Protein design: a perspective from simple tractable models.
Explore the source record for details and available documents.
Models, Chemical↗
SEARCH · Search PubMed
Results for “Chemical Engineering”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Creation and discovery of ligand-receptor pairs for transcriptional control with small molecules.
The nuclear receptor retinoid X receptor (RXR) is a ligand-activated transcription factor. To create receptors for a new ligand, a structure-based approach was used to generate a library of approximately 380,000 mutant RXR genes. To discover functional variants within the library, we used chemical complementation, a method of protein engineering that uses the power of genetic selection. Wild-type RXR has an EC50 of 500 nM for 9-cis retinoic acid (9cRA) and an EC50 of >10 microM for the synthetic retinoid-like compound LG335 in yeast. The library produced ligand-receptor pairs with LG335 that have a variety of EC50 values (40 nM to >2 microM) and activation levels (10-80% of wild-type RXR with 9cRA) in yeast. The variant I268V;A272V;I310L;F313M has an EC50 for LG335 of 40 nM and an EC50 for 9cRA of >10 microM in yeast. This variant has essentially the reverse ligand specificity of wild-type RXR and is transcriptionally active at a 10-fold-lower ligand concentration in yeast. This EC50 is 25-fold lower than the best receptor we have engineered through site-directed mutagenesis, Q275C;I310M;F313I. Furthermore, the variants' EC50 values and activation levels in yeast and mammalian cells correlate. This protein engineering method should be extendable to produce other functional ligand-receptor pairs, which can be selected and characterized from libraries within weeks. Coupling large library construction with chemical complementation could be used to engineer proteins that bind virtually any small molecule for conditional gene expression, applications in metabolic engineering, and biosensors and to engineer enzymes through genetic selection.
Amino Acid Substitution↗
Respiratory fluid mechanics and transport processes.
The field of respiratory flow and transport has experienced significant research activity over the past several years. Important contributions to the knowledge base come from pulmonary and critical care medicine, surgery, physiology, environmental health sciences, biophysics, and engineering. Several disciplines within engineering have strong and historical ties to respiration including mechanical, chemical, civil/environmental, aerospace and, of course, biomedical engineering. This review draws from a wide variety of scientific literature that reflects the diverse constituency and audience that respiratory science has developed. The subject areas covered include nasal flow and transport, airway gas flow, alternative modes of ventilation, nonrespiratory gas transport, aerosol transport, airway stability, mucus transport, pulmonary acoustics, surfactant dynamics and delivery, and pleural liquid flow. Within each area are a number of subtopics whose exploration can provide the opportunity of both depth and breadth for the interested reader.
Animals↗
Chemical characteristics and cytocompatibility of collagen-based scaffold reinforced by chitin fibers for bone tissue engineering.
Chitin is a kind of seemly material to match PLLA for a scaffold, which may create an appropriate environment for the regeneration of tissues. In this study, we prepared and evaluated a new nano-hydroxyapatite/collagen/PLLA (nHACP) scaffold reinforced by chitin fibers for bone-tissue engineering. The chitin fibers were crosslinked with PLLA by dicyclohexylcarbodimide (DCC). The chemical characteristics were evaluated by Fourier transformed infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The mechanical strength was measured by compressive tests. The fibers, crosslinked with PLLA, could enhance the compressive strength of the scaffold about four times. Human marrow mesenchymal stem cells (MSCs) culture showed that the reinforced nHACP scaffolds were more cytocompatible than that without reinforcement. The crosslinks hardly affected the cytocompatibility of the reinforced scaffolds. The results suggested that the reinforced scaffolds (DCC crosslinked) might be a promising candidate for bone-tissue engineering.
Animals↗
Spacer-engineered donor DNA enhances CRISPR-Cas9-mediated knockin to establish a chemical knockdown platform for endogenous proteins.
Precise installation of functional protein domains at endogenous loci is a powerful approach for interrogating protein functions, but its broad application is limited by the low efficiency of homology-directed repair (HDR)-mediated knockin during Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene editing. Here, we investigated a simple donor DNA engineering strategy that enhances HDR-mediated gene knockin by appending additional gRNA-recognizable spacer sequences to donor templates. Systematic analysis of linear dsDNA and plasmid donors showed that spacer position, length, and orientation influenced HDR efficiency, and that spacer-containing donors improved knockin across multiple genomic loci, insertion sizes, cell types and delivery modalities. Mechanistic analyses revealed that spacer-containing donors formed stable complexes with Cas9/gRNA and showed increased nuclear localization, supporting nuclear delivery as a key contributor to improved editing outcomes. We then applied this gene-editing strategy to establish a chemical knockdown platform by installing drug-responsive degrons at endogenous loci, generating cell lines in which GSK3β or Lin28A protein could be rapidly, potently and reversibly depleted by drug treatment. These platforms enable selective modulation of endogenous proteins and reveal cellular responses that may differ from those obtained using conventional genetic perturbation. Together, this work establishes a readily implementable framework that integrates improved gene editing with on-demand chemical knockdown of endogenous proteins.
CRISPR-Cas9↗
Producing bispecific and bifunctional antibodies.
Bispecific antibodies are artificially engineered monoclonal antibodies (MAbs) that consist of two distinct binding sites and are capable of binding two different antigens noncovalently. They can be produced by chemical cross-linkage, genetic engineering, or somatic hybridization. This chapter describes a rapid method using somatic fusion to generate hybrid hybridomas (quadromas). Two fluorescence-labeled hybridoma cell lines were fused with polyethylene glycol (PEG) to generate the quadroma. Generation of a quadroma secreting bsMAb against biotin and HRPO is described, along with a benzhydroxamic acid-agarose affinity chromatography procedure to purify the bsMAb-HRPO complex. This bsMAb can be used for ultrasensitive ELISA detection of biotinylated antigens. Essentially a similar method can be used for fusing any two hybridomas for therapeutic applications. Bifunctional antibodies are colinear molecules with one or more paratopes linked with diagnostic or therapeutic molecules. There are some limitations of therapeutic monoclonal antibodies in the clinic that can be overcome by engineering smaller and more effective antibody fragments. Here we describe a stepwise procedure for developing a bifunctional ScFv (bfScFv). We constructed a bfScFv from a hybridoma cell line using PCR strategies. The VL and VH gene segments are linked with a 45-bp linker and fused with a biotin mimic sequence at the 3' end. This engineered bifunctional antibody fragment gene could be expressed and the protein purified on a large scale in Escherichia coli as inclusion bodies. Such bifunctional antibody molecules could have useful applications in the area of immunodiagnostics and immunotherapy. Similar strategies can be used to incorporate a second single-chain antibody or any nonantibody entity such as a cytokine for therapeutic applications.
Animals↗
Incorporation of T and B epitopes of the circumsporozoite protein in a chemically defined synthetic vaccine against malaria.
We show here an effective and novel approach to engineer peptide-based vaccines using a chemically defined system, known as multiple peptide antigen systems (MAPs), to protect an inbred mouse strain from infection against rodent malaria. 10 mono- and di-epitope MAP models containing different arrangements and stoichiometry of functional B and/or T helper cell epitopes from the circumsporozoite protein of Plasmodium berghei were used to immunize A/J mice. While these mice did not respond to the mono-epitope MAP bearing only the B or T epitope, very high titers of antibody and protective immunity against sporozoite challenge were elicited by di-epitope MAPs, particularly those with the B and T epitopes in tandem and present in equimolar amounts. These results, obtained in a well-defined rodent malaria model, indicate that MAPs may overcome some of the difficulties in the development of synthetic vaccines, not only for malaria but also for other infectious diseases.
Amino Acid Sequence↗
[Hygienic aspects of the protection of water resources in the area of a regional industrial complex in organic synthesis manufacture].
Explore the source record for details and available documents.
Benzopyrenes↗
Biocommodity Engineering.
The application of biotechnology to the production of commodity products (fuels, chemicals, and materials) offering benefits in terms of sustainable resource supply and environmental quality is an emergent area of intellectual endeavor and industrial practice with great promise. Such "biocommodity engineering" is distinct from biotechnology motivated by health care at multiple levels, including economic driving forces, the importance of feedstocks and cost-motivated process engineering, and the scale of application. Plant biomass represents both the dominant foreseeable source of feedstocks for biotechnological processes as well as the only foreseeable sustainable source of organic fuels, chemicals, and materials. A variety of forms of biomass, notably many cellulosic feedstocks, are potentially available at a large scale and are cost-competitive with low-cost petroleum whether considered on a mass or energy basis, and in terms of price defined on a purchase or net basis for both current and projected mature technology, and on a transfer basis for mature technology. Thus the central, and we believe surmountable, impediment to more widespread application of biocommodity engineering is the general absence of low-cost processing technology. Technological and research challenges associated with converting plant biomass into commodity products are considered relative to overcoming the recalcitrance of cellulosic biomass (converting cellulosic biomass into reactive intermediates) and product diversification (converting reactive intermediates into useful products). Advances are needed in pretreatment technology to make cellulosic materials accessible to enzymatic hydrolysis, with increased attention to the fundamental chemistry operative in pretreatment processes likely to accelerate progress. Important biotechnological challenges related to the utilization of cellulosic biomass include developing cellulase enzymes and microorganisms to produce them, fermentation of xylose and other nonglucose sugars, and "consolidated bioprocessing" in which cellulase production, cellulose hydrolysis, and fermentation of soluble carbohydrates to desired products occur in a single process step. With respect to product diversification, a distinction is made between replacement of a fossil resource-derived chemical with a biomass-derived chemical of identical composition and substitution of a biomass-derived chemical with equivalent functional characteristics but distinct composition. The substitution strategy involves larger transition issues but is seen as more promising in the long term. Metabolic engineering pursuant to the production of biocommodity products requires host organisms with properties such as the ability to use low-cost substrates, high product yield, competitive fitness, and robustness in industrial environments. In many cases, it is likely to be more successful to engineer a desired pathway into an organism having useful industrial properties rather than trying to engineer such often multi-gene properties into host organisms that do not have them naturally. Identification of host organisms with useful industrial properties and development of genetic systems for these organisms is a research challenge distinctive to biocommodity engineering. Chemical catalysis and separations technologies have important roles to play in downstream processing of biocommodity products and involve a distinctive set of challenges relative to petrochemical processing. At its current nascent state of development, the definition and advancement of the biocommodity field can benefit from integration at multiple levels. These include technical issues associated with integrating unit operations with each other, integrating production of individual products into a multi-product biorefinery, and integrating biorefineries into the broader resource, economic, and environmental systems in which they function. We anticipate that coproduction of multiple products, for example, production of fuels, chemicals, power, and/or feed, is likely to be essential for economic viability. Lifecycle analysis is necessary to verify the sustainability and environmental quality benefits of a particular biocommodity product or process. We see biocommodity engineering as a legitimate focus for graduate study, which is responsive to an established personnel demand in an industry that is expected to grow in the future. Graduate study in biocommodity engineering is supported by a distinctive blend of intellectual elements, including biotechnology, process engineering, and resource and environmental systems.
Journal Article↗
Back to basics: thermodynamics in biochemical engineering.
Rational and efficient process development in chemical technology always makes heavy use of process analysis in terms of balances, kinetics, and thermodynamics. While the first two of these concepts have been extensively used in biotechnology, it appears that thermodynamics has received relatively little attention from biotechnologists. This state of affairs is one among several reasons why development and design of biotechnological processes is today mostly carried out in an essentially empirical fashion and why bioprocesses are often not as thoroughly optimized as many chemical processes. Since quite a large body of knowledge in the area of bio thermodynamics already existed in the early nineties, the Steering Committee of a European Science Foundation program on Process Integration in Biochemical Engineering identified a need to stimulate a more systematic use of thermodynamics in the area. To this effect, a bianual course for advanced graduate students and researchers was developed. The present contribution uses the course structure to provide an outline of the area and to characterize very briefly the achievements, the challenges, and the research needs in the various sub-topics.
Animals↗
Cancer incidence among Danish seafarers: a population based cohort study.
AIMS: Seafarers aboard oil and chemical tankers may be exposed to many chemicals, including substances like benzene that are known to be carcinogenic. Other seafarers are exposed to engine exhaust, different oil products, and chemicals used aboard and some years ago asbestos was also used extensively in ships. The aim of this study was to study cancer morbidity among Danish seafarers in relation to type of ship and job title. METHODS: A cohort of all Danish seafarers during 1986-1999 (33,340 men; 11,291 women) registered by the Danish Maritime Authority with an employment history was linked with the nationwide Danish Cancer Registry and followed up for cancer until the end of 2002. The number of person years at risk was 517,518. Standardised incidence ratios (SIR) were estimated by use of the corresponding national rates. RESULTS: The SIR of all cancers combined was higher than expected: 1.26 (95% CI 1.19 to 1.32) for men and 1.07 (95% CI 0.95 to 1.20) for women. This was mainly due to an excess of cancer of the larynx, lung, tongue, mouth, pharynx, oesophagus, pancreas, kidney, urinary bladder, colon, and bone as well as skin melanomas among men (the three latter borderline significantly increased), and an excess of cancer of the lung, rectum, and cervix uteri among women. The differences in risk pattern for lung cancer between the different job categories among men ranged in terms of SIR from 1.2 (95% CI 0.9 to 1.7) (engine officers) to 2.3 (1.6 to 3.3) (engine room crew), and 4.1 (2.1 to 7.4) among maintenance crew. Non-officers had a 1.5 times higher lung cancer risk than officers. No increased occurrence of all lymphatic and haematopoietic malignancies combined was found for employees on tankers, but the number of cases was limited to a total of 7. CONCLUSIONS: Danish seafarers, especially men, face an increased overall cancer risk, in particular a risk for lung cancer and other tobacco associated cancers.
Adult↗
The threat of mid-spectrum chemical warfare agents.
There is a spectrum of several threat agents, ranging from nerve agents and mustard agents to natural substances, such as biotoxins and new, synthetic, bioactive molecules produced by the chemical industry, to the classical biological warfare agents. The new, emerging threat agents are biotoxins produced by animals, plants, fungi, and bacteria. Examples of such biotoxins are botulinum toxin, tetanus toxin, and ricin. Several bioactive molecules produced by the pharmaceutical industry can be even more toxic than are the classical chemical warfare agents. Such new agents, like the biotoxins and bioregulators, often are called mid-spectrum agents. The threat to humans from agents developed by modern chemical synthesis and by genetic engineering also must be considered, since such agents may be more toxic or more effective in causing death or incapacitation than classical warfare agents. By developing effective medical protection and treatment against the most likely chemical and mid-spectrum threat agents, the effects of such agents in a war scenario or following a terrorist attack can be reduced.
Biological Products↗
Protein biotoxins of military significance.
There is a spectrum of several threat agents, ranging from nerve agents and mustard agents to natural substances, such as biotoxins and new, synthetic, bioactive molecules produced by the chemical industry, to the classical biological warfare agents. The new, emerging threat agents are biotoxins produced by animals, plants, fungi, and bacteria. Many types of organisms produce substances that are toxic to humans. Examples of such biotoxins are botulinum toxin, tetanus toxin, and ricin. Several bioactive molecules produced by the pharmaceutical industry can be even more toxic than are the classical chemical warfare agents. Such new agents, like the biotoxins and bioregulators, often are called mid-spectrum agents. The threat to humans from agents developed by modern chemical synthesis and by genetic engineering also must be considered, since such agents may be more toxic or more effective in causing death or incapacitation than classical warfare agents. By developing effective medical protection and treatment against the most likely chemical and mid-spectrum threat agents, the effects of such agents in a war scenario or following a terrorist attack can be reduced. Toxin-mediated diseases have made humans ill for millennia. Unfortunately, the use of biological agents as weapons of terror has now been realized, and separating naturally occurring disease from bioterroristic events has become an important public health goal. The key to timely identification of such attacks relies on education of primary care physicians, first responders, and public health officials.
Bacterial Toxins↗
Engineering the electronic structure of single-walled carbon nanotubes by chemical functionalization.
Explore the source record for details and available documents.
Journal Article↗
Plasma- and chemical-induced graft polymerization on the surface of starch-based biomaterials aimed at improving cell adhesion and proliferation.
Plasma and chemical induced graft polymerization of acrylic monomers on starch-based biomaterials has been performed with the aim to improve cell adhesion and proliferation on the surface of the polymers, in order to adequate their properties for bone tissue engineering scaffolding applications. Plasma and chemical surface activation was aimed to induce the polymerization of acrylic polar monomers being carried out by applying a radio frequency plasma and expose the samples to a mixture of Ar/O2, or by immersion in a H2O2/(NH4)2S2O8 solution with UV radiation, respectively. Both procedures were followed by the graft polymerization of the corresponding monomers. Polymer grafting was analyzed by Fourier transformed infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) and by contact angle measurements. Properties such as mechanical performance, swelling degree, and degradation behavior, as well as bioactivity, have been studied and compared for the different activation methods. Finally, preliminary cell adhesion and proliferation tests were performed, using goat bone marrow cells, showing a remarkable improvement with respect to original non-surface modified starch-based biomaterials.
Journal Article↗
Physico-chemical characteristics of corrosion scales in old iron pipes.
Corrosion scales play an important role in modifying water quality in drinking water distribution systems. The corrosion scales from old iron/steel pipes were analyzed for their structure and composition. Scales were studied both before and after drying. and goethite, magnetite and lepidocrocite were identified as the primary constituents of the dried samples. High concentrations of readily soluble ferrous phases were detected in wet-scale samples. The corrosion scales had a shell-like, enveloping layer, covering porous deposits of iron oxide phases. Our studies were able to identify important differences between corrosion scales found in two different water distribution systems. Further studies are needed to establish the role of corrosion scales in the mechanism of iron release from corroded pipes.
Corrosion↗
Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: homoacetate production.
Microbial processes for commodity chemicals have focused on reduced products and anaerobic conditions where substrate loss to cell mass and CO(2) are minimal and product yields are high. To facilitate expansion into more oxidized chemicals, Escherichia coli W3110 was genetically engineered for acetate production by using an approach that combines attributes of fermentative and oxidative metabolism (rapid growth, external electron acceptor) into a single biocatalyst. The resulting strain (TC36) converted 333 mM glucose into 572 mM acetate, a product of equivalent oxidation state, in 18 h. With excess glucose, a maximum of 878 mM acetate was produced. Strain TC36 was constructed by sequentially assembling deletions that inactivated oxidative phosphorylation (deltaatpFH), disrupted the cyclic function of the tricarboxylic acid pathway (deltasucA), and eliminated native fermentation pathways (deltafocA-pflB deltafrdBC deltaldhA deltaadhE). These mutations minimized the loss of substrate carbon and the oxygen requirement for redox balance. Although TC36 produces only four ATPs per glucose, this strain grows well in mineral salts medium and has no auxotrophic requirement. Glycolytic flux in TC36 (0.3 micromol.min(-1).mg(-1) protein) was twice that of the parent. Higher flux was attributed to a deletion of membrane-coupling subunits in (F(1)F(0))H(+)-ATP synthase that inactivated ATP synthesis while retaining cytoplasmic F(1)-ATPase activity. The effectiveness of this deletion in stimulating flux provides further evidence for the importance of ATP supply and demand in the regulation of central metabolism. Derivatives of TC36 may prove useful for the commercial production of a variety of commodity chemicals.
Acetates↗
Golden age of insecticide research: past, present, or future?
Insecticide research led to the first "complete" victories in combatting pests almost 50 years ago with the chlorinated hydrocarbons followed quickly by the organophosphates, methylcarbamates, and pyrethroids--all neuroactive chemicals. This Golden Age of Discovery was the source of most of our current insecticides. The challenge then became health and the environment, a Golden Age met with selective and degradable compounds. Next the focus shifted to resistance, novel biochemical targets, and new chemical approaches for pest control. The current Golden Age of Genetic Engineering has curtailed, but is unlikely to eliminate, chemical use on major crops. Insecticide research, having passed through several Golden Ages, is now in a renaissance of integrating chemicals and biologicals for sustainable pest control with human safety.
Animals↗