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PubMed2004

Quantum dots and other nanoparticles: what can they offer to drug discovery?

Nanocrystals (quantum dots) and other nanoparticles (gold colloids, magnetic bars, nanobars, dendrimers and nanoshells) have been receiving a lot of attention recently with their unique properties for potential use in drug discovery, bioengineering and therapeutics. In this review, structural, optical and biological assets of nanocrystals are summarized and their applications to drug discovery studies are discussed. Unique properties of these nanoparticles can offer new advancements in drug discovery.

Drug Design↗
PubMed1999

Bioinspired polymeric materials: in-between proteins and plastics.

Chemical and biological researchers are making rapid progress in the design and synthesis of non-natural oligomers and polymers that emulate the properties of natural proteins. Whereas molecular biologists are exploring biosynthetic routes to non-natural proteins with controlled material properties, synthetic polymer chemists are developing bioinspired materials with well-defined chemical and physical properties that function or self-organize according to defined molecular architectures. Bioorganic chemists, on the other hand, are developing several new classes of non-natural oligomers that are bridging the gap between molecular biology and polymer chemistry. These synthetic oligomers have both sidechain and length specificity, and, in some cases, demonstrate capability for folding, self-assembly, and specific biorecognition. Continued active exploration of diverse backbone and sidechain chemistries and connectivities in bioinspired oligomers will offer the potential for self-organized materials with greater chemical diversity and biostability than natural peptides. Taken together, advances in molecular bioengineering, polymer chemistry, and bioorganic chemistry are converging towards the creation of useful bioinspired materials with defined molecular properties.

Biopolymers↗
PubMed2003

Motifs, modules and games in bacteria.

Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology. From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games. Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks. They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses. The dynamical functioning of modules defines the organism's strategy to survive in a game, pitting cell against cell, and cell against environment. Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function. This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering.

Animals↗
PubMed2000

Sterol methyl transferase: enzymology and inhibition.

Sterol C-methylations catalyzed by the (S)-adenosyl-L-methionine: Delta(24)-sterol methyl transferase (SMT) have provided the focus for study of electrophilic alkylations, a reaction type of functional importance in C-C bond formation of natural products. SMTs occur generally in nature, but do not occur in animal systems, suggesting that the difference in sterol synthetic pathways can be exploited therapeutically and in insect-plant interactions. The SMT genes from several plants and fungi have been cloned, sequenced and expressed in bacteria or yeast and bioengineered into tobacco or tomato plants. These enzymes share significant amino acid sequence similarity in the putative sterol and AdoMet binding sites. Investigations of the molecular recognition of sterol fitness and studies with stereospecifically labeled substrates as well as various sterol analogs assayed with native or mutant SMTs from fungi and plants have been carried out recently in our own and other laboratories. These analyses have led to an active-site model, referred to as the 'steric-electric plug' model, which is consistent with a non-covalent mechanism involving the intermediacy of a 24beta-methyl (or ethyl) sterol bound to the ternary complex. Despite the seeming differences between fungal and plant SMT activities the recent data indicate that a distinct SMT or family of SMTs exist in these organisms which bind and transform sterols according to a similar mechanistic plan. Vascular plants have been found to express different complements of C(1)/C(2)-activities in the form of at least three SMT isoforms. This enzyme multiplicity can be a target of regulatory control to affect phytosterol homeostasis in transgenic plants. The state of our current understanding of SMT enzymology and inhibition is presented.

Amino Acid Sequence↗
PubMed2000

Bacillus thuringiensis and its use in transgenic insect control technologies.

The insecticidal activity of Bacillus thuringiensis (Bt) is mainly due to the production of crystals containing insecticidal crystal proteins (ICPs). These proteins are very selectively active against certain insect species, including some agronomically important pest species. Some ICP genes have been used for bioengineered crop protection, resulting in transgenic crop plants with excellent insect protection.

Bacillus thuringiensis Toxins↗
PubMed2004

Contribution of biomechanics, orthopaedics and rehabilitation: the past present and future.

Biomechanics is a field that has a very long history. From its beginnings in ancient Chinese and Greek literature, the field of orthopaedic biomechanics has grown in the areas of biomechanics of bone, articular cartilage, soft tissues, upper extremities, spine and so on. Bioengineers in collaboration with orthopaedic surgeons have applied biomechanical principles to study clinically relevant problems, improving patient treatment and outcome. In the past 30 years, my colleagues and I have focused our research on the biomechanics of musculoskeletal soft tissues, ligaments and tendons in particular. Therefore, in this review article, the function of the knee ligaments and the associated homeostatic responses secondary to immobilisation and exercise will be described. Research on healing of the medial collateral ligament (MCL) of the knee and possible future approaches in improving the healing of the knee ligaments will be presented. Finally, improvement of the understanding of ligament reconstruction, specifically of the anterior cruciate ligament (ACL), through the use of robotics technology will be included. Throughout the manuscript, specific scientific findings that have guided or changed the clinical management of injury to these soft tissues will be emphasised.

Anterior Cruciate Ligament↗
PubMed2003

Mechanisms and the current state of deep brain stimulation in neuropsychiatry.

Deep brain stimulation (DBS) is established as a therapy for movement disorders, and it is an investigational treatment in other neurologic conditions. DBS precisely targets neuroanatomical targets deep within the brain that are proposed to be centrally involved in the pathophysiology of some neuropsychiatric illnesses. DBS is nonablative, offering the advantages of reversibility and adjustability. This might permit therapeutic effectiveness to be enhanced or side effects to be minimized. Preclinical and clinical studies have shown effects of DBS locally, at the stimulation target, and at a distance, via actions on fibers of passage or across synapses. Although its mechanisms of action are not fully elucidated, several effects have been proposed to underlie the therapeutic effects of DBS in movement disorders, and potentially in other conditions as well. The mechanisms of action of DBS are the focus of active investigation in a number of clinical and preclinical laboratories. As in severe movement disorders, DBS may offer a degree of hope for patients with intractable neuropsychiatric illness. It is already clear that research intended to realize this potential will require a very considerable commitment of resources, energy, and time across disciplines including psychiatry, neurosurgery neurology, neuropsychology, bioengineering, and bioethics. These investigations should proceed cautiously.

Electric Stimulation Therapy↗
PubMed2006

Enzyme-nanoparticle functionalization of three-dimensional protein scaffolds.

Various surface modification techniques have been developed for patterning functional biomolecules in two dimensions, allowing enzymes, antibodies, and other compounds to be localized for applications in bioanalysis and bioengineering. Here, we report a strategy for extending high-resolution patterning of biomolecules to three dimensions. In this approach, three-dimensional protein scaffolds are created by a direct-write process in which multiphoton excitation promotes photochemical cross-linking of protein molecules from aqueous solution within specified volume elements. After scaffold fabrication, protein microstructures are functionalized with enzyme-gold nanoparticle conjugates via a targeting process based in part on electrostatic attraction between the low-isoelectric-point enzyme and the microstructure, fabricated from high-isoelectric-point proteins. High signal-to-background ratios (approximately 20:1) are demonstrated for fluorescent product streams created by dephosphorylation of the fluorogenic compound, fluorescein diphosphate, at microstructures decorated with alkaline phosphatase-gold nanoparticle conjugates. We also demonstrate feasibility for using such structures to quantify substrate concentrations in flowing streams with low-micromolar detection limits and to create sensor suites based on both enzyme-nanoparticle functionalization and intrinsic enzymatic activity of protein scaffolds. These topographically complex sensors and dosing sources have potential applications in microfluidics, sensor array fabrication, and real-time chemical modification of cell culture environments.

Enzymes↗
PubMed2003

Functional characterization of transgene integration patterns by halo fluorescence in situ hybridization: electroporation versus retroviral infection.

Gene transfer techniques are essential for bioengineering and gene therapy. Retroviral vectors constitute an important tool in this context as integrase-catalyzed genomic anchoring is one of the best defined results of nonhomologous recombination, occurring at loci with favorable expression properties. On the basis of a retroviral expression cassette, this study focuses on differences regarding the genomic targets after its transfer by either retroviral infection or electroporation. Fluorescence in situ hybridization (FISH) of clones generated by infection revealed for the majority an association of the transgene with the nuclear matrix while this was true only for a minority of single copy clones if the same construct was transferred by electroporation. Our results demonstrate that the process of integration is distinct for both gene transfer routes and confirm that retroviral survival strategies favor integration next to scaffold/matrix attachment regions. These results may be one key to explain recent consequences of gene therapy trials that have led to the deregulation of endogenous genes.

Animals↗
PubMed2006

Efficient metabolic engineering of GM3 on tumor cells by N-phenylacetyl-D-mannosamine.

Abnormal carbohydrates expressed on tumor cells, which are termed tumor-associated carbohydrate antigens (TACAs), are potential targets for the development of cancer vaccines. However, immune tolerance to TACAs has severely hindered progress in this area. To overcome this problem, we have developed a novel immunotherapeutic strategy based on synthetic cancer vaccines and metabolic engineering of TACAs on tumor cells. One critical step of this new strategy is metabolic engineering of cancer, namely, to induce expression of an artificial form of a TACA by supplying tumors with an artificial monosaccharide precursor. To identify the proper precursor for this application, N-propionyl, N-butanoyl, N-isobutanoyl, and N-phenylacetyl derivatives of d-mannosamine were synthesized, and their efficiency as biosynthetic precursors in modifying sialic acid and inducing expression of modified forms of GM3 antigen on tumor cells was investigated. For this purpose, tumor cells were incubated with different N-acyl-d-mannosamines, and modified forms of GM3 expressed on tumor cells were analyzed by flow cytometry using antigen-specific antisera. N-Phenylacetyl-d-mannosamine was efficiently incorporated in a time- and dose-dependent manner to bioengineer GM3 expression by several tumor cell lines, including K562, SKMEL-28, and B16-F0. Moreover, these tumor cell lines also exhibited ManPAc-dependent sensitivity to cytotoxicity mediated by anti-PAcGM3 immune serum and complement. These results provide an important validation for this novel therapeutic strategy. Because N-phenylacetyl GM3-protein conjugates are particularly immunogenic, the combination of an N-phenylacetyl GM3 conjugate vaccine with systemic N-phenylacetyl-d-mannosamine treatment is a promising immunotherapy for future development and application to melanoma and other GM3-bearing tumors.

Animals↗
PubMed2006

Characterization of a Thermobifida fusca beta-1,3-glucanase (Lam81A) with a potential role in plant biomass degradation.

Thermobifida fusca is a filamentous soil bacterium that plays a major role in the breakdown of plant biomass. In this paper, we report the cloning, expression, purification, and characterization of the T. fusca enzyme, Lam81A. The Carbohydrate Active Enzymes Database (http://afmb.cnrs-mrs.fr/CAZY/) indicates that Lam81A belongs to a relatively uncharacterized family of beta-1,3-glucanases, family GH-81 [Coutinho, P. M., and Henrissat, B. (1999) in Recent Advances in Carbohydrate Bioengineering (Gilbert, H. J., Davies, G., Henrissat, B., and Svensson, B., Eds.) pp 3-12, The Royal Society of Chemistry, Cambridge, U.K.]. Microarray analysis suggests that Lam81A plays a role in biomass degradation, where its natural substrate may be the plant cell wall polysaccharide, callose, which is a polymer of beta-1,3-linked glucose. Characterization of Lam81A has shown that the enzyme is specific for beta-1,3-linked glucose polysaccharides, is endohydrolytic, and utilizes an inverting mechanism for substrate hydrolysis. In addition, the enzyme has a broad pH optimum from 5.5 to 10, a temperature optimum of 50 degrees C, and demonstrates substrate inhibition, as well as showing a high basal level of expression.

Actinomycetales↗
PubMedDate not supplied

Molecular level investigations of the inter- and intramolecular interactions of pH-responsive artificial triblock proteins.

Intelligent materials that can undergo physical gelation in response to environmental stimuli have potential impacts in the bioengineering and biomedical fields where the entrapment of cellular or molecular species is desired. Here, we utilize atomic force microscopy (AFM) to perform molecular level investigations of designer artificial proteins that undergo physical gelation. These are engineered as triblock copolymers with independent interchain binding and solvent retention functions, namely, two terminal leucine zipper-like peptide sequences and a central alanylglycine rich sequence, respectively. AFM force measurements between probes and surfaces functionalized with molecules of this triblock protein revealed adhesive interactions that increased in average force and frequency as the pH was lowered from pH 11.2 to 7.4 to 4.5, reflecting an increase in the numbers of interacting molecular strands. In bulk solution, lowering the pH results in a viscous liquid to gel transition. The modular design of the triblock protein was also exploited for single molecule force spectroscopy investigations, which revealed altered intramolecular interactions in response to changes in pH. An increased understanding of the inter- and intramolecular forces involved in biomolecule driven gelation processes is not only of great fundamental interest in the study of the biomolecular systems involved but may also prove key in enabling the rational design of new generations of intelligent hydrogel systems.

Amino Acid Sequence↗
PubMedDate not supplied

Semisynthetic hydrophilic polyals.

Non-bioadhesive, fully biodegradable soluble polymers would be very instrumental in advanced biomedical applications, such as gene and drug delivery and tissue engineering. However, rational development of such materials is hindered by the complexity of macromolecule interactions with biological milieu. The prevalence of carbohydrates in naturally occurring interface structures suggests an alternative, biomimetic approach. Interface carbohydrates, regardless of their biological function, have common non-signaling substructures (e.g., acetal and ketal groups, secondary and primary alcohols). We hypothesized that hydrophilic polymers (polyals) consisting of acyclic units built of non-signaling carbohydrate substructures would be highly biocompatible and non-bioadhesive, while intrachain acetal or ketal groups would enable nonenzymatic biodegradation upon uptake by cells. Acyclic hydrophilic polyals can be prepared via either polymerization of suitable monomers or lateral cleavage of cyclic polyals (e.g., polysaccharides). In this study, model polyals were produced via lateral cleavage of polyaldoses and polyketoses. Best results were achieved using dextran B-512 as a precursor. The resultant poly[hydroxymethylethylene hydroxymethylformal], in agreement with the hypothesis, demonstrated excellent biological properties and technological flexibility. Materials of this type can potentially have several applications in pharmacology and bioengineering.

Animals↗
PubMedDate not supplied

Quorum-sensing-based toolbox for regulatable transgene and siRNA expression in mammalian cells.

Technologies for regulated expression of multiple transgenes in mammalian cells have gathered momentum for bioengineering, gene therapy, drug discovery, and gene-function analyses. Capitalizing on recently developed mammalian transgene modalities (QuoRex) derived from Streptomyces coelicolor, we have designed a flexible and highly compatible expression vector set that enables desired transgene/siRNA control in response to the nontoxic butyrolactone SCB1. The construction-kit-like expression portfolio includes (i) multicistronic (pTRIDENT), (ii) autoregulated, (iii) bidirectional (pBiRex), (iv) oncoretro- and lentiviral transduction, and (v) RNA polymerase II-based siRNA transcription-fine-tuning vectors for straightforward implementation of QuoRex-controlled (trans)gene modulation in mammalian cells.

Animals↗
PubMedDate not supplied

An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research.

Advances in biomedical research require a new generation of researchers having a strong background in both the life and physical sciences and a knowledge of computational, mathematical, and engineering tools for tackling biological problems. The NIH-NSF Bioengineering and Bioinformatics Summer Institute at the University of Pittsburgh (BBSI @ Pitt; www.ccbb.pitt.edu/bbsi) is a multi-institutional 10-week summer program hosted by the University of Pittsburgh, Duquesne University, the Pittsburgh Supercomputing Center, and Carnegie Mellon University, and is one of nine Institutes throughout the nation currently participating in the NIH-NSF program. Each BBSI focuses on a different area; the BBSI @ Pitt, entitled "Simulation and Computer Visualization of Biological Systems at Multiple Scales", focuses on computational and mathematical approaches to understanding the complex machinery of molecular-to-cellular systems at three levels, namely, molecular, subcellular (microphysiological), and cellular. We present here an overview of the BBSI @ Pitt, the objectives and focus of the program, and a description of the didactic training activities that distinguish it from other traditional summer research programs. Furthermore, we also report several challenges that have been identified in implementing such an interdisciplinary program that brings together students from diverse academic programs for a limited period of time. These challenges notwithstanding, presenting an integrative view of molecular-to-system analytical models has introduced these students to the field of computational biology and has allowed them to make an informed decision regarding their future career prospects.

Computational Biology↗
PubMedDate not supplied

Expression of Vitreoscilla hemoglobin in Escherichia coli enhances ribosome and tRNA levels: a flow field-flow fractionation study.

Asymmetrical flow field-flow fractionation (FFF) was used to separate and quantitate 70S ribosomes, the 30S and 50S subunits, and tRNA in one single analytical procedure. The method was applied to an investigation of the effect of Vitreoscilla hemoglobin (VHb) on the translational machinery of the recombinant Escherichia coli cells. The number of active 70S ribosomes per cell increased dramatically, more than 2-fold, as did also the tRNA levels for the VHb-expressing strain relative to VHb-negative control at the end of a 30-h fed-batch cultivation. This was accompanied by a corresponding 61% increase of a cloned marker enzyme activity. The results clearly indicate that VHb promotes the level of translational components. There should be many other cases in bioengineering where it is important to relate the protein production level in a bioreactor to the ribosome and tRNA levels.

Aerobiosis↗
PubMed1999

Novel optical methodologies in studying mechanical signal transduction in mammalian cells.

For the last 3 decades evidence has been accumulating that some types of mammalian cells respond to their mechanically active environment by altering their morphology, growth rate, and metabolism. The study of such responses is very important in understanding, physiological and pathological conditions ranging from bone formation to atherosclerosis. Obtaining this knowledge has been the goal for an active research area in bioengineering termed cell mechanotransduction. The advancement of optical methodologies used in cell biology research has given the tools to elucidate cellular mechanisms that would otherwise be impossible to visualize. Combined with molecular biology techniques, they give engineers invaluable tools in understanding the chemical pathways involved in mechanotransduction. Herein we briefly review the current knowledge on mechanical signal transduction in mammalian cells, focusing on the application of novel optical techniques in the ongoing research.

Animals↗
PubMed2003

Palladium(II) complex as a sequence-specific peptidase: hydrolytic cleavage under mild conditions of X-Pro peptide bonds in X-Pro-Met and X-Pro-His segments.

The X-Pro peptide bond (in which X represents any amino acid residue) in peptides and proteins is resistant to cleavage by most proteolytic enzymes. We show that [Pd(H(2)O)(4)](2+) ion can selectively hydrolyze this tertiary peptide bond within the X-Pro-Met and X-Pro-His sequence segments. The hydrolysis requires an equimolar amount of the Pd(II) reagent and occurs under mild conditions-at temperature as low as 20 degrees C (with half-life of 1.0 h at pH 2.0) and at pH as high as 7.0 (with half-life of 4.2 h at pH 7.0 and 40 degrees C). The secondary peptide bond, exemplified by X-Gly in the X-Gly-Met and X-Gly-His sequence segments, however, is cleaved only in weakly acidic solution (pH < 4.0) and more slowly (half-life is 4.2 h at pH 2.0 and 60 degrees C). We explain the sequence-specificity of X-Pro cleavage by NMR spectroscopic analysis of the coordination of the X-Pro-Met segment to the Pd(II) ion. We give indirect evidence for the mechanism of cleavage by analyzing the conformation of the scissile X-Pro peptide bond, and by comparing the rate constants for the cleavage of the tertiary X-Pro peptide bond, the tertiary X-Sar peptide bond (Sar is N-methyl glycine), and the typical secondary X-Gly peptide bond in a set of analogous oligopeptides. Methionine and histidine side chains provide the recognition by selectively binding (anchoring) the Pd(II) ion. The proline residue provides the enhanced activity because its tertiary X-Pro peptide bond favors the cleavage-enhancing binding of the Pd(II) ion to the peptide oxygen atom and prevents the cleavage-inhibiting binding of the Pd(II) ion upstream of the anchoring (histidine or methionine) residue. Cleavage can be switched from the residue-selective to the sequence-specific mode by simply adjusting the pH of the aqueous solution. In acidic solutions, any X-Y bond in X-Y-Met and X-Y-His segments is cleaved because the cleavage is directed by anchoring methionine and histidine residues. In mildly acidic and neutral solutions, only the X-Pro bond in X-Pro-Met and X-Pro-His sequences is cleaved because of an interplay between the anchoring residue and the proline residue preceding it. Because Pro-Met and Pro-His sequences are rare in proteins, this sequence-specific cleavage is potentially useful for the removal of the fusion tags from the bioengineered fusion proteins.

Amino Acid Sequence↗