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Surface engineering approaches to micropattern surfaces for cell-based assays.

The ability to produce patterns of single or multiple cells through precise surface engineering of cell culture substrates has promoted the development of cellular bioassays that provide entirely new insights into the factors that control cell adhesion to material surfaces, cell proliferation, differentiation and molecular signaling pathways. The ability to control shape and spreading of attached cells and cell-cell contacts through the form and dimension of the cell-adhesive patches with high precision is important. Commitment of stem cells to different specific lineages depends strongly on cell shape, implying that controlled microenvironments through engineered surfaces may not only be a valuable approach towards fundamental cell-biological studies, but also of great importance for the design of cell culture substrates for tissue engineering. Furthermore, cell patterning is an important tool for organizing cells on transducers for cell-based sensing and cell-based drug discovery concepts. From a material engineering standpoint, patterning approaches have greatly profited by combining microfabrication technologies, such as photolithography, with biochemical functionalization to present to the cells biological cues in spatially controlled regions where the background is rendered non-adhesive ("non-fouling") by suitable chemical modification. The focus of this review is on the surface engineering aspects of biologically motivated micropatterning of two-dimensional (flat) surfaces with the aim to provide an introductory overview and critical assessment of the many techniques described in the literature. In particular, the importance of non-fouling surface chemistries, the combination of hard and soft lithography with molecular assembly techniques as well as a number of less well known, but useful patterning approaches, including direct cell writing, are discussed.

Adsorption↗

A study of the specificity of barley chymotrypsin inhibitor 2 by cysteine engineering of the P1 residue.

A combination of oligonucleotide-directed mutagenesis and chemical modification was used to produce reactive site (P1) variants of chymotrypsin inhibitor II (CI2) in an attempt to create more potent inhibitors and examine inhibitory specificity. Mutagenesis to introduce a unique cysteine (CI2M59C) followed by modification to S-carboxamidocysteine with iodoacetamide produced a 7-fold more potent inhibitor of subtilisin BPN' than the wild type inhibitor. Modification with iodoacetic acid, which gives a negatively charged P1 residue (S-carboxymethylcysteine), generates a weaker inhibitor of subtilisin BPN' and chymotrypsin. Further chemical modification experiments of CI2M59C with a series of iodoalkanes of increasing chain lengths was used to determine the optimal P1 side chain length required for potent inhibition of porcine pancreatic elastase. A trend was observed which implies that for CI2 the original methionine residue or its isostere S-ethylcysteine are most effective residues at this position and not alanine as might have been expected from the substrate specificity. The mutant CI2M59C did not inhibit human neutrophil elastase. The iodoalkane modifications not only resulted in recovery of inhibitory activity but also proved to be substantially more potent inhibitors of human neutrophil elastase than wild-type CI2.

Chymotrypsin↗

Engineering of improved microbes and enzymes for bioremediation.

Bioremediation with microorganisms is an attractive alternative to conventional techniques, such as incineration and chemical treatment, for disposing of pollutants. Recent progress in molecular biology, microbiology, and genetics is providing the driving force towards engineering improved microbes and enzymes for bioremediation. A number of genetic engineering approaches have been developed in the past several years that have proven useful in introducing/evolving the desired properties for different biodegradative pathways or enzymes. The initial excitement generated in this area should continue to pave the way for rational or irrational design of microbes or enzymes with novel remedial properties.

Amino Acid Sequence↗

Effects of chlorinated aliphatic hydrocarbons on the fidelity of cell division in human CYP2E1 expressing cells.

Chlorinated organic chemicals are widely used in industry and are present in the environment. Five chlorinated aliphatic hydrocarbons, namely 1-2-dichloroethane, 1,1,2-trichloroethane, trichloroethylene, 2,3-dichlorobutane and 1-chlorohexane were investigated to determine their influence upon the fidelity of cell division in cultured mammalian cells. In order to determine the influence of these chemical compounds upon the fidelity of cell division, a technique known as differential staining of chromosomes and spindle was performed with one genetically engineered cell line and its parental cell line. The genetically engineered cell line used in this study expressed a human P450 enzyme, CYP2E1. Four chemicals, 1-2-dichloroethane, trichloroethylene, 2,3-dichlorobutane and 1-chlorohexane required metabolic bioactivations in order to induce spindle damage in cultured mammalian cells whereas 1,1,2-trichloroethane was a direct-acting spindle poison.

Animals↗

Characterization of bottom ash in municipal solid waste incinerators for its use in road base.

Incineration of municipal solid wastes (MSWs) produces by-products which can be broadly classified as bottom and fly ashes. Since MSW incineration started, possibilities other than landfilling the incineration residues have been sought; most initiatives in this sense tend to use these residues as aggregate substitute in pavements and other road construction elements. The main goal of the present work is the physical and chemical characterization of the local incineration bottom ash towards its eventual re-utilization. The study includes not only the specific aspects regarding its role as pavement element, but also the assessment of the environmental effects. Therefore, together with the determination of physical (moisture content, apparent and bulk densities, crystallinity, etc.) and engineering properties (particle size distribution, abrasion and impact resistance, etc.), full chemical characterization of the bottom ash and the study of leaching as a function of aging time have been undertaken. The results obtained indicate that the metal content of both the raw bottom ash and its leachates fulfill the environmental regulations provided that the bottom ash is stored for at least one month. Engineering properties of the bottom ash are close to those of natural aggregates and, thus, road-construction use of these residues seems to be feasible.

Compressive Strength↗

Protein engineering study of protein L by simulation.

We examine the ability of our recently introduced minimalist protein model to reproduce experimentally measured thermodynamic and kinetic changes upon sequence mutation in the well-studied immunoglobulin-binding protein L. We have examined five different sequence mutations of protein L that are meant to mimic the same mutation type studied experimentally: two different mutations which disrupt the natural preference in the beta-hairpin #1 and beta-hairpin #2 turn regions, two different helix mutants where a surface polar residue in the alpha-helix has been mutated to a hydrophobic residue, and a final mutant to further probe the role of nonnative hydrophobic interactions in the folding process. These simulated mutations are analyzed in terms of various kinetic and thermodynamic changes with respect to wild type, but in addition we evaluate the structure-activity relationship of our model protein based on the phi-value calculated from both the kinetic and thermodynamic perspectives. We find that the simulated thermodynamic phi-values reproduce the experimental trends in the mutations studied and allow us to circumvent the difficult interpretation of the complicated kinetics of our model. Furthermore, the level of resolution of the model allows us to directly predict what experiments seek in regard to protein engineering studies of protein folding--namely the residues or portions of the polypeptide chain that contribute to the crucial step in the folding of the wild-type protein.

Bacterial Proteins↗

Development of metabolically engineered Saccharomyces cerevisiae cells for the production of lactic acid.

Interesting challenges from metabolically engineered Saccharomyces cerevisiae cells arise from the opportunity to obtain yeast strains useful for the production of chemical(s). In this paper, we describe the accumulation of lactic acid in the culture medium of growing, engineered yeast cells expressing a mammalian lactate dehydrogenase gene (LDH-A). High and reproducible productions (20 g/L) and productivities (up to 11 g/L/h) of lactic acid have been obtained by modulating the physiological growth conditions. Since yeast cells are acid tolerant and survive at very low pH values, the production of lactate can be avoided. In perspective, the approaches described could be useful for the production of lactic acid, outflanking the problems related to the synthesis from bacteria cells. In fact, during industrial productions, there is an inhibitory effect on the metabolic activities of the growing bacteria (i.e., Lactobacillus spp.) caused by the acid produced and by the low pH value. Thus, strategies to prevent the lowering of pH are conventional operations. These processes allow the production of lactate(s) and require the purification of the acid from its salt. The biotechnological implications of this study are also discussed.

Animals↗

Evaluation of emission toxicity of urban bus engines: compressed natural gas and comparison with liquid fuels.

Emissions from a spark-ignition (SI) heavy-duty (HD) urban bus engine with a three-way catalyst (TWC), fuelled with compressed natural gas (CNG), were chemically analyzed and tested for genotoxicity. The results were compared with those obtained in a previous study on an equivalent diesel engine, fuelled with diesel oil (D) and a blend of the same with 20% vegetable oil (B20). Experimental procedures were identical, so that emission levels of the CNG engine were exactly comparable to the ones of the diesel engine. The experimental design was focused on carcinogenic compounds and genotoxic activity of exhausts. The results obtained show that the SI CNG engine emissions, with respect to the diesel engine fuelled with D, were nearly 50 times lower for carcinogenic polycyclic aromatic hydrocarbons (PAHs), 20 times lower for formaldehyde, and more than 30 times lower for particulate matter (PM). A 20-30 fold reduction of genotoxic activity was estimated from tests performed. A very high reduction of nitrogen oxides (NO(X)) was also measured. The impact of diesel powered transport on urban air quality, and the potential benefits deriving from the use of CNG for public transport, are discussed.

Air Pollutants↗

Studies on the biosynthesis of antibiotics.

In the framework of studies on the biosynthesis of several antibiotics, specifically asukamycin, acarbose, reductiomycin, actinorhodin, and granaticin, a variety of different approaches to biosynthetic problems are illustrated. These include multiple labeling with stable isotopes in conjunction with modern methods of nmr analysis, as illustrated by the development of a new triple-quantum 2D-INADEQUATE experiment for biosynthetic studies, the use of stereochemical probes, as illustrated by the synthesis and stereochemical analysis of chiral [13C, 2H]malonate, and combinations of genetic and chemical approaches, as illustrated by examples of the production of new hybrid antibiotics by genetic engineering.

Anti-Bacterial Agents↗

Ex planta phytoremediation of trichlorophenol and phenolic allelochemicals via an engineered secretory laccase.

Plant roots release a range of enzymes capable of degrading chemical compounds in their immediate vicinity. We present a system of phytoremediation ex planta based on the overexpression of one such enzyme, a secretory laccase. Laccases catalyze the oxidation of a broad range of phenolic compounds, including polychlorinated phenols such as 2,4,6-trichlorophenol (TCP), that are among the most hazardous and recalcitrant pollutants in the environment. We isolated a secretory laccase cDNA of LAC1, which is specifically expressed in the roots of Gossypium arboreum (cotton). Transgenic Arabidopsis thaliana plants overexpressing LAC1 exhibited enhanced resistance to several phenolic allelochemicals and TCP. The secretory laccase activity in these plants was responsible for the conversion of sinapic acid into a mono-lactone type dimer and for the transformation of TCP.

Arabidopsis↗

Mice with the enhanced green fluorescent protein gene knocked in to chromosome 11 exhibit normal transmission ratios.

Meiotic recombination between homologous chromosomes can be suppressed within a chosen segment by a regional inversion. In mice, this feature can be engineered and conveniently used in genetic screens to maintain chemically induced mutations within the homologous chromosome. The efficiency of an inversion-based mutagenesis screen can be substantially enhanced provided that the inversion chromosome and its wild-type (WT) homologue are both visibly tagged by two different coat color markers. Dual tagging eliminates labor associated with molecular genotyping. Previously, we reported the generation of the In(11)10Brd strain of mice carrying K14-agouti tagging a 30-cM inversion between the Trp53 and Egfr loci on mouse chromosome 11. Since K14-agouti causes yellowing of ears and tails, the In(11)10Brd mice are easily distinguishable from their WT littermates. In this paper, we describe the construction of a second strain of mice that carry the enhanced green fluorescent protein (EGFP) transgene at the Egfr locus. The EGFP carriers are visually recognizable by emitting green fluorescent light upon UV illumination. We found that the EGFP function was transmitted from one generation to another with expected Mendelian frequencies, and no detrimental effects of EGFP expression were detected in hemizygous or homozygous animals. The EGFP mice together with the previously generated In(11)10Brd inversion carriers constitute a complete set of reagents required for initiation of a regional ENU mutagenesis screen to address functionally more than one-third of mouse chromosome 11.

Animals↗

In-situ investigation of the adsorption of globular model proteins on stimuli-responsive binary polyelectrolyte brushes.

Binary brushes constituted from two incompatible polymers can be used in the form of ultrathin polymeric layers as a versatile tool for surface engineering to tune physicochemical surface characteristics such as wettability, surface charge, chemical composition, and morphology and furthermore to create responsive surface properties. Mixed brushes of oppositely charged weak polyelectrolytes represent a special case of responding surfaces that are sensitive to changes in the pH value of the aqueous environment and therefore represent interesting tools for biosurface engineering. The polyelectrolyte brushes used for this study were composed of two oppositely charged polyelelctrolytes poly(2-vinylpyridine) (P2VP) and poly(acrylic acid) (PAA). The in-situ properties and surface characteristics such as as surface charge, surface tension, and extent of swelling of these brush layers are functions of the pH value of the surrounding aqueous solution. To test the behavior of the mixed polylelctrolyte brushes in contact with biosystems, protein adsorption experiments with globular model proteins were performed at different pH values and salt concentrations (confinement of counterions) of the buffer solutions. The influence of the pH value, buffer salt concentration, and isoelectric points (IEP) of the brush and protein on the adsorbed amount and the interfacial tension during protein adsorption as well as the protein adsorption mechanism postulated in reference to recently developed theories of protein adsorption on polyelectrolyte brushes is discussed. In the salted regime, protein adsorption was found to be similar to the often-described adsorption at hydrophobic surfaces. However, in the osmotic regime the balance of electrostatic repulsion and a strong entropic driving force, "counterion release", was found to be the main influence on protein adsorption.

Acrylic Resins↗

Incremental truncation as a strategy in the engineering of novel biocatalysts.

The application and success of combinatorial approaches to protein engineering problems have increased dramatically. However, current directed evolution strategies lack a combinatorial methodology for creating libraries of hybrid enzymes which lack high homology or for creating libraries of highly homologous genes with fusions at regions of non-identity. To create such hybrid enzyme libraries, we have developed a series of combinatorial approaches that utilize the incremental truncation of genes, gene fragments or gene libraries. For incremental truncation, Exonuclease III is used to create a library of all possible single base-pair deletions of a given piece of DNA. Incremental truncation libraries (ITLs) have applications in protein engineering as well as protein folding, enzyme evolution, and the chemical synthesis of proteins. In addition, we are developing a methodology of DNA shuffling which is independent of DNA sequence homology.

Amino Acid Motifs↗

Local versus nonlocal interactions in protein folding and stability--an experimentalist's point of view.

One of the classic important issues in protein folding and stability is the relative roles of noncovalent short-range (local) and long-range (nonlocal) interactions. Interest in this topic has been reinforced by recent developments in the analytical theory of protein folding and in lattice-based computer simulations. During the past few years, a wealth of experimental information relevant to this issue has been accumulating. In this review, we focus specifically on experimental aspects, discussing some general ideas that arise from the results obtained by many different groups using a variety of approaches. We also discuss a new experimental strategy that allows us to engineer the contribution of local interactions, and we discuss the first results obtained.

Computer Simulation↗

Competitive interaction between two different spherical sinks.

Competitive interactions within diverse mixed populations of chemically active sites are prevalent throughout nature, science, and engineering. Their effects are readily seen in the distribution of dead and surviving aerobic cells within a thick biofilm and particle shape changes during the growth and coarsening of crystals. Even in the most dilute case, competition for a reactant requires at least two spheres/cells, and the solution of the two-spherical sink problem is of interest for several reasons. The solution accurately describes lower cell concentration behavior (10(8) cells/l), and like the Smoluchowski diffusion-reaction treatment for a single sphere, the analysis is extremely helpful in understanding the fundamental phenomena of the effect on the first spherical sink of the presence of a second different spherical sink. In addition these exact solutions are required for the systematic extension to higher density behavior by rigorous expansions in the spherical sink densities. The method of the twin spherical expansion is used with a formal matrix elimination scheme to generate an exact solution for two distinct spherical sinks of differing sizes and kinetics. The two sinks exist in a medium, which supplies a reactant to the sinks via Fickian diffusion. The two sinks compete for the same reactant with different first-order reactions occurring at the surface of each sink. Earlier work focused on two spherical sinks of the same size with identical surface reaction kinetics. This work has been advanced to allow for diversity in the theory of cellular or reactive sink competition. A number of interesting higher order interactive phenomena are observed in this paper when the different reactive sinks are in close proximity. (c) 2004 American Institute of Physics.

Chemical Phenomena↗

Genetic engineering of plant lipids.

Vegetable oils are a major component of human diets, comprising as much as 25% of average caloric intake. Until recently, it was not possible to exert significant control over the chemical composition of vegetable oils derived from different plants. However, the advent of genetic engineering has provided novel opportunities to tailor the composition of plant-derived lipids so that they are optimized with respect to food functionality and human dietary needs. In order to exploit this new capability, it is essential for food scientists and nutritionists to define the lipid compositions that would be most desirable for various purposes.

Dietary Fats, Unsaturated↗

Thermoresponsive terpolymeric films applicable for osteoblastic cell growth and noninvasive cell sheet harvesting.

A novel multifunctional linear block copolymer, poly(N-isopropylacrylamide-co-acrylic acid)-b-poly( L-lactic acid) (NAL), was synthesized to expand the concept of cell sheet engineering by using its thermoresponsive property and processibility. The chemical structure of synthesized NAL was confirmed by Fourier transform infrared spectroscopy, and its molar mass (103,500 g.mol(-1)) and molar mass distribution were determined by matrix-assisted laser desorption/ionization-time of flight mass spectroscopy. NAL copolymer was fabricated into thin films by spin-casting. Spin-cast NAL films displayed thermoresponsive properties as demonstrated by surface wettability and topology changes from relatively more hydrophobic (contact angle of 56 degrees) and rougher at 37 degrees C to relatively more hydrophilic (contact angle of 40 degrees) and smoother at 22 degrees C, as assessed by contact angle measurement and atomic force microscopy, respectively. Murine osteoblastic MC3T3-E1 cells displayed comparable adhesion but slower proliferation on NAL films than on poly(L-lactic acid) (PLLA) films and tissue culture polystyrene (TCPS). Within 9 days of cell culture, the highest alkaline phosphatase activity of MC3T3-E1 cells occurred later (on day 9) on NAL films than on PLLA films and TCPS (on day 6). A well-established MC3T3-E1 cell sheet was successfully detached from NAL films, in the absence of enzymes, within about 5 min by simply lowering the temperature from 37 degrees C to room temperature. NAL copolymer has potential for use in the controlled release of therapeutic agents while simultaneously supporting cell growth. In addition, it may be applicable for noninvasive two- or three-dimensional cell sheet harvesting.

Alkaline Phosphatase↗