Solution structure and interaction of cupiennin 1a, a spider venom peptide, with phospholipid bilayers

The solution structure of cupiennin 1a, a 35 residue, basic antibacterial peptide isolated from the venom of the spider Cupiennius salei, has been determined by nuclear magnetic resonance (NMR) spectroscopy. The peptide was found to adopt a helix−hinge−helix structure in a membrane mimicking solvent. The hinge may play a role in allowing the amphipathic N-terminal helix and polar C-terminal helix to orient independently upon membrane binding, in order to achieve maximal antibacterial efficacy. Solid-state 31P and 2H NMR was used to further study the effects of cupiennin 1a on the dynamic properties of lipid membranes, using zwitterionic chain deuterated dimyristoylphosphatidylcholine (d54-DMPC) and anionic dimyristoylphosphatidylglycerol (DMPG) multilamellar vesicles. In d54-DMPC alone, cupiennin 1a caused a decrease in the 31P chemical shift anisotropy, indicating some interaction with the lipid head groups, and a decrease in order over the entire acyl chain. In contrast, for the mixed (d54-DMPC/DMPG) lipid system cupiennin 1a appeared to induce lateral separation of the two lipids as evidenced by the 31P spectra, in which the peptide preferentially interacted with DMPG. Little effect was observed on the deuterated acyl chain order parameters in the d54-DMPC/DMPG model membranes. Furthermore, 31P NMR relaxation measurements confirmed a differential effect on the lipid motions depending upon the membrane composition. Therefore, subtle differences are likely in the mechanism by which cupiennin 1a causes membrane lysis in either prokaryotic or eukaryotic cells, and may explain the specific spectrum of activity.

A telematics solution for the remote follow-up of malnourished children in underserved areas

The identification of malnourished children living under extreme poverty conditions in isolated areas is crucial to trigger urgent interventions like supplementary or therapeutic feeding. This work aims to strengthen the task of following-up malnourished maternal-child population in rural areas of developing countries like Nicaragua. The solution facilitates low-cost health nutritional remote monitoring to support rural communities at the point of care. Thus, the system allows medical staff to communicate with brigades, who transmit anthropometric measurements, such as weight and height of the children, from communities which are sited about 12 km. far away. A hybrid WiMAX/WiFi architecture was deployed to provide affordable communications between the isolated communities and the health center. Furthermore, a free PBX software and an open information system, installed at the health center, support WiFi based mobile communications and information management to support the care needs of maternal-child population at risk.

The design, computer modeling, solution structure, and biological evaluation of synthetic analogs of bryostatin 1

The bryostatins are a unique family of emerging cancer chemotherapeutic candidates isolated from marine bryozoa. Although the biochemical basis for their therapeutic activity is not known, these macrolactones exhibit high affinities for protein kinase C (PKC) isozymes, compete for the phorbol ester binding site on PKC, and stimulate kinase activity in vitro and in vivo. Unlike the phorbol esters, they are not first-stage tumor promoters. The design, computer modeling, NMR solution structure, PKC binding, and functional assays of a unique class of synthetic bryostatin analogs are described. These analogs (7b, 7c, and 8) retain the putative recognition domain of the bryostatins but are simplified through deletions and modifications in the C4-C14 spacer domain. Computer modeling of an analog prototype (7a) indicates that it exists preferentially in two distinct conformational classes, one in close agreement with the crystal structure of bryostatin 1. The solution structure of synthetic analog 7c was determined by NMR spectroscopy and found to be very similar to the previously reported structures of bryostatins 1 and 10. Analogs 7b, 7c, and 8 bound strongly to PKC isozymes with Ki = 297, 3.4, and 8.3 nM, respectively. Control 7d, like the corresponding bryostatin derivative, exhibited weak PKC affinity, as did the derivative, 9, lacking the spacer domain. Like bryostatin, acetal 7c exhibited significant levels of in vitro growth inhibitory activity (1.8–170 ng/ml) against several human cancer cell lines, providing an important step toward the development of simplified, synthetically accessible analogs of the bryostatins.

Actin-Bundling Protein Isolated from Pollen Tubes of Lily : Biochemical and Immunocytochemical Characterization

A 135-kD actin-bundling protein was purified from pollen tubes of lily (Lilium longiflorum) using its affinity to F-actin. From a crude extract of the pollen tubes, this protein was coprecipitated with exogenously added F-actin and then dissociated from F-actin by treating it with high-ionic-strength solution. The protein was further purified sequentially by chromatography on a hydroxylapatite column, a gel-filtration column, and a diethylaminoethyl-cellulose ion-exchange column. In the present study, this protein is tentatively referred to as P-135-ABP (Plant 135-kD Actin-Bundling Protein). By the elution position from a gel-filtration column, we estimated the native molecular mass of purified P-135-ABP to be 260 kD, indicating that it existed in a dimeric form under physiological conditions. This protein bound to and bundled F-actin prepared from chicken breast muscle in a Ca2+-independent manner. The binding of 135-P-ABP to actin was saturated at an approximate stoichiometry of 26 actin monomers to 1 dimer of P-135-ABP. By transmission electron microscopy of thin sections, we observed cross-bridges between F-actins with a longitudinal periodicity of 31 nm. Immunofluorescence microscopy using rhodamine-phalloidin and antibodies against the 135-kD polypeptide showed that P-135-ABP was colocalized with bundles of actin filaments in lily pollen tubes, leading us to conclude that it is the factor responsible for bundling the filaments.

Membrane healing and restoration of contractility after mechanical injury in isolated skeletal muscle fibers of the frog.

In single isolated skeletal muscle fibers of the frog, we studied (i) the recovery from large sarcolemmal mechanical injuries of the response to electric stimulation and (ii) the integrity of the sarcolemma under the light microscope. In Ringer's solution, the damaged cells stopped contracting and deteriorated completely within 1 hr. In the presence of phosphatidylcholine (0.025 g/ml in Ringer's solution), the injured cells initially responded with local twitches. Within 0.5 hr, contractility and membrane integrity started to recover and both were back to control levels within 3 hr. When these cells were placed back in normal Ringer's solution, they remained viable and active for several hours. Our results suggest that phosphatidylcholine can protect muscle fibers from the effects of sarcolemmal injury.

Isolation and characterization of novel cyclotides from Viola hederaceae - Solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide

Based on a newly established sequencing strategy featured by its efficiency, simplicity, and easy manipulation, the sequences of four novel cyclotides (macrocyclic knotted proteins) isolated from an Australian plant Viola hederaceae were determined. The three-dimensional solution structure of V. hederaceae leaf cyclotide-1 ( vhl-1), a leaf-specific expressed 31-residue cyclotide, has been determined using two-dimensional H-1 NMR spectroscopy. vhl-1 adopts a compact and well defined structure including a distorted triple-stranded β- sheet, a short 310 helical segment and several turns. It is stabilized by three disulfide bonds, which, together with backbone segments, form a cyclic cystine knot motif. The three-disulfide bonds are almost completely buried into the protein core, and the six cysteines contribute only 3.8% to the molecular surface. A pH titration experiment revealed that the folding of vhl-1 shows little pH dependence and allowed the pK(a) of 3.0 for Glu(3) and ∼ 5.0 for Glu(14) to be determined. Met(7) was found to be oxidized in the native form, consistent with the fact that its side chain protrudes into the solvent, occupying 7.5% of the molecular surface. vhl-1 shows anti-HIV activity with an EC50 value of 0.87 μ m.

Isolation, solution structure, and insecticidal activity of Kalata B2, a circular protein with a twist: Do Mobius strips exist in nature?

A large number of macrocyclic miniproteins with diverse biological activities have been isolated from the Rubiaceae, Violaceae, and Cucurbitaceae plant families in recent years. Here we report the three-dimensional structure determined using H-1 NMR spectroscopy and demonstrate potent insecticidal activity for one of these peptides, kalata B2. This peptide is one of the major components of an extract from the leaves of the plant Oldenlandia affinis. The structure consists of a distorted triple-stranded beta-sheet and a cystine knot arrangement of the disulfide bonds and is similar to those described for other members of the cyclotide family. The unique cyclic and knotted nature of these molecules makes them a fascinating example of topologically complex proteins. Examination of the sequences reveals that they can be separated into two subfamilies, one of which contains a larger number of positively charged residues and has a bracelet-like circularization of the backbone. The second subfamily contains a backbone twist due to a cis-peptidyl-proline bond and may conceptually be regarded as a molecular Mobius strip. Kalata B2 is the second putative member of the Mobius cyclotide family to be structurally characterized and has a cis-peptidyl-proline bond, thus validating the suggested name for this subfamily of cyclotides. The observation that kalata B2 inhibits the growth and development of Helicoverpa armigera larvae suggests a role for the cyclotides in plant defense. A comparison of the sequences and structures of kalata B1 and B2 provides insight into the biological activity of these peptides.

Developments and extensions of Roth's method of double Fourier series with applications to the solution of electromagnetic field problems

The first part of the thesis compares Roth's method with other methods, in particular the method of separation of variables and the finite cosine transform method, for solving certain elliptic partial differential equations arising in practice. In particular we consider the solution of steady state problems associated with insulated conductors in rectangular slots. Roth's method has two main disadvantages namely the slow rate of con­vergence of the double Fourier series and the restrictive form of the allowable boundary conditions. A combined Roth-separation of variables method is derived to remove the restrictions on the form of the boundary conditions and various Chebyshev approximations are used to try to improve the rate of convergence of the series. All the techniques are then applied to the Neumann problem arising from balanced rectangular windings in a transformer window. Roth's method is then extended to deal with problems other than those resulting from static fields. First we consider a rectangular insulated conductor in a rectangular slot when the current is varying sinusoidally with time. An approximate method is also developed and compared with the exact method.The approximation is then used to consider the problem of an insulated conductor in a slot facing an air gap. We also consider the exact method applied to the determination of the eddy-current loss produced in an isolated rectangular conductor by a transverse magnetic field varying sinusoidally with time. The results obtained using Roth's method are critically compared with those obtained by other authors using different methods. The final part of the thesis investigates further the application of Chebyshdev methods to the solution of elliptic partial differential equations; an area where Chebyshev approximations have rarely been used. A poisson equation with a polynomial term is treated first followed by a slot problem in cylindrical geometry.

Simplified design method for energy dissipating devices in retrofitting of seismically isolated bridges

Abstract: Highway bridges have great values in a country because in case of any natural disaster they may serve as lines to save people’s lives. Being vulnerable under significant seismic loads, different methods can be considered to design resistant highway bridges and rehabilitate the existing ones. In this study, base isolation has been considered as one efficient method in this regards which in some cases reduces significantly the seismic load effects on the structure. By reducing the ductility demand on the structure without a notable increase of strength, the structure is designed to remain elastic under seismic loads. The problem associated with the isolated bridges, especially with elastomeric bearings, can be their excessive displacements under service and seismic loads. This can defy the purpose of using elastomeric bearings for small to medium span typical bridges where expansion joints and clearances may result in significant increase of initial and maintenance cost. Thus, supplementing the structure with dampers with some stiffness can serve as a solution which in turn, however, may increase the structure base shear. The main objective of this thesis is to provide a simplified method for the evaluation of optimal parameters for dampers in isolated bridges. Firstly, performing a parametric study, some directions are given for the use of simple isolation devices such as elastomeric bearings to rehabilitate existing bridges with high importance. Parameters like geometry of the bridge, code provisions and the type of soil on which the structure is constructed have been introduced to a typical two span bridge. It is concluded that the stiffness of the substructure, soil type and special provisions in the code can determine the employment of base isolation for retrofitting of bridges. Secondly, based on the elastic response coefficient of isolated bridges, a simplified design method of dampers for seismically isolated regular highway bridges has been presented in this study. By setting objectives for reduction of displacement and base shear variation, the required stiffness and damping of a hysteretic damper can be determined. By modelling a typical two span bridge, numerical analyses have followed to verify the effectiveness of the method. The method has been used to identify equivalent linear parameters and subsequently, nonlinear parameters of hysteretic damper for various designated scenarios of displacement and base shear requirements. Comparison of the results of the nonlinear numerical model without damper and with damper has shown that the method is sufficiently accurate. Finally, an innovative and simple hysteretic steel damper was designed. Five specimens were fabricated from two steel grades and were tested accompanying a real scale elastomeric isolator in the structural laboratory of the Université de Sherbrooke. The test procedure was to characterize the specimens by cyclic displacement controlled tests and subsequently to test them by real-time dynamic substructuring (RTDS) method. The test results were then used to establish a numerical model of the system which went through nonlinear time history analyses under several earthquakes. The outcome of the experimental and numerical showed an acceptable conformity with the simplified method.

Renal and vascular effects of the natriuretic peptide isolated from Crotalus durissus cascavella venom

Crotalus durissus cascavella is a snake that is usually found in the scrublands of northeast Brazil. The components of its venom may have effects on the vascular and renal systems. Recently, a new bradykinin inhibitory peptide has been identified in the venom of the Crotalinae family. The aim of the present study was to investigate the renal and vascular effects of the natriuretic peptide isolated from the venom of Crotalus durissus cascavella (NP2_Casca). The chromatographic profile showed the fractionation of substances identified as convulxin, gyroxin, crotoxin and crotamine, as well as fractions V and VI. The electrophoretic profile of fraction V consisted of several bands ranging from approximately 6 kDa to 13 kDa, while fraction VI showed only two main electrophoretic bands with molecular weights of approximately 6 and 14 kDa. Reverse-phase chromatography showed that NP2_Casca corresponds to about 18% of fraction VI and that this fraction is the main natriuretic peptide. NP2_Casca was compared to other natriuretic peptides from other sources of snake venom. All amino acid sequences that were compared showed a consensus region of XGCFGX, XLDRIX and XSGLGCX. The group treated with NP2-Casca showed an increase in perfusion pressure, renal vascular resistance, urinary flow and glomerular filtration rate. The percent of total and proximal tubular transport of sodium was reduced significantly after administration of the peptide. The mean arterial pressure showed a dose-dependent decrease after infusion of NP2_Casca, and an increase in nitrite production. In the aortic ring assay, NP2_Casca caused a relaxant effect in endothelium-intact thoracic aortic rings precontracted with phenylephrine in the presence and absence of isatin. NP2_Casca failed to relax the aortic rings precontracted with an isosmotic potassium Krebs-Henseleit solution. In conclusion, the natriuretic peptide isolated from Crotalus durissus cascavella venom produced renal and vascular effects. NP2_Casca reduced total and proximal sodium tubular transport, leading to an increase in sodium excretion, thereby demonstrating a diuretic action. A hypotensive effect was displayed in an arterial pressure assay, with an increase in nitrite production, suggesting a possible vasoactive action. (C) 2008 Elsevier Ltd. All rights reserved.

Sequential exhaustive extraction of a Mollisol soil, and characterizations of humic components, including humin, by solid and solution state NMR.

A comprehensive sequential extraction procedure was applied to isolate soil organic components using aqueous solvents at different pH values, base plus urea (base-urea), and finally dimethylsulfoxide (DMSO) plus concentrated H2SO4 (DMSO-acid) for the humin-enriched clay separates. The extracts from base-urea and DMSO-acid would be regarded as 'humin' in the classical definitions. The fractions isolated from aqueous base, base-urea and DMSO-acid were characterized by solid and solution state NMR spectroscopy. The base-urea solvent system isolated ca. 10% (by mass) additional humic substances. The combined base-urea and DMSO-acid solvents isolated ca. 93% of total organic carbon from the humin-enriched fine clay fraction (<2 ?m). Characterization of the humic fractions by solid-state NMR spectroscopy showed that oxidized char materials were concentrated in humic acids isolated at pH 7, and in the base-urea extract. Lignin-derived materials were in considerable abundance in the humic acids isolated at pH 12.6. Only very small amounts of char-derived structures were contained in the fulvic acids and fulvic acids-like material isolated from the base-urea solvent. After extraction with base-urea, the 0.5 m NaOH extract from the humin-enriched clay was predominantly composed of aliphatic hydrocarbon groups, and with lesser amounts of aromatic carbon (probably including some char material), and carbohydrates and peptides. From the combination of solid and solution-state NMR spectroscopy, it is clear that the major components of humin materials, from the DMSO-acid solvent, after the exhaustive extraction sequence, were composed of microbial and plant derived components, mainly long-chain aliphatic species (including fatty acids/ester, waxes, lipids and cuticular material), carbohydrate, peptides/proteins, lignin derivatives, lipoprotein and peptidoglycan (major structural components in bacteria cell walls). Black carbon or char materials were enriched in humic acids isolated at pH 7 and humic acids-like material isolated in the base-urea medium, indicating that urea can liberate char-derived material hydrogen bonded or trapped within the humin matrix.

Multi-organ support device for combined extracorporeal carbon dioxide removal and hemofiltration treatments with pump-free solution for ultrafiltration

The use of extracorporeal organ support (ECOS) devices is increasingly widespread, to temporarily sustain or replace the functions of impaired organs in critically ill patients. Among ECOS, respiratory functions are supplied by extracorporeal life support (ECLS) therapies like extracorporeal membrane oxygenation (ECMO) and extracorporeal carbon dioxide removal (ECCO2R), and renal replacement therapies (RRT) are used to support kidney functions. However, the leading cause of mortality in critically ill patients is multi-organ dysfunction syndrome (MODS), which requires a complex therapeutic strategy where extracorporeal treatments are often integrated to pharmacological approach. Recently, the concept of multi-organ support therapy (MOST) has been introduced, and several forms of isolated ECOS devices are sequentially connected to provide simultaneous support to different organ systems. The future of critical illness goes towards the development of extracorporeal devices offering multiple organ support therapies on demand by a single hardware platform, where treatment lines can be used alternately or in conjunction. The aim of this industrial PhD project is to design and validate a device for multi-organ support, developing an auxiliary line for renal replacement therapy (hemofiltration) to be integrated on a platform for ECCO2R. The intended purpose of the ancillary line, which can be connected on demand, is to remove excess fluids by ultrafiltration and achieve volume control by the infusion of a replacement solution, as patients undergoing respiratory support are particularly prone to develop fluid overload. Furthermore, an ultrafiltration regulation system shall be developed using a powered and software-modulated pinch-valve on the effluent line of the hemofilter, proposed as an alternative to the state-of-the-art solution with peristaltic pump.

The Cratylia Mollis Seed Lectin Induces Membrane Permeability Transition In Isolated Rat Liver Mitochondria And A Cyclosporine A-insensitive Permeability Transition In Trypanosoma Cruzi Mitochondria.

Previous results provided evidence that Cratylia mollis seed lectin (Cramoll 1,4) promotes Trypanosoma cruzi epimastigotes death by necrosis via a mechanism involving plasma membrane permeabilization to Ca(2+) and mitochondrial dysfunction due to matrix Ca(2+) overload. In order to investigate the mechanism of Ca(2+) -induced mitochondrial impairment, experiments were performed analyzing the effects of this lectin on T. cruzi mitochondrial fraction and in isolated rat liver mitochondria (RLM), as a control. Confocal microscopy of T. cruzi whole cell revealed that Cramoll 1,4 binding to the plasma membrane glycoconjugates is followed by its internalization and binding to the mitochondrion. Electrical membrane potential (∆Ψm ) of T. cruzi mitochondrial fraction suspended in a reaction medium containing 10 μM Ca(2+) was significantly decreased by 50 μg/ml Cramoll 1,4 via a mechanism insensitive to cyclosporine A (CsA, membrane permeability transition (MPT) inhibitor), but sensitive to catalase or 125 mM glucose. In RLM suspended in a medium containing 10 μM Ca(2+) this lectin, at 50 μg/ml, induced increase in the rate of hydrogen peroxide release, mitochondrial swelling, and ∆Ψm disruption. All these mitochondrial alterations were sensitive to CsA, catalase, and EGTA. These results indicate that Cramoll 1, 4 leads to inner mitochondrial membrane permeabilization through Ca(2+) dependent mechanisms in both mitochondria. The sensitivity to CsA in RLM characterizes this lectin as a MPT inducer and the lack of CsA effect identifies a CsA-insensitive MPT in T. cruzi mitochondria.

Genome Sequence Of Bacillus Safensis Cfa06, Isolated From Biodegraded Petroleum In Brazil.

Bacillus safensis is a microorganism recognized for its biotechnological and industrial potential due to its interesting enzymatic portfolio. Here, as a means of gathering information about the importance of this species in oil biodegradation, we report a draft genome sequence of a strain isolated from petroleum.

Identification Of Corynebacterium Spp. Isolated From Bovine Intramammary Infections By Matrix-assisted Laser Desorption Ionization-time Of Flight Mass Spectrometry.

Corynebacterium species (spp.) are among the most frequently isolated pathogens associated with subclinical mastitis in dairy cows. However, simple, fast, and reliable methods for the identification of species of the genus Corynebacterium are not currently available. This study aimed to evaluate the usefulness of matrix-assisted laser desorption ionization/mass spectrometry (MALDI-TOF MS) for identifying Corynebacterium spp. isolated from the mammary glands of dairy cows. Corynebacterium spp. were isolated from milk samples via microbiological culture (n=180) and were analyzed by MALDI-TOF MS and 16S rRNA gene sequencing. Using MALDI-TOF MS methodology, 161 Corynebacterium spp. isolates (89.4%) were correctly identified at the species level, whereas 12 isolates (6.7%) were identified at the genus level. Most isolates that were identified at the species level with 16 S rRNA gene sequencing were identified as Corynebacterium bovis (n=156; 86.7%) were also identified as C. bovis with MALDI-TOF MS. Five Corynebacterium spp. isolates (2.8%) were not correctly identified at the species level with MALDI-TOF MS and 2 isolates (1.1%) were considered unidentified because despite having MALDI-TOF MS scores >2, only the genus level was correctly identified. Therefore, MALDI-TOF MS could serve as an alternative method for species-level diagnoses of bovine intramammary infections caused by Corynebacterium spp.