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PubMed1999

[Action of hydrostatic pressure on proteins: emergence of high pressure biotechnology, potential pharmaceutical and medical applications].

High pressure engineering of proteins is an emerging biotechnology. The role of pressure in the control of protein stability and reactivity is reviewed. It is shown that a better understanding of the behavior of proteins under extreme pressure and temperature conditions may help to improve biochemical processes under non conventional medial/conditions for enzyme-catalyzed production of fine chemicals and the use of modified proteins of medical or pharmaceutical interest. Moreover, high pressure can be used instead of heart or chemicals for sterilization.

Biomedical Engineering↗
PubMed2005

Foundations for engineering biology.

Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. Unfortunately, our ability to quickly and reliably engineer biological systems that behave as expected remains quite limited. Foundational technologies that make routine the engineering of biology are needed. Vibrant, open research communities and strategic leadership are necessary to ensure that the development and application of biological technologies remains overwhelmingly constructive.

Biological Evolution↗
PubMed2005

Hyaluronan and sulphated hyaluronan micropatterns: effect of chemical and topographic cues on lymphatic endothelial cell alignment and proliferation.

While tissue engineered blood vessels have entered surgical practice, the construction of artificial lymphatic vessels has never been attempted due to the small dimensions and fragility of lymphatic vessels. A possible alternative would be to obtain a new growth of interrupted lymphatic vessels. We have previously reported that lymphatic endothelial cells align when cultured on striped micropatterns of hyaluronan (Hyal) and aminosilanized glass. We here report a comparative study in which lymphatic endothelial cells have been plated on micropatterns with stripes of different width and height obtained by the photoimmobilization of Hyal and its sulphated derivative (HyalS) on aminosilanized glass to verify whether their response correlated with surface-chemistry andlor topography. On Hyal micropatterns, cells adhered to aminosilanized glass, avoiding Hyal stripes and molding their shape in accordance to the micropattern topography. Stress fibers, integrins and focal adhesion kinase organized accordingly. HyalS micropatterns with the same topography were unable to guide cell response, cells randomly adhered to HyalS and glass stripes, and polarization was attained only by increasing stripe height. These data indicate that surface chemistry is the main cue responsible for lymphatic endothelial cell guidance. When surface chemistry of stripes promotes cell adhesion as well as that of the substrate, topographical parameters become prevalent. Micropatterns with defined chemical and topographical properties may contribute to the design of new platforms for controlled cell growth in tissue engineering of lymphatic vessels.

Actins↗
PubMedDate not supplied

The use of biosensor technology for the engineering of antibodies and enzymes.

Recently developed scientific instrumentation featuring surface plasmon resonance detection allows the detection of biomolecular interactions in real time and without chemical modification of the binding partners. These biosensors are proving invaluable tools in protein engineering, particularly in research aimed at the isolation and improvement of protein binders and catalysts from macromolecular repertoires containing billions of individual members. This article reviews the use of biosensor technology for the isolation and characterization of engineered antibodies and enzymes.

Animals↗
PubMed2001

Reverse engineering of metabolic pathways from observed data using genetic programming.

Recent work has demonstrated that genetic programming is capable of automatically creating complex networks (such as analog electrical circuits and controllers) whose behavior is modeled by linear and non-linear continuous-time differential equations and whose behavior matches prespecified output values. The concentrations of substances participating in networks of chemical reactions are also modeled by non-linear continuous-time differential equations. This paper demonstrates that it is possible to automatically create (reverse engineer) a network of chemical reactions from observed time-domain data. Genetic programming starts with observed time-domain concentrations of input substances and automatically creates both the topology of the network of chemical reactions and the rates of each reaction within the network such that the concentration of the final product of the automatically created network matches the observed time-domain data. Specifically, genetic programming automatically created metabolic pathways involved in the phospholipid cycle and the synthesis and degradation of ketone bodies.

Biomedical Engineering↗
PubMed2001

A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering.

A mixed-integer linear program (MILP) is described that can enumerate all the ways fluxes can distribute in a metabolic network while still satisfying the same constraints and objective function. The multiple solutions can be used to (1) generate alternative flux scenarios that can account for limited experimental observations, (2) forecast the potential responses to mutation (e.g., new reaction pathways may be used), and (3) (as illustrated) design (13)C NMR experiments such that different potential flux patterns in a mutant can be distinguished. The experimental design is enabled by using the MILP results as an input to an isotopomer mapping matrices (IMM)-based program, which accounts for the network circulation of (13)C from a precursor such as glucose. The IMM-based program can interface to common plotting programs with the result that the user is provided with predicted NMR spectra that are complete with splittings and Lorentzian line-shape features. The example considered is the trafficking of carbon in an Escherichia coli mutant, which has pyruvate kinase activity deleted for the purpose of eliminating acetate production. Similar yields and extracellular measurements would be manifested by the flux alternatives. The MILP-IMM results suggest how NMR experiments can be designed such that the spectra of glutamate for two flux distribution scenarios differ significantly.

Algorithms↗
PubMed2003

A metabolic network analysis & NMR experiment design tool with user interface-driven model construction for depth-first search analysis.

A Windows program for metabolic engineering analysis and experimental design has been developed. A graphical user interface enables the pictorial, "on-screen" construction of a metabolic network. Once a model is composed, balance equations are automatically generated. Model construction, modification and information exchange between different users is thus considerably simplified. For a given model, the program can then be used to predict all the extreme point flux distributions that optimize an objective function while satisfying balances and constraints by using a depth-first search strategy. One can also find the minimum reaction set that satisfies different conditions. Based on the identified flux distributions or linear combinations, the user can simulate the NMR and GC/MS spectra of selected signal molecules. Alternately, spectra vectorization allows for the automated optimization of labeling experiments that are intended to distinguish between different, yet plausible flux extreme point distributions. The example provided entails predicting the flux distributions associated with deleting pyruvate kinase and designing 13C NMR experiments that can maximally discriminate between the flux distributions.

Computer Simulation↗
PubMed2005

Depopulated bovine ureteric xenograft for complex haemodialysis vascular access.

OBJECTIVES: To assess performance of a de-cellularised bovine ureter vascular graft for haemodialysis in patients for whom conventional access was not possible. METHODS: The Syner Graft Vascular Graft Model 100 (SGVG 100) is a bovine ureter modified by a tissue-engineering depopulation technology and uniquely it is not chemically cross-linked. SGVG 100 was implanted in patients with a failed fistula or vascular access grafts. Graft patency was the primary outcome; secondary outcomes included adverse events and associated treatments. RESULTS: 25 SGVG 100 were implanted in 23 patients; mean age was 59+/-14 years. Mean follow-up was 370 days. The mean time to occlusion (19 events) was 215+/-141 days with patency re-established in 14 of 18 surgical interventions. Thirty angioplasties were performed on 14 SGVG 100 for luminal/anastomotic stenosis. Two grafts demonstrated areas of dilation; however, both grafts continue to be usable at last reported follow-up (930 and 602 days) with no further changes in graft size. Primary patency, assisted primary patency, secondary patency, and freedom from infection were 29, 45, 81, and 95% at 1 year, respectively. CONCLUSIONS: This report demonstrates SGVG 100 is a stable vascular access conduit, providing a suitable graft alternative when autologous vein is not available.

Adult↗
PubMed2006

Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study.

Cytochrome P450 BM-3 from Bacillus megaterium is an extensively studied enzyme for industrial applications. A major focus of current protein engineering research is directed to improving the catalytic performance of P450 BM-3 toward nonnatural substrates of industrial importance in the presence of organic solvents or cosolvents. For the latter reason, it is important to study the effect of organic cosolvent molecules on the structure and dynamics of the enzyme, in particular, the effect of cosolvent molecules on the active site's structure and dynamics. In this paper, we have studied, using molecular dynamics (MD) simulations, the F87A mutant of P450 BM-3 in the presence of DMSO as cosolvent, to understand the role of the F87A substitution for its catalytic activity. This mutant exhibits an altered regioselectivity and substrate specificity compared with wild-type; however, it has lower tolerance toward DMSO. The simulation results offer an explanation for the DMSO sensitivity of the F87A mutant. Our simulation results show that the F87 side chain prevents the disturbance of the water molecule bound to the heme iron by DMSO molecules. The absence of the phenyl ring in F87A mutant promotes interactions of the DMSO molecule with the heme iron resulting in water displacement by DMSO at the catalytic heme center.

Bacillus megaterium↗
PubMed2002

Protein engineering of oxygenases for biocatalysis.

Oxygenase enzymes have seen limited practical applications because of their complexity, poor stabilities, and often low catalytic rates. However, their ability to perform difficult chemistry with high selectivity and specificity has kept oxygenases at the forefront of engineering efforts. Growing understanding of structure-function relationships and improved protein engineering methods are paving the way for applications of oxygenases in chemical synthesis and bioremediation.

Animals↗
PubMed1999

Turning over a new leaf. Tobacco.

Anticipating a diminishing market for cigarettes and other tobacco products in the future, researchers around the country are studying alternative uses for tobacco plants. The most promising field of research for tobacco involves the genetic engineering of tobacco plants to produce various substances such as industrial chemicals, pharmaceuticals, and consumer product ingredients. Tobacco has been called the "fruit fly of the plant kingdom" because of the ease with which it can be genetically engineered. There are countless possibilities for the use of tobacco, but current efforts are concentrating on engineering tobacco to produce vaccines, human enzymes, and plastics. Tobacco researchers have been successful in expressing bovine lysozyme, an enzyme with antibacterial properties, and insulin.

Biotechnology↗
PubMed2007

Synthesis and characterization of the novel transfection reagent poly(amino ester glycol urethane).

Poly(ester urethane) (PEU) is a class of biodegradable polymer that has been applied as tissue-engineering scaffolds with minimum toxicity. Despite its unique biocompatibility, there have been no reports in modifying the PEU backbone to design a soluble, PEU-based DNA carrier. We have developed a method of incorporating tertiary amines and poly(ethylene glycol) (PEG) into PEU to synthesize a soluble poly(amino ester glycol urethane) (PaEGU) as a novel transfection reagent. Parallel to this, we have synthesized poly(amino ester) (PaE) and poly(amino ester urethane) (PaEU) as the control polymers. The test transfection reagent PaEGU and the control PaE were similar in their properties of being soluble and buffering pH in water and their capabilities of self-assembling with DNA and transfecting the target cells. Significantly, PaEGU exhibited faster hydrolysis kinetics than PaE, half-lives of 19 and 36 h for PaEGU and PaE, respectively, underlying PaEGU's unique property of low cytotoxicity. However, in comparison to PaEGU, the other control polymer, PaEU, was not readily dissolved in water, indicating the importance of PEG units in PaEGU in increasing polymer hydrophilicity. This study demonstrated a useful synthesis scheme for the PEU-based transfection reagent PaEGU. The combination of tertiary amine, ester, PEG, and urethane units in the polymer backbone constitutes a feasible approach for the future design of low-toxicity gene transfer vectors.

Biocompatible Materials↗
PubMed2003

Metabolic engineering for improved fermentation of pentoses by yeasts.

The fermentation of xylose is essential for the bioconversion of lignocellulose to fuels and chemicals, but wild-type strains of Saccharomyces cerevisiae do not metabolize xylose, so researchers have engineered xylose metabolism in this yeast. Glucose transporters mediate xylose uptake, but no transporter specific for xylose has yet been identified. Over-expressing genes for aldose (xylose) reductase, xylitol dehydrogenase and moderate levels of xylulokinase enable xylose assimilation and fermentation, but a balanced supply of NAD(P) and NAD(P)H must be maintained to avoid xylitol production. Reducing production of NADPH by blocking the oxidative pentose phosphate cycle can reduce xylitol formation, but this occurs at the expense of xylose assimilation. Respiration is critical for growth on xylose by both native xylose-fermenting yeasts and recombinant S, cerevisiae. Anaerobic growth by recombinant mutants has been reported. Reducing the respiration capacity of xylose-metabolizing yeasts increases ethanol production. Recently, two routes for arabinose metabolism have been engineered in S. cerevisiae and adapted strains of Pichia stipitis have been shown to ferment hydrolysates with ethanol yields of 0.45 g g(-1) sugar consumed, so commercialization seems feasible for some applications.

Aerobiosis↗
PubMed2007

The stability of engineered thermostable neutral proteases from Bacillus stearothermophilus in organic solvents and detergents.

Engineered extremely thermostable variants of the thermolysin-like protease from Bacillus stearothermophilus possessing an introduced disulfide bond G8C/N60C (double mutant, DM) and six additional amino acid substitutions in the exposed loop region 56-69 (Boilysin, BLN) have been probed with respect to stability toward water-miscible organic solvents and detergents. The solvent concentrations where 50% of enzyme activity were irreversibly lost (C(50)) decreased in the order methanol > 2-propanol > dimethylsulfoxide > dioxane > acetonitrile > dimethylformamide > acetone. The C(50) values were remarkably higher for the thermostable variants than for the wild-type enzymes. Therefore, the stabilization of this loop region also protects the molecule from irreversible inactivation by solvents, and inactivation seems to follow principally the same mechanism as thermal inactivation. However, in contrast to thermal inactivation where the corresponding T(50) values of DM and BLN differed by 10 K, the differences of the C(50) values of DM and BLN were not significant. Detergents had great effects on proteolytic activities which were dependent on the individual detergent and its concentration, but mostly without significant differences between the enzyme variants. These effects were inactivating (SDS, sulfobetaine) or strongly activating (CTAB, CHAPS). Triton X-100 and Tween 20 were activating or inactivating at low and high concentrations, respectively. In all detergents, stabilities of the enzymes were strongly decreased. However, the more thermostable variants were affected by the detergents to the same extent as the wild-type enzymes suggesting that the mechanism of detergent inactivation is different from that of thermal inactivation.

Amino Acid Sequence↗
PubMed2005

Histological evaluation of decellularised porcine aortic valves: matrix changes due to different decellularisation methods.

OBJECTIVE: Several decellularisation techniques have been developed to produce acellular matrix scaffolds for the purpose of tissue engineering, mostly comprising (non-)ionic detergents or enzymatic extraction methods. However, the effect of chemically induced decellularisation on the major structural and adhesion molecules as well as glycosaminoglycans, and the possible replenishment of lost compounds have escaped attention. METHODS: Porcine aortic valves were treated with two different methods: detergent Triton X-100 and enzymatic Trypsine cell extraction. (Immuno-) histochemistry was used to address changes in extracellular matrix constitution (elastin, collagen, glycosaminoglycans, chondroitin sulfate, fibronectin and laminin) and the production of extracellular matrix components by seeded endothelial cells. RESULTS: The Trypsine treated group showed a fragmentation and distortion of elastic fibers. Changes in collagen distribution were observed in both groups. An almost complete washout of glycosaminoglycans and chondroitin sulfate was observed in the Triton and Trypsin treated group, but the latter with a smaller glycosaminoglycans reduction. Both treatments resulted in a considerable washout of the adhesion molecules laminin and fibronectin. Furthermore, seeded endothelial cells were capable of synthesising laminin, fibronectin and chondroitin sulfate. CONCLUSIONS: Chemically induced decellularisation by Triton or Trypsine resulted in changes in the extracellular matrix constitution, which could lead to problems in valve functionality and cell growth and migration. Seeded endothelial cells were capable of synthesising extracellular matrix components lost by cell extraction. Further studies on tissue engineering should focus more on the effect of chemically induced cell extraction on the extracellular matrix of the remaining scaffold and the in vitro or in vivo replenishment of lost compounds.

Animals↗
PubMed1996

Hammerhead ribozyme engineering.

Of all the catalytic RNAs the hammerhead ribozyme is the most chemically modified and structurally studied. Such studies have resulted in improvements in the nuclease resistance of ribozymes, reductions in their size, and improvements in their catalytic efficiency. These improvements have facilitated the use of ribozymes for therapeutic applications, and have allowed us to study how the three-dimensional structure of the enzyme and its array of functional groups interact to create a catalytic site where a phosphodiester bond is cleaved.

Base Sequence↗
PubMed2004

Fibrillation of carrier protein albebetin and its biologically active constructs. Multiple oligomeric intermediates and pathways.

We showed that the genetically engineered carrier-protein albebetin and its biologically active constructs with interferon-alpha(2) octapeptide LKEKKYSP or differentiation factor hexapeptide TGENHR are inherently highly amyloidogenic at physiological pH. The kinetics of fibrillation were monitored by thioflavine-T (ThT) binding and the morphological changes by atomic force microscopy. Fibrillation proceeds via multiple pathways and includes a hierarchy of amyloid structures ranging from oligomers to protofilaments and fibrils. Comparative height and volume microscopic measurements allowed us to identify two distinct types of oligomeric intermediates: pivotal oligomers ca. 1.2 nm in height comprised of 10-12 monomers and on-pathway amyloid-competent oligomers ca. 2 nm in height constituted of 26-30 molecules. The former assemble into chains and rings with "bead-on-string morphology", in which a "bead" corresponds to an individual oligomer. Once formed, the rings and chains remain in solution simultaneously with fibrils. The latter give rise to protofilaments and fibrils, and their formation is concomitant with an increasing level of ThT binding. The amyloid nature of filamentous structures was confirmed by a pronounced ThT and Congo red binding and beta-sheet-rich far-UV circular dichroism. We suggest that transformation of the pivotal oligomers into the amyloid-prone ones is a limiting stage in amyloid assembly. Peptides, either fused to albebetin or added into solution, and an increased ionic strength promote fibrillation of albebetin (net charge of -12) by counterbalancing critical electrostatic repulsions. This finding demonstrates that the fibrillation of newly designed polypeptide-based products can produce multimeric amyloid species with a potentially "new" functionality, raising questions about their safety.

Amyloid↗
PubMed2003

An experimental study of the regeneration of the intervertebral disc with an allograft of cultured annulus fibrosus cells using a tissue-engineering method.

STUDY DESIGN: Cultured annulus fibrosus cells within an atelocollagen honeycomb-shaped scaffold with a membrane seal were allografted into the lacunas of intervertebral discs of which the nucleus pulposus had been vaporized using an indocyanine green dye-enhanced laser. Regeneration of the intervertebral disc was assessed based on the viability and histologic status of the allografted annulus fibrosus cells, as well as the prevention of narrowing disc space. OBJECTIVES: To study the regeneration of intervertebral disc after laser discectomy using tissue-engineering methods. SUMMARY OF BACKGROUND DATA: Intervertebral disc is the most avascular tissue in the human body, and its ability to regenerate is as low as that of articular cartilage. When nucleotomy is carried out, little regeneration of the annulus fibrosus is observed; consequently, intervertebral disc degeneration is inevitable. METHODS: Annulus fibrosus cells isolated from 20 Japanese white rabbits were labeled with a PKH-26 fluorescent dye and seeded within an atelocollagen honeycomb-shaped scaffold with a membrane seal. Annulus fibrosus cells cultured in atelocollagen honeycomb-shaped scaffold with a membrane seal for 1 week were allografted into the lacunas of intervertebral discs of recipient rabbit of which the nucleus pulposus had been vaporized using an ICG dye-enhanced laser. Soft radiograph photographs of the lumbar spine of these anesthetized rabbits were taken, the disc space measured, and the lumbar spine extracted 2, 4, 8, and 12 weeks after the operation. The proliferation of allografted annulus fibrosus cells with 5-bromo-2'-deoxyuridine/PKH-26 fluorescent labels was assessed using consecutive frozen sections, and safranin-O staining carried out for histologic evaluation. RESULTS: The allografted annulus fibrosus cells were viable and showed proliferation activity with a hyaline-like cartilage being produced. The narrowing of the intervertebral disc space of the cell translation group was significantly prevented, as shown, up to 12 postoperative weeks. CONCLUSION: The annulus fibrosus cells cultured in an ACHMS-scaffold were allografted into the lacunae of nucleus pulposus (obtained using laser vaporization), as well as the hole of annulus fibrosus (obtained by laser fiber insertion) of rabbit intervertebral discs. These cells were viable and showed cell proliferation in the disc tissues of recipients.

Animals↗