepatica was used as a solid-phase immunosorbent for the purification of T1 antigen from homogenised mature F hepatica. Material fractionated by this technique was successfully used in enzyme-linked immunoassays to detect antibodies to F hepatica in sera from sheep and cattle. Species differences in response to infection by F hepatica were demonstrated.

Antibodies to the structural polypeptides of measles virus following acute infection and in SSPE

A solid-phase radioimmunoassay was used to determine the specificity of IgG antibodies from normal sera, sera and CSF from patients with SSPE for the structural polypeptides of measles virus. The polypeptide specificity of antibodies from these sources were qualitatively similar; these results indicate antigenic cross-reactivity between SSPE-derived (Mantooth) and non-SSPE-derived strains of measles virus and stimulation of antibody formation by comparable antigens.

Development of Novel Activity-Based Probes for the Detection of Serine Proteases

Cystic Fibrosis (CF) is a genetic disease featuring a chronic cycle of inflammation and infection in the airways of sufferers. Mutations lead to altered ion transport, which in turn causes dehydrated airways and reduced mucociliary clearance which predisposes the patient to infection, resulting in a severe immune response and tissue destruction (1). Airway dehydration is primarily caused by the hyperabsorption of sodium by the epithelial sodium channel (ENaC) (2). ENaC is activated by the action of a number of predominantly trypsin-like Channel Activating Proteases (CAPs) including prostasin, matriptase and furin (3). Additional proteases known to activate ENaC include human airway trypsin (3), plasmin, neutrophil elastase and chymotrypsin (4).

Activity profiling is a valuable technique which involves the use of small inhibitory molecules called Activity-Based Probes (ABPs) which can be used to covalently label the active site of proteases and provide a range of information regarding its structure, catalytic mechanism, location and function within biological systems. The development of novel ABPs for CAPs, would enhance understanding of the role of these proteases in CF airways disease and in particular their role in ENaC activation and airway dehydration. This project investigates the application of a range of novel broad-spectrum ABPs targeting the various subclasses of serine proteases, to include those proteases involved in ENaC activation. Additionally, the application of more selective ABPs in detecting specific serine proteases is investigated.

Compounds were synthesised by Solid-Phase Peptide Synthesis (SPPS) using a standard Fmoc/tBu strategy. Kinetic evaluation of synthesised ABPs against various serine proteases was determined by fluorogenic steady-state enzyme assays. Furthermore, application of ABPs and confirmation of irreversible nature of the compounds was carried out through SDS-PAGE and electroblotting techniques.

Synthesised compounds showed potent irreversible inhibition of serine proteases within their respective targeting class (NAP855 vs Trypsin k3/Ki = 2.60 x 106 M-1 min-1, NFP849 vs Chymotrypsin k3/Ki = 1.28 x 106 M-1 min-1 and NVP800 vs Neutrophil Elastase k3/Ki = 6.41 x 104 M-1 min-1). Furthermore ABPs showed little to no cross-reactivity between classes and so display selectivity between classes. The irreversible nature of compounds was further demonstrated through labelling of proteases, followed by separation and detection via SDS-PAGE and electroblotting techniques. Targeted labelling of active proteases only, was demonstrated by failure of ABPs to detect previously inactivated proteases. Extension of the substrate recognition site within probes resulted in an increased potency and selectivity in the detection of the target proteases. Successful detection of neutrophil elastase from CF sputum samples by NVP800, demonstrated the application of compounds within biological samples and their potential use in identifying further proteases involved in ENaC activation and airway dehydration in CF patients.

A comparative study on the thermophysical properties for two bis[(trifluoromethyl)sulfonyl]imide-based ionic liquids containing the trimethyl-sulfonium or the trimethyl-ammonium cation in molecular solvents

Herein, we present a comparative study of the thermophysical properties of two homologous ionic liquids, namely, trimethyl-sulfonium bis[(trifluoromethyl) sulfonyl]imide, [S₁₁₁][TFSI], and trimethyl-ammonium bis[(trifluoromethyl)sulfonyl]imide, [HN₁₁₁][TFSI], and their mixtures with propylene carbonate, acetonitrile, or gamma butyrolactone as a function of temperature and composition. The influence of solvent addition on the viscosity, conductivity, and thermal properties of IL solutions was studied as a function of the solvent mole fraction from the maximum solubility of IL, x_s, in each solvent to the pure solvent. In this case, x_s is the composition corresponding to the maximum salt solubility in each liquid solvent at a given temperature from 258.15 to 353.15 K. The effect of temperature on the transport properties of each binary mixture was then investigated by fitting the experimental data using Arrhenius' law and the Vogel-Tamman-Fulcher (VTF) equation. The experimental data shows that the residual conductivity at low temperature, e.g., 263.15 K, of each binary mixture is exceptionally high. For example, conductivity values up to 35 and 42 mS·cm^-1 were observed in the case of the [S ₁₁₁][TFSI] + ACN and [HN₁₁₁][TFSI] + ACN binary mixtures, respectively. Subsequently, a theoretical approach based on the conductivity and on the viscosity of electrolytes was formulated by treating the migration of ions as a dynamical process governed by ion-ion and solvent-ion interactions. Within this model, viscosity data sets were first analyzed using the Jones-Dole equation. Using this theoretical approach, excellent agreement was obtained between the experimental and calculated conductivities for the binary mixtures investigated at 298.15 K as a function of the composition up to the maximum solubility of the IL. Finally, the thermal characterization of the IL solutions, using DSC measurements, showed a number of features corresponding to different solid-solid phase transitions, T_S-S, with extremely low melting entropies, indicating a strong organizational structure by easy rotation of methyl group. These ILs can be classified as plastic crystal materials and are promising as ambient-temperature solid electrolytes. © 2013 American Chemical Society.

pLR-HL: a novel amphibian Bowman-Birk-type trypsin inhibitor from the skin secretion of the broad-folded frog, Hylarana latouchii

In this study, we report a novel heptadecapeptide (LIGGCWTKSIPPKPCLV) of the pLR/ranacyclin family, named pLR-HL, whose structure was deduced from its biosynthetic precursor-encoding cDNA cloned from the skin secretion-derived cDNA library of the broad-folded frog, Hylarana latouchii, by employing a "shotgun" cloning technique. It contains a disulphide loop between Cys5 and Cys15 which is consistent with Bowman-Birk-type protease inhibitors. The primary structure of pLR-HL deduced from the cDNA sequence was confirmed by fractionating the skin secretion using reverse phase HPLC and subsequent analysis using MALDI-TOF mass spectrometry and LC/MS/MS fragmentation sequencing. On the basis of the establishment of unequivocal amino acid sequence, a synthetic replicate was synthesised by solid-phase Fmoc chemistry, and it displayed a moderately potent trypsin inhibition with a Ki of 143 nM. The substitution of Lys-8 by Phe (Phe8 -pLR-HL) resulted in abolition of trypsin inhibition but generation of modest inhibition on chymotrypsin with a Ki of 2.141 μM. Additionally, both the disulphide loops of pLR-HL and Phe8 -pLR-HL were synthesised and tested. Both of the catalytic loops retained similar inhibitory potencies towards trypsin or chymotrypsin in comparison with the original intact molecules. Thus, the replacement of reactive site residues could alter the specificity of these protease inhibitors, while the canonical reactive loop alone can independently constitute biologically-active moiety.

Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly

Adaptor protein complex 2 alpha and beta-appendage domains act as hubs for the assembly of accessory protein networks involved in clathrin-coated vesicle formation. We identify a large repertoire of beta-appendage interactors by mass spectrometry. These interact with two distinct ligand interaction sites on the beta-appendage (the "top" and "side" sites) that bind motifs distinct from those previously identified on the alpha-appendage. We solved the structure of the beta-appendage with a peptide from the accessory protein Eps15 bound to the side site and with a peptide from the accessory cargo adaptor beta-arrestin bound to the top site. We show that accessory proteins can bind simultaneously to multiple appendages, allowing these to cooperate in enhancing ligand avidities that appear to be irreversible in vitro. We now propose that clathrin, which interacts with the beta-appendage, achieves ligand displacement in vivo by self-polymerisation as the coated pit matures. This changes the interaction environment from liquid-phase, affinity-driven interactions, to interactions driven by solid-phase stability ("matricity"). Accessory proteins that interact solely with the appendages are thereby displaced to areas of the coated pit where clathrin has not yet polymerised. However, proteins such as beta-arrestin (non-visual arrestin) and autosomal recessive hypercholesterolemia protein, which have direct clathrin interactions, will remain in the coated pits with their interacting receptors.

Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE

Evidence that persistent environmental pollutants may target the male reproductive system is increasing. The male reproductive system is regulated by secretion of testosterone by testicular Leydig cells, and perturbation of Leydig cell function may have ultimate consequences. 3-Methylsulfonyl-DDE (3-MeSO₂-DDE) is a potent adrenal toxicants formed from the persistent insecticide DDT. Although studies have revealed the endocrine disruptive effect of 3-MeSO₂-DDE, the underlying mechanisms at cellular level in steroidogenic Leydig cells remains to be established. The current study addresses the effect of 3-MeSO₂-DDE on viability, hormone production and proteome response of primary neonatal porcine Leydig cells. The AlamarBlue™ assay was used to evaluate cell viability. Solid phase radioimmunoassay was used to measure concentration of hormones produced by both unstimulated and Luteinizing hormone (LH)-stimulated Leydig cells following 48h exposure. Protein samples from Leydig cells exposed to a non-cytotoxic concentration of 3-MeSO₂-DDE (10μM) were subjected to nano-LC-MS/MS and analyzed on a Q Exactive mass spectrometer and quantified using label-free quantitative algorithm. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) were carried out for functional annotation and identification of protein interaction networks. 3-MeSO₂-DDE regulated Leydig cell steroidogenesis differentially depending on cell culture condition. Whereas its effect on testosterone secretion at basal condition was stimulatory, the effect on LH-stimulated cells was inhibitory. From triplicate experiments, a total of 6804 proteins were identified in which the abundance of 86 proteins in unstimulated Leydig cells and 145 proteins in LH-stimulated Leydig cells was found to be significantly regulated in response to 3-MeSO₂-DDE exposure. These proteins not only are the first reported in relation to 3-MeSO₂-DDE exposure, but also display small number of proteins shared between culture conditions, suggesting the action of 3-MeSO₂-DDE on several targeted pathways, including mitochondrial dysfunction, oxidative phosphorylation, EIF2-signaling, and glutathione-mediated detoxification. Further identification and characterization of these proteins and pathways may build our understanding to the molecular basis of 3-MeSO₂-DDE induced endocrine disruption in Leydig cells.