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Fluorescein angiography basic science and engineering.

Fluorescein angiography is an application of the physical phenomenon of fluorescence, which is phosphorescence in which the quantum mechanical decay curve is so rapid that it appears instantaneous, and it consequently has no afterglow. Sodium fluorescein is excited by light energy between 465 and 490 nm, and it decays into a lower state emitting light energy between 520 and 530 nm as fluorescent radiation. The free electrons available for excitation are reduced by chemical bonding between the fluorescein dye and plasma proteins to which up to 80% of the dye is bound in the bloodstream, thus reducing overall fluorescence. Optimalization of the observed and recorded fluorescence is afforded by providing exciter and barrier filters with as little overlap as possible to reduce or eliminate contrast reducing pseudofluorescence.

Chemical Phenomena↗

Hazardous jarosite use in developing non-hazardous product for engineering application.

Jarosite released from zinc metal extraction process is hazardous in nature and its world wide disposal has become a major environmental concern. In this study, an attempt has been made to immobilise and recycle the jarosite released from Hindustan Zinc Limited, India, using CCRs, so called fly ash, and clay soil. Results revealed that the particle size of jarosite was finer than that of CCRs and had higher porosity and water holding capacity due to fine textured materials resulting in high surface area (10,496.18 +/- 30.90 cm(2)/g). Jarosite contain higher concentration of toxic elements (lead, zinc, sulphur, cadmium, chromium and copper) than that of CCRs. Concentrations of radionuclides such as (226)Ra, (40)K and (228)Ac in jarosite found less than in CCRs are similar to that of soil. Statistically designed experiments on solidified/stabilised (s/s) sintered jarosite--CCRs products confirmed that the compressive strength of jarosite bricks reached as high as 140 kg/cm2 with 14.5% water absorption capacity at the combination of 3:1 ratio of jarosite and clay, respectively, but, concentrations of all the toxic elements recommended by United States Environmental Protection Agency (USEPA)--Toxicity Leachate Characteristics Procedure (TCLP) standard are not within the permissible limits. However, it is confirmed that the toxic elements leaching potentials of s/s-sintered products developed using 2:1 jarosite clay ratio with 15% CCRs comply with the USEPA-TCLP limits and also meet the quality for engineering applications.

Adsorption↗

Influence of particulate trap oxidizers on emission of mutagenic compounds by diesel automobiles.

Diesel exhaust particles are known to contain mutagenic and carcinogenic chemicals. The aim of this study was to determine whether, and to what extent, catalytic particulate trap oxidizers on light-duty diesel engines may reduce the emission of particle-associated mutagenic chemicals into the environment. Exhaust particles were collected from Mercedes Benz and Volkswagen diesel automobiles, equipped with or without the manufacturer's exhaust traps, while running on a chassis dynamometer under specified load conditions. Exhaust particles were collected from a dilution tunnel onto 20" X 20" Teflon-coated fiberglass filters. Mutagenesis tests of dichloromethane (DCM) extracts of the particles were conducted using the Ames Salmonella bacterial test system. The mutation rate was calculated in terms of histidine revertants per mile of travel during a set of standard test cycles. With both vehicles the traps produced an 87-92% reduction in the total amount of particulate material collected by the filters. There was no significant change in the specific mutagenic activity (revertants per microgram of DCM particle extract) with or without the traps. These studies support the notion that installation of exhaust traps which reduce particulate emission on diesel-powered vehicles will also reduce the emission of particle-associated mutagenic and carcinogenic materials into the environment.

Air Pollution↗

Structure-transport relationships in porous media.

An understanding of adsorption, transport, and reaction processes occurring within porous materials is central to the design and optimisation of chemical processing operations such as gas separations, catalysis, and soil remediation. To address many of the important questions in these areas the process engineer needs to characterise heterogeneities in both the physical and chemical properties of porous media, and to identify the importance of these properties in determining the operating characteristics of the system under consideration. In this paper three examples, each considering different types of structure-transport correlation, are discussed: (1) single and binary component adsorption processes in zeolites, (2) structure and transport heterogeneity in porous catalyst pellets, and (3) the characterisation of the interparticle space in packed beds of particles.

Magnetic Resonance Imaging↗

Site-protected fixation and immobilization of Escherichia coli cells displaying surface-anchored beta-lactamase.

Bacteria displaying heterologous receptors or enzymes on their surface hold great potential as whole-cell adsorbents and biocatalysts, respectively. For industrial applications, such surface-engineered cells need to be killed and chemically fixed to prevent disintegration and leakage of the displayed proteins under process conditions. It is also highly desirable to couple the chemically stabilized cells onto a solid support matrix for additional mechanical stability, flexibility in reactor choice, and easy separation from processed medium. Recently, we described the development of a readily scalable methodology for cell killing, fixation, and outer membrane stabilization via glutaraldehyde fixation followed by secondary crosslinking (Freeman, A., Abramov, S. and Georgiou, G. 1996. Biotechnol. Bioeng. 52: 625-630). Glutaraldehyde treatment was also found, however, to reduce the specific activity of a model enzyme, beta-lactamase displayed on the surface of E. coli. Here, we show that crosslinking carried out in the presence of beta-lactamase inhibitors, namely phenyl boronic acid or sodium borate, protects the active site from chemical modification resulting in up to threefold higher specific activities without affecting the cell-stabilizing effect of the glutaraldehyde treatment. To prepare an immobilized whole cell biocatalyst, residual unreacted surface aldehyde groups were employed to immobilize covalently the fixed bacteria onto chitosan-coated cellulose powder. The binding of the bacteria onto chitosan-coated cellulose was quantitative up to cell loading of 83 mg dry cell weight/g of support. Cell immobilization did not introduce mass transfer limitations and created only a modest reduction in Vmax. Thus, chemical crosslinking, affected in presence of reversible active-site inhibitors and coupled with cell immobilization on chitosan-coated cellulose represents a widely useful methodology for the process application of recombinant bacteria displaying surface-anchored heterologous proteins.

Biotechnology↗

Accessibility of N-acyl-D-mannosamines to N-acetyl-D-neuraminic acid aldolase.

N-Acetyl-D-neuraminic acid (NeuNAc) aldolase is an important enzyme for the metabolic engineering of cell-surface NeuNAc using chemically modified D-mannosamines. To explore the optimal substrates for this application, eight N-acyl derivatives of D-mannosamine were prepared, and their accessibility to NeuNAc aldolase was quantitatively investigated. The N-propionyl-, N-butanoyl-, N-iso-butanoyl-, N-pivaloyl-, and N-phenylacetyl-D-mannosamines proved to be as good substrates as, or even better than, the natural N-acetyl-D-mannosamine, while the N-trifluoropropionyl and benzoyl derivatives were poor. It was proposed that the electronic effects might have a significant influence on the enzymatic aldol condensation reaction of D-mannosamine derivatives, with electron-deficient acyl groups having a negative impact. The results suggest that N-propionyl-, N-butanoyl-, N-iso-butanoyl-, and N-phenylacetyl-D-mannosamines may be employed to bioengineer NeuNAc on cells.

Carbohydrate Conformation↗

The endophytic fungus Trametes hirsuta as a novel alternative source of podophyllotoxin and related aryl tetralin lignans.

The aryl tetralin lignans are synthesized by Podophyllum sps. and are in great demand worldwide due to their use in synthesis of topoisomerase inhibitors. However, the sustained production of these aryl tetralin lignans requires large-scale harvesting from the natural environments, which has resulted in the plant-endangered status. In view of the difficulties in their total chemical synthesis, cultivation and failure of metabolic engineering approaches, there is a need to search for alternative sources of production of aryl tetralin lignans. We unequivocally established the methodology for isolation, identification, and characterization of a novel fungal endophyte (Trametes hirsuta) that produces aryl tetralin lignans consistently as shown by HPLC, LC-MS, LC/MS-MS and (1)H NMR. The lignans produced by the microorganism are biologically active, and exhibit potent antioxidant, anticancer and radioprotective properties. This strategy promises to improve the production of these therapeutically important compounds at lower costs.

Cell Fractionation↗

Nucleic acid molecular switches.

Natural and artificial ribozymes can catalyse a diverse range of chemical reactions. Through recent efforts in enzyme engineering, it has become possible to tailor the activity of ribozymes to respond allosterically to specific effector compounds. These allosteric ribozymes function as effector-dependent molecular switches that could find application as novel genetic-control elements, biosensor components or precision switches for use in nanotechnology.

Allosteric Regulation↗

Prediction of posttranslational modifications using intact-protein mass spectrometric data.

We present a Web-based application that uses whole-protein masses determined by mass spectrometry to identify putative co- and posttranslational proteolytic cleavages and chemical modifications. The protein cleavage and modification engine (PROCLAME) requires as input an intact mass measurement and a precursor identification based on peptide mass fingerprinting or tandem mass spectrometry. This approach predicts mass-modifying events using a depth-first tree search, bounded by a set of rules controlled by a custom-built fuzzy logic engine, to explore a large number of possible combinations of modifications accounting for the experimental mass. Candidates are saved during a search if they are within a user-specified instrument mass accuracy; the total number of possible candidates searched is based on a specified fuzzy cutoff score. Candidates are scored and ranked using a simple probabilistic model. There is generally not enough information in an intact mass measurement to determine a single unique protein characterization; however, the program provides utility by expediting the identification of sets of putative events consistent with the mass data and ranking them for further investigation. This approach uses a simple, intuitive rule base and lends itself to discovery of unannotated posttranslational events. We have assessed the program with both in silico-generated test data and with published data from an analysis of large ribosomal subunit proteins, both from the yeast S. cerevisiae. Results indicate a high degree of sensitivity and specificity in characterizing proteins whose masses resulted from reasonable proteolysis and covalent modification scenarios. The application is available on the web at http://proclame.unc.edu.

Computational Biology↗

Effects of alpha-tocopherol, beta-carotene, and soy isoflavones on lipid oxidation of structured lipid-based emulsions.

Structured lipids (SLs) are triacylglycerols that have been modified to change the fatty acid composition and/or positional distribution in the glycerol backbone by chemically and/or enzymatically catalyzed reactions and/or genetic engineering. Ten percent oil-in-water emulsions were formulated with a canola oil/caprylic acid SL and stabilized with 0.5% whey protein isolate (WPI) or sucrose fatty acid ester (SFE). The effects of alpha-tocopherol, beta-carotene, genistein, and daidzein (added at 0.02 wt % of oil) on lipid oxidation were evaluated over a 15-day period in emulsion samples. Significantly (p < 0.05) less total oxidation (calculated from peroxide value and anisidine value measurements) occurred in the WPI emulsions compared to their SFE counterparts. In this study, alpha-tocopherol, beta-carotene, and both soy isoflavones exhibited prooxidant activities in SFE emulsions. Because of their ability to exhibit prooxidant activity under certain conditions, manufacturers must experiment with these compounds before adding them to SL-based products as functional ingredients.

Antioxidants↗

Porcine collagen crosslinking, degradation and its capability for fibroblast adhesion and proliferation.

Porcine dermal collagen permanently crosslinked with hexamethylene diisocyanate was investigated for its suitability as a dermal tissue engineering matrix. It was found that the chemically crosslinked collagen had far fewer free lysine groups per collagen molecule than did the uncrosslinked matrix. The ability of the matrix to support human primary fibroblast outgrowth from explants was compared for matrices that had been presoaked in various solutions, including fibroblast media, cysteine and phosphate buffered saline (PBS). It was found that superior cell outgrowth was obtained after soaking with fibroblast media and PBS. The fibroblast attachment properties of the matrix were compared against tissue culture plastic and PET. The collagen matrix showed the least amount of cell retention compared to the other to matrices, however, the general trends were similar for all three scaffolds. Longer term cultures on the collagen showed fibroblasts covering the matrix stacking up on each other and bridging natural hair follicles. However, it was also observed that the fibroblasts were not able to penetrate into the matrix structure. This was believed to result from the chemical crosslinking, as shown by the resistance of the matrix to degradation by collagenases.

Absorbable Implants↗

Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians.

A large family of cytotoxic cyclic peptides exemplified by the patellamides has been isolated from ascidians harboring the obligate cyanobacterial symbionts Prochloron spp.. Genome sequence analysis of these symbionts has revealed that Prochloron spp. synthesize patellamides by a ribosomal pathway. To understand how this pathway evolved to produce a suite of related metabolites, we analyzed 46 prochloron-containing ascidians from the tropical Pacific Ocean for the presence of patellamide biosynthetic genes and taxonomic markers. Here, we show that Prochloron spp. generate a diverse library of patellamides using small, hypervariable cassettes within a conserved genetic background. Each symbiont strain contains a single pathway, and mixtures of symbionts within ascidians lead to the accumulation of chemical libraries. We used this information to engineer the production of a new cyclic peptide in Escherichia coli, thereby demonstrating the power of comparative analysis of closely related symbiotic pathways to direct the genetic synthesis of new molecules.

Amino Acid Sequence↗

Combinatorial biosynthesis of antitumor indolocarbazole compounds.

Rebeccamycin and staurosporine are natural products with antitumor properties, which belong to the family of indolocarbazole alkaloids. An intense effort currently exists for the generation of indolocarbazole derivatives for the treatment of several diseases, including cancer and neurodegenerative disorders. Here, we report a biological process based on combinatorial biosynthesis for the production of indolocarbazole compounds (or their precursors) in engineered microorganisms as a complementary approach to chemical synthesis. We have dissected and reconstituted the entire biosynthetic pathway for rebeccamycin in a convenient actinomycete host, Streptomyces albus. This task was achieved by coexpressing different combinations of genes isolated from the rebeccamycin-producing microorganism. Also, a gene (staC) was identified in staurosporine-producing microbes and was shown to have a key role to differentiate the biosynthetic pathways for the two indolocarbazoles. Last, incorporation of the pyrH and thal genes, encoding halogenases from different microorganisms, resulted in production of derivatives with chlorine atoms at novel positions. We produced >30 different compounds by using the recombinant strains generated in this work.

Antineoplastic Agents↗

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Base Sequence↗

Targeted energy transfer through discrete breathers in nonlinear systems.

We propose a simple, novel mechanism for inducing highly selective and efficient energy transfer and focusing in certain discrete nonlinear systems. Under a precise condition of nonlinear resonance, when a specific amount of energy is injected as a discrete breather at a donor system, it can be transferred as a discrete breather to another weakly coupled acceptor system. This general mechanism could be relevant for energy transfer in bioenergetics and electron transfer in chemical reactions and could be used for engineering functional materials and devices.

Journal Article↗

The SAM framework: modeling the effects of management factors on human behavior in risk analysis.

Complex engineered systems, such as nuclear reactors and chemical plants, have the potential for catastrophic failure with disastrous consequences. In recent years, human and management factors have been recognized as frequent root causes of major failures in such systems. However, classical probabilistic risk analysis (PRA) techniques do not account for the underlying causes of these errors because they focus on the physical system and do not explicitly address the link between components' performance and organizational factors. This paper describes a general approach for addressing the human and management causes of system failure, called the SAM (System-Action-Management) framework. Beginning with a quantitative risk model of the physical system, SAM expands the scope of analysis to incorporate first the decisions and actions of individuals that affect the physical system. SAM then links management factors (incentives, training, policies and procedures, selection criteria, etc.) to those decisions and actions. The focus of this paper is on four quantitative models of action that describe this last relationship. These models address the formation of intentions for action and their execution as a function of the organizational environment. Intention formation is described by three alternative models: a rational model, a bounded rationality model, and a rule-based model. The execution of intentions is then modeled separately. These four models are designed to assess the probabilities of individual actions from the perspective of management, thus reflecting the uncertainties inherent to human behavior. The SAM framework is illustrated for a hypothetical case of hazardous materials transportation. This framework can be used as a tool to increase the safety and reliability of complex technical systems by modifying the organization, rather than, or in addition to, re-designing the physical system.

Accidents, Traffic↗

Gene integration and expression and extracellular secretion of Erwinia chrysanthemi endoglucanase CelY (celY) and CelZ (celZ) in ethanologenic Klebsiella oxytoca P2.

The development of methods to reduce costs associated with the solubilization of cellulose is essential for the utilization of lignocellulose as a renewable feedstock for fuels and chemicals. One promising approach is the genetic engineering of ethanol-producing microorganisms that also produce cellulase enzymes during fermentation. By starting with an ethanologenic derivative (strain P2) of Klebsiella oxytoca M5A1 with the native ability to metabolize cellobiose, the need for supplemental beta-glucosidase was previously eliminated. In the current study, this approach has been extended by adding genes encoding endoglucanase activities. Genes celY and celZ from Erwinia chrysanthemi have been functionally integrated into the chromosome of P2 using surrogate promoters from Zymomonas mobilis for expression. Both were secreted into the extracellular milieu, producing more than 20,000 endoglucanase units (carboxymethyl cellulase activity) per liter of fermentation broth. During the fermentation of crystalline cellulose with low levels of commercial cellulases of fungal origin, these new strains produced up to 22% more ethanol than unmodified P2. Most of the beneficial contribution was attributed to CelY rather than to CelZ. These results suggest that fungal enzymes with substrate profiles resembling CelY (preference for long-chain polymers and lack of activity on soluble cello-oligosaccharides of two to five glucosyl residues) may be limiting in commercial cellulase preparations.

Base Sequence↗