Evolution of holometabola insect digestive systems: physiological and biochemical aspects

This review takes into account primarily the work done in our laboratory with insects from the major Holometabola orders. Only the most significant data for each insect will be presented and a proposal on the evolution of Holometabola insect digstive systems will be advanced.

Automated systems in the identification and determination of methicillin resistance among coagulase negative staphylococci

Coagulase-negative staphylococci (CoNS) are an important cause of nosocomial bacteremia, specially in patients with indwelling devices or those submitted to invasive medical procedures. The identification of species and the accurate and rapid detection of methicillin resistance are directly dependent on the quality of the identification and susceptibility tests used, either manual or automated. The objective of this study was to evaluate the accuracy of two automated systems MicroScan and Vitek - in the identification of CoNS species and determination of susceptibility to methicillin, considering as gold standard the biochemical tests and the characterization of the mecA gene by polymerase chain reaction, respectively. MicroScan presented better results in the identification of CoNS species (accuracy of 96.8 vs 78.8%, respectively); isolates from the following species had no precise identification: Staphylococcus haemolyticus, S. simulans, and S. capitis. Both systems were similar in the characterization of methicillin resistance. The higher discrepancies for gene mec detection were observed among species other than S. epidermidis (S. hominis, S. saprophyticus, S. sciuri, S. haemolyticus, S. warneri, S. cohnii), and those with borderline MICs.

Application of biochemical and polymerase chain reaction assays for identification of Campylobacter isolates from non-human primates

A multiplex polymerase chain reaction (PCR) assay was performed on 167 thermophilic campylobacters isolated from non-human primates. Samples were first identified by phenotypic methods resulting in 64 Campylobacter jejuni and 103 C. coli strains. Four strains identified biochemically as C. coli, were then determined to be C. jejuni by PCR. Comparison of methodologies showed that the main discrepancies were attributed to the hippurate hydrolysis test and sensitivity to cephalothin and nalidixic acid. Analysis of data showed that the application of phenotypic methods should be supplemented by a molecular method to offer a more reliable Campylobacter identification.

Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2) and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2), which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

Implementation of Quantitative Reaction-based Model Refinement

Building a computational model for complex biological systems is an iterative process. It starts from an abstraction of the process and then incorporates more details regarding the specific biochemical reactions which results in the change of the model fit. Meanwhile, the model’s numerical properties such as its numerical fit and validation should be preserved. However, refitting the model after each refinement iteration is computationally expensive resource-wise. There is an alternative approach which ensures the model fit preservation without the need to refit the model after each refinement iteration. And this approach is known as quantitative model refinement. The aim of this thesis is to develop and implement a tool called ModelRef which does the quantitative model refinement automatically. It is both implemented as a stand-alone Java application and as one of Anduril framework components. ModelRef performs data refinement of a model and generates the results in two different well known formats (SBML and CPS formats). The development of this tool successfully reduces the time and resource needed and the errors generated as well by traditional reiteration of the whole model to perform the fitting procedure.

Mass transfer and reaction kinetics in single droplet systems

As reactive extraction grown more and more popular in a variety of technological applications, optimizing its performance becomes more and more important. The process of complex formation is affected by a great number of both physical and chemical properties of all the components involved, and sometimes their interference with one another makes improving the effectiveness of such processes very difficult. In this Master’s Theses, the processes of complex formation between the aqueous phase - represented by copper sulfate water solution, and organic phase – represented by Acorga M5640 solvent extractor, were studied in order to establish the effect these components have on reactive extraction performance and to determine which step is bottlenecking the process the most.

Biochemical and histological investigations of viral localisation in the hypersensitive reaction of Phaselous vulgaris L. var Pinto to tobacco mosaic virus infection

STOBBS, Lorne,W ABSTRACT Biochemical and Histological Investigations of viral localisation in the hypersensitive reaction of Phaseolus vulgaris L. var Pinto to tobacco mosaic virus infection. The infection of Phaseolus vulgaris L. var Pinto with tobacco mosaic virus (TMV) results in the production of distinct necrotic lesions confining the virus to restricted areas of the leaf surface. Biochemical and histological changes in the leaf tissue as a result of infection have been described. Trace accumulations of fluorescent metabolites, detected prior to lesion expression represent metabolites produced, by the cell in response to virus infection. These substances, are considered to undergo oxidation and in diffusing into adjacent cells, react with cellular constituents causing the death of these cells. Such cellular necrosis in advance of infection effectively limits virus spread. Chromatographic studies on extracts from TMV infected Pinto bean leaf tissue suggests that a number of extra-fluorescent metabolites produced on lesion'expression represent end products of phenolic oxidation r,eactionsoccurring earlier in these cells. Inhibition of phenolic oxidation by ascorbate infiltration or elevated temperature treatment resulted in the absence of extra-fluorescent metabolites and the continued movement of virus in the absence of necrosis. Further studies with i ascorbate infiltration indicated that irreversible necrotic events were determined as early as 12 tci 18 hrs after viral inoculation. Histochemical tests indicated that callose formation was initiated at this time, and occurred in response to necrotisation. Inhibition of necrosis by either ascorbate infiltration or elevated temp8rature treatment resulted in the absence of callose deposition. Scanning electron'micrographs of infected tissue revealed severe epidermal and palisade cell damage. Histochemical tests indicated extensive callose formation in cells bordering the lesion, and suggested the role of callose iTh the blockage of intercellular connections limiting virus movement. The significance of these cellular changes is discussed. ii

Biochemical and molecular characterization of pathogenic vibrios from hatcheries and aquaculture farms

Vibrio are important during hatchery rearing. aquaculture phase and post-harvest quality of shrimps. Vibrio spp are of concern to shrimp farmers and hatchery operators because certain species can cause Vibriosis. Vibrio species are of concern to humans because certain species cause serious diseases.With the progress in aquaculture, intensive systems used for shrimp aquaculture create an artificial environment that increases bacterial growth. To maintain the productivity of such an intensive aquaculture, high inputs of fish protein have to be employed for feeding together with high levels of water exchange and the massive use of antibiotics/ probiotics / chemicals. It seems that the combination of these conditions favours the proliferation of vibrios and enhances their virulence and disease prevalence. The risk of a microbial infection is high, mainly at larval stages. The effect and severity are related to Vibrio species and dose, water, feed, shrimp quality and aquaculture management.Consumption of seafood can occasionally result in food-bome illnesses due to the proliferation of indigenous pathogens like Vibrio.Of the l2 pathogenic Vibrio species, 8 species are known to be directly food associated. Strict quality guidelines have been laid by the importing nations, for the food products that enter their markets. The microbiological quality requirement for export of frozen shrimp products is that V.cholerae, V.parahaemolyticus and V. vulnificus should be absent in 25g of the processed shrimp (Export Inspection Council of India, 1995). The mere presence of these pathogenic Vibrios is sufficient for the rejection of the exported product.The export rejections cause serious economic loss to the shrimp industry and might harm the brand image of the shrimp products from the countiy.There is a need for an independent study on the incidence of different pathogenic vibrios in shrimp aquaculture and investigate their biochemical characteristics to have a better understanding about the growth and survival of these organisms in the shrimp aquaculture niche. PCR based methods (conventional PCR, duplex PCR, multiplex-PCR and Real Time PCR) for the detection of the pathogenic Vibrios is important for rapid post-harvest quality assessment. Studies on the genetic heterogeneity among the specific pathogenic vibrio species isolated from shrimp aquaculture system provide; valuable information on the extent of genetic diversity of the pathogenic vibrios, the shrimp aquaculture system.So the present study was undertaken to study the incidence of pathogenic Vibrio spp. in Penaeus monodon shrimp hatcheries and aquaculture farms, to carry out biochemical investigations of the pathogenic Vibrio spp isolated from P. monodon hatchery and. aquaculture environments, to assess the effect of salt (NaCl) on the growth and enzymatic activities of pathogenic Vibrio spp., to study the effect of preservatives, and chemicals on the growth of pathogenic Vibrio spp. and to employ polymerase chain reaction (PCR) methods for the detection of pathogenic V ibrio spp.Samples of water (n=7) and post-larvae (n=7) were obtained from seven Penaeus monodon hatcheries and samples of water (n=5), sediment (n=5) and shrimp (n=5) were obtained from five P. monodon aquaculture farms located on the East Coast of lndia. The microbiological examination of water, sediment, post-larvae and shrimp samples was carried out employing standard methods and by using standard media.The higher bacterial loads were obtained in pond sediments which can be attributed to the accumulation of organic matter at the pond bottom which stimulated bacterial growth.Shrimp head. (4.78 x 105 +/- 3.0 x 104 cfu/g) had relatively higher bacterial load when compared to shrimp muscle 2.7 x 105 +/- 1.95 x 104 cfu/g). ln shrimp hatchery samples, the post-larvae (2.2 x 106 +/- 1.9 x 106 cfu/g) had higher bacterial load than water (5.6 x 103 +/- 3890 cfu/ml).The mean E.coli counts were higher in aquaculture pond sediment (204+/-13 cfu/g) and pond water (124+/-88 cfu/ml). Relatively lower Escherichia coli counts were obtained from shrimp samples (12+/-11 to 16+/-16.7 cfu/g). The presence of E.coli in aquaculture environment might have been from the source water. E.coli was not detected in hatchery waters and post-larvae.

Physicochemical and Biochemical Characterization of Enzymes Immobilized on lnorganic Matrices

Biotechnology is currently considered as a useful altemative to conventional process technology in industrial and catalytic fields. The increasing awareness of the need to create green and sustainable production processes in all fields of chemistry has stimulated materials scientists to search for innovative catalysts supports. lmmobilization of enzymes in inorganic matrices is very useful in practical applications due to the preserved stability and catalytic activity of the immobilized enzymes under extreme conditions. Nanostructured inorganic, organic or hybrid organic-inorganic nanocomposites present paramount advantages to facilitate integration and miniaturization of the devices (nanotechnologies), thus affording a direct connection between the inorganic, organic and biological worlds. These properties, combined with good chemical stability, make them competent candidates for designed biocatalysts, protein-separation devices, drug delivery systems, and biosensors Aluininosilicate clays and layered double hydroxides, displaying, respectively, cation and anion exchange properties, were found to be attractive materials for immobilization because of their hydrophilic, swelling and porosity properties, as well as their mechanical and thermal stability.The aim of this study is the replacement of inorganic catalysts by immobilized lipases to obtain purer and healthier products.Mesocellular silica foams were synthesized by oil-in-water microemulsion templating route and were functionalized with silane and glutaraldehyde. " The experimental results from IR spectroscopy and elemental analysis demonstrated the presence of immobilized lipase and also functionalisation with silane and glutaraldehyde on the supports.The present work is a comprehensive study on enzymatic synthesis of butyl isobutyrate through esterification reaction using lipase immobilized onto mesocellular siliceous foams and montmorillonite K-10 via adsorption and covalent binding. Moreover, the irnrnobil-ization does not modify the nature of the kinetic mechanism proposed which is of the Bi-Bi Ping—Pong type with inhibition by n-butanol. The immobilized biocatalyst can be commercially exploited for the synthesis of other short chain flavor esters. Mesocellular silica foams (MCF) were synthesized by microemusion templating method via two different routes (hydrothermal and room temperature). and were functionalized with silane and glutaraldehyde. Candida rugosa lipase was adsorbed onto MCF silica and clay using heptane as the coupling medium for reactions in non-aqueous media. I From XRD results, a slight broadening and lowering of d spacing values after immobilization and modification was observed in the case of MCF 160 and MCF35 but there was no change in the d-spacing in the case of K-10 which showed that the enzymes are adsorbed only on the external surface. This was further confirmed from the nitrogen adsorption measurements

Organocatalytic domino reaction of cyanosulfones: access to complex cyclohexane systems with quaternary carbon centers

When ε-nitro-a,β-unsaturated esters are added to conjugated cyanosulfones in the presence of a bifunctional thiourea catalyst, a highly stereoselective domino reaction occurs to generate complex cyclohexanes with up to four stereogenic centers, one of which is quaternary in nature. Therefore, it is demonstrated that, like nitro compounds, sulfones can undergo an asymmetric intramolecular conjugate addition to r,β- unsaturated esters in the presence of a bifunctional organocatalyst.

Breakup effects in fusion and total reaction cross sections of weakly bound systems

We use a new technique to investigate the systematic behavior of near barrier complete fusion, total fusion and total reaction cross sections of weakly bound systems. A dimensionless fusion excitation function is used as a benchmark to which renormalized fusion data are compared and dynamic breakup effects can be disentangled from static effects. The same reduction procedure is used to study the effect of the direct reaction mechanisms on the total reaction cross section.

Reaction functions for weakly bound systems

We propose a new technique to analyze total reaction cross sections. In this technique, which has been previously applied to fusion reactions, the experimental data are used to build a dimensionless reaction function, which does not depend oil the system size or details of the optical potential. In this way, total reaction cross sections for different systems can be directly compared. We employ this technique to perform a systematic study of reaction cross sections of weakly bound systems in different mass ranges, and compare their reaction functions with the ones of tightly bound systems with similar masses. We show that breakup reactions and neutron transfers in halo systems lead to large reaction functions, well above the ones of typical tightly or weakly bound stable systems. (C) 2009 Elsevier B.V. All rights reserved.

Total reaction cross-sections for light weakly bound systems

We have measured the elastic scattering cross-section for (8)Li + (9)Be and (8)Li + (51)V systems at 19.6 MeV and 18.5 MeV, respectively. We have also extracted total reaction cross sections from the elastic scattering analysis for several light weakly bound systems using the optical model with Woods-Saxon and double-folding-type potentials. Different reduction methods for the total reaction cross-sections have been applied to analyze and compare simultaneously all the systems.

Reaction-diffusion systems coupled at the boundary and the Morse-Smale property

We study an one-dimensional nonlinear reaction-diffusion system coupled on the boundary. Such system comes from modeling problems of temperature distribution on two bars of same length, jointed together, with different diffusion coefficients. We prove the transversality property of unstable and stable manifolds assuming all equilibrium points are hyperbolic. To this end, we write the system as an equation with noncontinuous diffusion coefficient. We then study the nonincreasing property of the number of zeros of a linearized nonautonomous equation as well as the Sturm-Liouville properties of the solutions of a linear elliptic problem. (C) 2008 Elsevier Inc. All rights reserved.

The plant energy-dissipating mitochondrial systems: Depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots

The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved. © The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.