ARAX: a graph-based modular reasoning tool for translational biomedicine

MOTIVATION

With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but progress has been hindered by the lack of an expressive analysis workflow language for translational reasoning and by the lack of a reasoning engine-supporting that language-that federates semantically integrated knowledge-bases.

RESULTS

We introduce ARAX, a new reasoning system for translational biomedicine that provides a web browser user interface and an application programming interface (API). ARAX enables users to encode translational biomedical questions and to integrate knowledge across sources to answer the user's query and facilitate exploration of results. For ARAX, we developed new approaches to query planning, knowledge-gathering, reasoning and result ranking and dynamically integrate knowledge providers for answering biomedical questions. To illustrate ARAX's application and utility in specific disease contexts, we present several use-case examples.

AVAILABILITY AND IMPLEMENTATION

The source code and technical documentation for building the ARAX server-side software and its built-in knowledge database are freely available online (https://github.com/RTXteam/RTX). We provide a hosted ARAX service with a web browser interface at arax.rtx.ai and a web API endpoint at arax.rtx.ai/api/arax/v1.3/ui/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Demography and space-use of Eastern Red-backed Salamanders (Plethodon cinereus) between mature and successional forests

Space-use and demographic processes are critical to the persistence of populations across space and time. Despite their importance, estimates of these processes are often derived from a limited number of populations spanning broad habitat or environmental gradients. With increasing appreciation of the role fine-scale environmental variation in microgeographic adaptation, there is a need and value to assessing within-site variation in space-use and demographic patterns. In this study, we analyze 3 years of spatial capture-recapture data on the Eastern Red-backed Salamander collected from a mixed-use deciduous forest site in central Ohio, USA. Study plots were situated in both a mature forest stand and successional forest stand separated by <100-m distance. Our results showed that salamander density was reduced on successional plots, which corresponded with greater distance between nearest neighbors, less overlap in core use areas, greater space-use, and greater shifts in activity centers when compared to salamanders occupying the mature habitat. By contrast, individual growth rates of salamanders occupying the successional forest were significantly greater than salamanders in the mature forest. These estimates result in successional plot salamanders reaching maturity more than 1 year earlier than salamanders on the mature forest plots and increasing their estimated lifetime fecundity by as much as 43%. The patterns we observed in space-use and individual growth are likely the result of density-dependent processes, potentially reflecting differences in resource availability or quality. Our study highlights how fine-scale, within-site variation can shape population demographics. As research into the demographic and population consequences of climate change and habitat loss and alteration continue, future research should take care to acknowledge the role that fine-scale variation may play, especially for abiotically sensitive organisms with limited vagility.

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

BACKGROUND

Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API).

RESULTS

To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building-and hosting a web API for querying-a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink.

CONCLUSION

RTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json . The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2 .

Prey-driven behavioral habitat use in a low-energy ambush predator

Food acquisition is an important modulator of animal behavior and habitat selection that can affect fitness. Optimal foraging theory predicts that predators should select habitat patches to maximize their foraging success and net energy gain, likely achieved by targeting areas with high prey availability. However, it is debated whether prey availability drives fine-scale habitat selection for predators. We assessed whether an ambush predator, the timber rattlesnake (Crotalus horridus), exhibits optimal foraging site selection based on the spatial distribution and availability of prey. We used passive infrared camera trap detections of potential small mammal prey (Peromyscus spp., Tamias striatus, and Sciurus spp.) to generate variables of prey availability across the study area and used whether a snake was observed in a foraging location or not to model optimal foraging in timber rattlesnakes. Our models of small mammal spatial distributions broadly predicted that prey availability was greatest in mature deciduous forests, but T. striatus and Sciurus spp. exhibited greater spatial heterogeneity compared with Peromyscus spp. We found the spatial distribution of cumulative small mammal encounters (i.e., overall prey availability), rather than the distribution of any one species, to be highly predictive of snake foraging. Timber rattlesnakes appear to forage where the probability of encountering prey is greatest. Our study provides evidence for fine-scale optimal foraging in a low-energy, ambush predator and offers new insights into drivers of snake foraging and habitat selection.

Towards a seamful ethics of Covid-19 contact tracing apps?

In the early months of 2020, the deadly Covid-19 disease spread rapidly around the world. In response, national and regional governments implemented a range of emergency lockdown measures, curtailing citizens' movements and greatly limiting economic activity. More recently, as restrictions begin to be loosened or lifted entirely, the use of so-called contact tracing apps has figured prominently in many jurisdictions' plans to reopen society. Critics have questioned the utility of such technologies on a number of fronts, both practical and ethical. However, little has been said about the ways in which the normative design choices of app developers, and the products that result therefrom, might contribute to ethical reflection and wider political debate. Drawing from scholarship in critical design and human-computer interaction, this paper examines the development of a QR code-based tracking app called Zwaai ('Wave' in Dutch), where its designers explicitly positioned the app as an alternative to the predominant Bluetooth and GPS-based approaches. Through analyzing these designers' choices, this paper argues that QR code infrastructures can work to surface a set of ethical-political seams, two of which are discussed here-responsibilization and networked (im)permanence-that more 'seamless' protocols like Bluetooth actively aim to bypass, and which may go otherwise unnoticed by existing ethical frameworks.

The logic of domains

The logic of domains has become a key organizing principle for contemporary computing projects and in broader science policy. The logic parses collectives of expertise into 'domains' that are to be studied or engaged in order to inform computational advancements and/or interventions on the domains themselves. The concept of a domain is set against a proposition that there is a more general, domain independent or agnostic technique that can serve to intermediate the domains. This article contrasts instances of this discourse, organizing and techne, drawing from cases in artificial intelligence, software engineering, and science policy to illustrate three ongoing figurations of the logic as i) experimental research, ii) formalization in method and software tools, and iii) a de facto organizing principle for science policy and technology development.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.

Transmission and fluorescence X-ray absorption spectroscopy cell/flow reactor for powder samples under vacuum or in reactive atmospheres

X-ray absorption spectroscopy is an element-specific technique for probing the local atomic-scale environment around an absorber atom. It is widely used to investigate the structures of liquids and solids, being especially valuable for characterization of solid-supported catalysts. Reported cell designs are limited in capabilities-to fluorescence or transmission and to static or flowing atmospheres, or to vacuum. Our goal was to design a robust and widely applicable cell for catalyst characterizations under all these conditions-to allow tracking of changes during genesis and during operation, both under vacuum and in reactive atmospheres. Herein, we report the design of such a cell and a demonstration of its operation both with a sample under dynamic vacuum and in the presence of gases flowing at temperatures up to 300 °C, showing data obtained with both fluorescence and transmission detection. The cell allows more flexibility in catalyst characterization than any reported.

Nanoparticle distribution during systemic inflammation is size-dependent and organ-specific

This study comprehensively investigates the changing biodistribution of fluorescent-labelled polystyrene latex bead nanoparticles in a mouse model of inflammation. Since inflammation alters systemic circulatory properties, increases vessel permeability and modulates the immune system, we theorised that systemic inflammation would alter nanoparticle distribution within the body. This has implications for prospective nanocarrier-based therapies targeting inflammatory diseases. Low dose lipopolysaccharide (LPS), a bacterial endotoxin, was used to induce an inflammatory response, and 20 nm, 100 nm or 500 nm polystyrene nanoparticles were administered after 16 hours. HPLC analysis was used to accurately quantify nanoparticle retention by each vital organ, and tissue sections revealed the precise locations of nanoparticle deposition within key tissues. During inflammation, nanoparticles of all sizes redistributed, particularly to the marginal zones of the spleen. We found that LPS-induced inflammation induces splenic macrophage polarisation and alters leukocyte uptake of nanoparticles, with size-dependent effects. In addition, spleen vasculature becomes significantly more permeable following LPS treatment. We conclude that systemic inflammation affects nanoparticle distribution by multiple mechanisms, in a size dependent manner.

pH-responsive polymeric micelle carriers for siRNA drugs

The ability of small interfering RNA (siRNA) to efficiently silence the expression of specific genes provides the basis for exciting new therapies based on RNA interference (RNAi). The efficient intracellular delivery of siRNA from cell uptake through the endosomal trafficking pathways into the cytoplasm remains a significant challenge. Previously we described the synthesis of a new family of diblock copolymer siRNA carriers using controlled reversible addition-fragmentation chain transfer (RAFT) polymerization. The carriers were composed of a positively charged block of dimethylaminoethyl methacrylate (DMAEMA) to mediate siRNA binding and a second pH-responsive endosome releasing block composed of DMAEMA and propylacrylic acid (PAA) in roughly equimolar ratios and butyl methacylate (BMA). Here we describe the development of a new generation of siRNA delivery polymers based on this design that exhibit enhanced transfection efficiency and low cytotoxicity. This design incorporates a longer endosomolytic block with increased hydrophobic content to induce micelle formation. These polymers spontaneously form spherical micelles in the size range of 40 nm with CMC (critical micelle concentration) values of approximately 2 μg/mL based on dynamic light scattering (DLS), (1)H NMR, electron microscopy, and selective partitioning of the small molecule pyrene into the hydrophobic micelle core. The siRNA binding to the cationic shell block did not perturb micelle stability or significantly increase particle size. The self-assembly of the diblock copolymers into particles was shown to provide a significant enhancement in mRNA knockdown at siRNA concentrations as low as 12.5 nM. Under these conditions, the micelle-based systems showed an 89% reduction in GAPDH mRNA levels as compared to only 23% (10 nM siRNA) for the nonmicelle system. The reduction in mRNA levels becomes nearly quantitative as the siRNA concentration is increased to 25 nM and higher. Flow cytometry analysis of fluorescent-labeled siRNA showed uptake in 90% of cells and a 3-fold increase in siRNA per cell compared to a standard lipid transfection agent. These results demonstrate the potential utility of this carrier design for siRNA drug delivery.

'Smart' delivery systems for biomolecular therapeutics

OBJECTIVE

There is a strong need for drug delivery systems that can deliver biological signals from biomaterials and tissue engineering scaffolds, and a particular need for new delivery systems that can efficiently deliver biomolecules to intracellular targets. Viruses and pathogens have evolved potent molecular machinery that sense the lowered pH gradient of the endosomal compartment and become activated to destabilize the endosomal membrane, thereby enhancing protein or DNA transport to the cytoplasmic compartment. A key feature of many of these biological delivery systems is that they are reversible, so that the delivery systems are not directly toxic. These delivery systems have the ability to change their structural and functional properties and thus display remarkable 'smart' material properties. The objective of this presentation is to review the initial development of smart polymeric carriers that mimic these biological delivery systems and combine similar pH-sensitive, membrane-destabilizing activity for the delivery of therapeutic biomolecules.

DESIGN

We have developed new 'smart' polymeric carriers to more effectively deliver and broaden the available types of biomolecular therapeutics. The polymers are hydrophilic and stealth-like at physiological pH, but become membrane-destabilizing after uptake into the endosomal compartment where they enhance the release of therapeutic cargo into the cytoplasm. They can be designed to provide a range of pH profiles and membrane-destabilizing activities, allowing their molecular properties to be matched to specific drugs and loading ranges. A versatile set of linker chemistries is available to provide degradable conjugation sites for proteins, nucleic acids, and/or targeting moieties.

RESULTS

The physical properties of several pH-responsive polymers were examined. The activity and pH profile can be manipulated by controlling the length of hydrophobic alkyl segments. The delivery of poly(propyl acrylic acid) (PPAA)-containing lipoplexes significantly enhanced wound healing through the interconnected effects of altered extracellular matrix organization and greater vascularization. PPAA has also been shown to enhance cytoplasmic delivery of a model protein therapeutic. Polymeric carriers displaying pH-sensitive, membrane-destabilizing activity were also examined. The pH profile is controlled by the choice of the alkylacrylic acid monomer and by the ratio of the carboxylate-containing alkylacrylic acid monomer to alkylacrylate monomer. The membrane destabilizing activity is controlled by the lengths of the alkyl segment on the alkylacrylic acid monomer and the alkylacrylate monomer, as well as by their ratio in the final polymer chains.

CONCLUSION

The molecular mechanisms that proteins use to sense and destabilize provide interesting paradigms for the development of new polymeric delivery systems that mimic biological strategies for promoting the intracellular delivery of biomolecular drugs. The key feature of these polymers is their ability to directly enhance the intracellular delivery of proteins and DNA, by destabilizing biological membranes in response to vesicular compartment pH changes. The ability to deliver a wide variety of protein and nucleic acid drugs to intracellular compartments from tissue engineering and regenerative scaffolds could greatly enhance control of important processes such as inflammation, angiogenesis, and biomineralization.

Plasma lithography--thin-film patterning of polymers by RF plasma polymerization II: Study of differential binding using adsorption probes

In this study we present methods to physico-chemically modify micropatterned cell culture substrates that were manufactured using plasma lithography to incorporate affinity structures for specific cell binding. The surfaces consist of a pattern of a fluorocarbon plasma polymer with feature sizes between 5 and 100 microm on a background of a non-fouling tetraglyme (tetraethylene glycol dimethyl ether) plasma polymer. The tetraglyme polymer blocks virtually all non-specific binding of proteins, and it is non-adhesive for a fluorocarbon-polyethylene glycol (FC-PEG) surfactant designed to act as a 'hydrophobic anchor' for peptides. The surfactant shows a strong affinity for the fluorocarbon polymer pattern, thus enabling us to form a pattern of the surfactant-conjugated peptide. To verify this, we have synthesized a conjugate between histamine (as a model for a more complex peptide) and a commercially available FC-PEG surfactant. Disuccinimidyl carbonate was used to activate the terminal -OH group of the polyethylene glycol headgroup for the reaction with the amine-containing molecule. Affinity pattern formation can easily be achieved by immersion of the patterned substrates in a solution of the peptide-surfactant conjugate. Time of flight secondary ion mass spectroscopy in the imaging mode was used to verify that the surfactant localizes on the pattern, while the background remains bare. A model protein, bovine serum albumin, showed the same behavior. This suggests that these surfaces can be used for the formation of patterns of cell-adhesive proteins. These substrates will be used to investigate the influence of the cell size and shape of vascular smooth muscle cells on their physiology.

Plasma lithography--thin-film patterning of polymeric biomaterials by RF plasma polymerization I: Surface preparation and analysis

Plasma lithography, combining plasma deposition with photolithography, is described as a versatile method to manufacture all-polymeric substrates with thin-film patterns for applications in biomedical engineering. Patterns of a hydrophobic fluorocarbon plasma polymer with feature sizes between 5 and 100 microm were deposited on a base substrate in a lift-off process: an intermediate tetraglyme plasma polymer layer provides non-fouling properties to the base substrate. Careful analysis of critical process parameters identified the narrow window of process conditions that led to the formation of functional surface patterns. High pattern fidelity, aspect ratios, and resolution of the patterns are demonstrated by atomic force microscopy. Electron spectroscopy for chemical analysis (ESCA) and secondary ion mass spectroscopy (SIMS) were used to characterize the surfaces, showing good retention of the original chemical structure of the pattern components throughout the process. SIMS imaging was used for specific chemical imaging of the components. Potential applications for the patterned polymer films, e.g., for studying cell behavior in vitro in dependence of shape and size of adhering cells, are discussed.

Blocking adhesion to cell and tissue surfaces by the chemisorption of a poly-L-lysine-graft-(poly(ethylene glycol); phenylboronic acid) copolymer

A family of graft copolymers that can sterically inhibit interactions between biological surfaces was developed. These copolymers contained phenylboronic acid (PBA) groups as saccharide-binding moieties on a poly-(L-lysine) backbone and poly(ethylene glycol) (PEG) grafted as adhesion-resisting side chains. These copolymers spontaneously chemisorbed to a saccharide-containing resin, and this binding was sterically controlled by the PEG grafting ratio. Copolymers with optimal grafting ratios spontaneously assembled on red blood cell surfaces and sterically prevented their agglutination by lectins and by antibodies to blood groups. The simple conjugation scheme created a PBA moiety with a pKa ca. 6, which can bind cis-diols much more strongly at physiological pH than typical PBA moieties, whose pKas are typically greater than 8. These surfactant copolymers can be employed to PEGylate cell or tissue surfaces by simply incubating the surfaces with an aqueous polymer solution, and have many potential applications such as preventing antibody binding to transplanted cells.

Isolation, quantitation, and characterization of a stable complex formed by Lp[a] binding to triglyceride-rich lipoproteins

Lipoprotein [a] (Lp[a]) is a cholesterol-rich lipoprotein resembling LDL to which a large polymorphic glycoprotein, apolipoprotein [a] (apo[a]), is covalently coupled. Lp[a] usually exists as a free-standing particle in normolipidemic subjects; however, it can associate noncovalently with triglyceride-rich lipoproteins in hypertriglyceridemic (HTG) subjects. In this study, 10-78% of the Lp[a] present in five HTG subjects was found in the triglyceride-rich lipoprotein (TRL) fraction. The Lp[a]-TRL complex was resistant to dissociation by ultracentrifugation (UCF) alone, but was quantitatively dissociated by UCF in the presence of 100 mM proline. Of this dissociated Lp[a], 70-88% was in the form of a lipoprotein resembling conventional Lp[a]. Incubation of Lp[a]-depleted TRL with native Lp[a] resulted in a reconstituted Lp[a]-TRL complex that closely resembled the native isolates in all examined properties. Complex formation was inhibited by several compounds in the order proline > tranexamate > epsilon-aminocaproate >> arginine > lysine. Neither plasminogen nor LDL inhibited binding of Lp[a] to TRL. We observed the preferential binding of Lp[a] containing higher apparent molecular weight apo[a] polymorphs to TRL both in native and reconstituted Lp[a]-TRL complexes. A disproportionate amount of Lp[a] was bound to the larger TRL particles. Although most apo[a] bound to TRL was in the form of conventional Lp[a] particles, lipid-free recombinant apo[a] was observed to bind TRL. These results provide unequivocal evidence of the existence of an Lp[a]-TRL complex under pathophysiologic conditions. The metabolic fate of the Lp[a]-TRL complex, which is more abundant in hypertriglyceridemia, may be different from that of conventional Lp[a], and may contribute uniquely to the progression or severity of cardiovascular disease.

A pH-sensitive polymer that enhances cationic lipid-mediated gene transfer

The efficient release of nonviral gene carriers from endosomes is an important step for the successful delivery of DNA into the cell nucleus. A synthetic pH-sensitive anionic polymer, poly(propylacrylic acid) (PPAA), was designed to aid in endosomal escape of nonviral vectors and improve the transfection efficiencies with these vectors. Transfection of NIH3T3 fibroblasts with ternary physical mixtures of the cationic lipid DOTAP, pCMVbeta plasmid DNA, and PPAA showed marked enhancement of both gene expression levels and fraction of cells transfected compared to binary control mixtures of DOTAP and DNA. PPAA also significantly improved the serum-stability of DOTAP/DNA vectors. The DOTAP/DNA/PPAA vectors maintained high levels of transfection in media containing up to 50% serum. The striking enhancement of transfection efficiency with cationic lipid/DNA/PPAA mixtures, along with the enhanced serum-stability, suggests that PPAA may provide significant improvements for the in vivo intracellular delivery of drugs such as DNA, oligonucleotides, proteins, and peptides.

Hydrogels for biomedical applications

This paper reviews the composition and synthesis of hydrogels, the character of their absorbed water, and permeation of solutes within their swollen matrices. The most important properties of hydrogels relevant to their biomedical applications are also identified, in particular for use of hydrogels as drug and cell carriers, and as tissue engineering matrices.

Control of shape and size of vascular smooth muscle cells in vitro by plasma lithography

The ability to control the shape and size of cells is an important enabling technique for investigating influences of geometrical variables on cell physiology. Herein we present a micropatterning technique ("plasma lithography") that uses photolithography and plasma thin-film polymerization for the fabrication of cell culture substrates with a cell-adhesive pattern on a cell-repellent (non-fouling) background. The micron-level pattern was designed to isolate individual vascular smooth muscle cells (SMC) on areas with a projected area of between 25 and 3600 microm(2) in order to later study their response to cytokine stimulation in dependence of the cell size and shape as an indication for the phenotypic state of the cells. Polyethylene terephthalate substrates were first coated with a non-fouling plasma polymer of tetraglyme (tetraethylene glycol dimethyl ether). In an organic lift-off process, we then fashioned square- and rectangular-shaped islands of a thin fluorocarbon plasma polymer film of approximately 12-nm thickness. Electron spectroscopy for chemical analysis and secondary ion mass spectroscopy were used to optimize the deposition conditions and characterize the resulting polymers. Secondary ion mass spectroscopy imaging was used to visualize the spatial distribution of the polymer components of the micropatterned surfaces. Rat vascular SMC were seeded onto the patterned substrates in serum-free medium to show that the substrates display the desired properties, and that cell shape can indeed be controlled. For long-term maintenance of these cells, the medium was augmented with 10% calf serum after 24 h in culture, and the medium was exchanged every 3 days. After 2 weeks, the cells were still confined to the areas of the adhesive pattern, and when one or more cells spanned more than one island, they did not attach to the intervening tetraethylene glycol dimethyl ether (tetraglyme) background. Spreading-restricted cells formed a well-ordered actin skeleton, which was most dense along the perimeter of the cells. The shape of the nucleus was also influenced by the pattern geometry. These properties make the patterned substrates suitable for investigating if the phenotypic reversion of SMC can be influenced by controlling the shape and size of SMC in vitro.

New antibody purification procedure using a thermally responsive poly(N-isopropylacrylamide)-dextran derivative conjugate

Through their specificity and affinity, antibodies are useful tools in research and medicine. In this study, we investigated a new type of chromatographic method using a thermosensitive polymer for the purification of antibodies against a dextran derivative (DD), as a model. The thermally reversible soluble-insoluble poly(N-isopropylacrylamide)-dextran derivative conjugate, named poly(NIPAAm)-DD, has been synthesized by conjugating amino-terminated poly(N-isopropylacrylamide) to a DD via ethyl-3-(3-dimethylaminopropyl)-carbodiimide. On one hand, this report describes the two steps of poly(NIPAAm)-DD conjugation and characterization. On the other hand, the poly(NIPAAm)-DD conjugate was used as a tool to purify polyclonal antibodies in serum samples from rabbits subcutaneously immunized with the derivatized dextran. Antibodies were purified and quantified by immunoenzymatic assays. Our results indicate that antibodies recognized both DD and poly(NIPAAm)-DD. In contrast, they did not bind to native poly(NIPAAm) or poly(NIPAAm) conjugated with another anionic dextran. We conclude that the conjugation of a polysaccharide to poly(NIPAAm) leads to an original and efficient chromatographic method to purify antibodies. Moreover, this novel method of purification is rapid, sensitive, inexpensive and could be used to purify various types of antibodies.

Insoluble ionic complexes of polyacrylic acid with a cationic drug for use as a mucoadhesive, ophthalmic drug delivery system

We have developed a new mucoadhesive drug delivery formulation based on an ionic complex of partially neutralized poly(acrylic acid) (PAA) and a highly potent beta blocker drug, levobetaxolol x hydrochloride (LB x HCl), for use in the treatment of glaucoma. PAA was neutralized with sodium hydroxide to varying degrees of neutralization. Aqueous solutions containing concentrations of LB x HCl equivalent to the degree of PAA neutralization were added to the PAA solutions and formed insoluble complexes, which were isolated. The complex formation was followed by turbidimetric titration, and the complexes were characterized by IR and 1H NMR spectroscopy. Complexes were prepared with varying degrees of drug loading, such that the same PAA chain would have free -COOH groups for mucoadhesion along with ionic complexes of LB x H+ with COO- groups. Thin films of the complexes dissociated to release the drug by ion exchange with synthetic tear fluid. The films shrunk continuously during release of the drug and dissolved completely in 1 h. Solid inserts of these films could be useful as a mucoadhesive ophthalmic drug delivery system.

Release of PEGylated granulocyte-macrophage colony-stimulating factor from chitosan/glycerol films

We have prepared a new formulation for mucosal delivery of GM-CSF or PEGylated GM-CSF based on a chitosan carrier plus added glycerol to control the rate of release of the protein. Thin dry films comprised of various weight ratios of chitosan to glycerol and containing either granulocyte-macrophage colony-stimulating factor (GM-CSF) or PEGylated GM-CSF, PEG-(GM-CSF), were prepared. The amount of GM-CSF or PEG-(GM-CSF) released from the chitosan/glycerol films was determined using size exclusion high performance liquid chromatography (HPLC-SEC). The amount of PEG-(GM-CSF) released from the films decreased with an increase in the amount of glycerol present in the film. In parallel with this, films with higher glycerol content exhibited a lower degree of equilibrium swelling when immersed in release media. pH measurements of the release media and analysis of the dried films by Fourier-transform infrared spectroscopy (FTIR) suggested that the amount of residual acetic acid in the dry films decreased as the glycerol content increased. This indicates that glycerol may act by displacing and releasing bound acetic acid from the chitosan molecules, resulting in chitosan--glycerol hydrogen bond formation as the film dries. Further, it was found that the release rate and the amount of PEG-(GM-CSF) released decreased with increasing molecular weight of the conjugated PEG. This effect was not observed with films containing physical mixtures of PEG and GM-CSF. The decrease in the fraction of PEG-(GM-CSF) released with increasing PEG molecular weight is believed to be due to the increased steric hindrance of the PEGylated protein molecule during its diffusion out of the swollen chitosan/glycerol film.

Size-dependent control of the binding of biotinylated proteins to streptavidin using a polymer shield

Many medical and biotechnological processes rely on controlling and manipulating the molecular-recognition capabilities of proteins. This can be achieved using small molecules capable of competing for protein binding or by changing environmental parameters that affect protein structure and hence binding. An alternative is provided by stimuli-responsive polymers that change reversibly from a water-soluble expanded coil to a water-insoluble collapsed globule upon small changes in temperature, pH or light intensity: when attached to proteins in the vicinity of their binding sites, they reversibly block and release small ligands. Here we show how this approach can be extended to achieve size-selective binding of large, macromolecular ligands. We use the thermally responsive polymer poly(N,N-diethylacrylamide) (PDEAAm), and attach it to the protein streptavidin approximately 20 A from the binding site for biotinylated proteins. Below the lower critical solution temperature of PDEAAm, the polymer is in its extended state and acts as a 'shield' to block the binding of large biotinylated proteins; above this temperature, it collapses and exposes the binding site, thereby allowing binding. We find that the degree of shielding depends on both the size of the biotinylated protein and the size of PDEAAm, suggesting that 'smart' polymer shields could be tailored to achieve a wide range of size-dependent ligand discrimination for use in affinity separations, biosensors and diagnostics technologies.

Mechanistic investigation of smart polymer-protein conjugates

Many affinity separation and diagnostic applications rely upon both capture and release steps. There is thus a need for methods to enhance the reversibility of biomolecular interactions. We have previously demonstrated that stimuli-responsive polymers can be used to gate biomolecular reactions when conjugated near the active site of proteins. Here we have used a new smart polymer, N,N-dimethyl acrylamide-co-4-phenylazophenylacrylate that has allowed a mechanistic investigation of the smart polymer switches. This polymer was conjugated via a vinyl sulfone terminus to cysteine residues of genetically engineered streptavidin mutant E116C, where the polymer is conjugated close to the biotin-binding site, and streptavidin mutant S139C, where the conjugation site is distant. The biotin binding switching activity was strongly dependent on conjugation position, as the E116C conjugate displayed a large thermal response while the S139C conjugate displayed only small effects. Kinetic measurements of biotin release demonstrated that the off-rate of biotin was unperturbed and that the thermally triggered release of biotin with the E116C conjugate was due to the blocking the reassociation of biotin. The addition of free polymer to purified E116C conjugates was also shown to increase the blocking and release properties of the switch. This effect was site dependent, suggesting that the conjugated polymers were directing a physical aggregation near the binding site that effectively enhanced the switching activity. These investigations provide mechanistic insight that can be utilized to design better molecular switches for a variety of stimuli-responsive polymer-protein conjugates.

A reverse microemulsion polymerization method for preparation of bioadhesive polyacrylic acid nanoparticles for mucosal drug delivery: loading and release of timolol maleate

Polyacrylic acid nanoparticles were successfully synthesized using a reverse microemulsion polymerization process. They had a narrow size range, averaging approximately 50 nm, and were stable in buffer. The particles were isolated and lyophilized in dry powder form, and were redispersible as individual particles in buffer. The drug timolol maleate was loaded into the nanoparticles from aqueous drug solutions and, when the drug-loaded particles were dispersed in a phosphate buffer solution, the drug slowly released over several hours from the nanoparticles.

Founder's Award, Society for Biomaterials. Sixth World Biomaterials Congress 2000, Kamuela, HI,May 15-20, 2000. Really smart bioconjugates of smart polymers and receptor proteins

Over the past 18 years we have been deeply involved with the synthesis and applications of stimuli-responsive polymer systems, especially polymer-biomolecule conjugates. This article summarizes our work with one of these conjugate systems, specifically polymer-protein conjugates. We include conjugates prepared by random polymer conjugation to lysine amino groups, and also those prepared by site-specific conjugation of the polymer to specific amino acid sites that are genetically engineered into the known amino acid sequence of the protein. We describe the preparation and properties of thermally sensitive random conjugates to enzymes and several affinity recognition proteins. We have also prepared site-specific conjugates to streptavidin with temperature-sensitive polymers, pH-sensitive polymers, and light-sensitive polymers. The preparation of these conjugates and their many fascinating applications are reviewed in this article.

Mucoadhesive drug carriers based on complexes of poly(acrylic acid) and PEGylated drugs having hydrolysable PEG-anhydride-drug linkages

We have designed a new mucoadhesive drug delivery formulation based on H-bonded complexes of poly(acrylic acid) (PAA) or poly(methacrylic acid) (PMAA) with the poly(ethylene glycol) (PEG), of a (PEG)-drug conjugate. The PEGylated prodrugs are synthesized with degradable PEG-anhydride-drug bonds for eventual delivery of free drug from the formulation. In this work we have used indomethacin as the model drug which is PEGylated via anhydride bonds to the PEG. The complexes are designed first to dissociate as the formulation swells in contact with mucosal surfaces at pH 7.4, releasing PEG-indomethacin, which then hydrolyses to release free drug and free PEG. We found that as MW of PAA increases, the dissociation rate of the complex decreases, which results in decreased rate of release of the drug. On the other hand, the drug release from PEG-indomethacin alone and from solid mixture of PEG-indomethacin+PAA was much faster than that from the H-bonded complexes. Due to the differences in the thermal stability, PMAA complex exhibited slightly faster drug release than that of the PAA complex of comparable MW. These H-bonded complexes of degradable PEGylated drugs with bioadhesive polymers should be useful for mucosal drug delivery.

Bioconjugates of intelligent polymers and recognition proteins for use in diagnostics and affinity separations

Polymers that respond to small changes in environmental stimuli with large, sometimes discontinuous changes in their physical state or properties are often called "intelligent" or "smart" polymers. We have conjugated these polymers to different recognition proteins, including antibodies, protein A, streptavidin, and enzymes. These bioconjugates have been prepared by random polymer conjugation to lysine amino groups on the protein surface, and also by site-specific conjugation of the polymer to specific amino acid sites, such as cysteine sulfhydryl groups, that are genetically engineered into the known amino acid sequence of the protein. We have conjugated several different smart polymers to streptavidin, including temperature-, pH-, and light-sensitive polymers. The preparation of these conjugates and their many fascinating applications are reviewed here.

The stabilization and release of hirudin from liposomes or lipid-assemblies coated with hydrophobically modified dextran

Hirudin is a 65-amino acid peptide and the most potent and specific known inhibitor of thrombin (K(i) = 0.2 pM). The short elimination half-life of hirudin from the body (1 hour) necessitates the use of a sustained and controlled delivery system. A proliposome method was used to entrap hirudin in liposomes coated with palmitoyl dextran-coated liposomes and lipid-assemblies. In vitro release studies of hirudin were performed using the lipid systems enclosed in dialysis membranes or deposited in the pores of a vascular graft. The activity of hirudin and released hirudin was measured using a thrombin chromogenic substrate assay. Entrapment efficiencies of hirudin in lipid-assemblies approached 100%, however, the release of hirudin from these systems was rapid with 90% released in 17 hours. Entrapment efficiencies of hirudin in coated-liposomes ranged from 5% to 55% and were dependent on several variables. Palmitoyl dextran- coated-liposomes showed a burst of 30% hirudin released in 5 hours with an additional 10% to 35% released over the next 600 hours. In all samples, 30-40% of the hirudin remained associated with the lipid-systems even after 600 hours. The released hirudin retained only 33% of its ability to inhibit thrombin when released from uncoated liposomes. However, hirudin retained 95% of its thrombin inhibitory activity when released from palmitoyl dextran-coated liposomes. Coated liposomes were found to stabilize hirudin and result in greater retention of hirudin's ability to inhibit thrombin's enzymatic activity, although the mechanism is not yet understood.

Molecular engineering of proteins and polymers for targeting and intracellular delivery of therapeutics

There are many protein and DNA based therapeutics under development in the biotechnology and pharmaceutical industries. Key delivery challenges remain before many of these biomolecular therapeutics reach the clinic. Two important barriers are the effective targeting of drugs to specific tissues and cells and the subsequent intracellular delivery to appropriate cellular compartments. In this review, we summarize protein engineering work aimed at improving the stability and refolding efficiency of antibody fragments used in targeting, and at constructing new streptavidin variants which may offer improved performance in pre-targeting delivery strategies. In addition, we review recent work with pH-responsive polymers that mimic the membrane disruptive properties of viruses and toxins. These polymers could serve as alternatives to fusogenic peptides in gene therapy formulations and to enhance the intracellular delivery of protein therapeutics that function in the cytoplasm.

Site-specific polymer-streptavidin bioconjugate for pH-controlled binding and triggered release of biotin

Low molecular weight copolymers of acrylic acid (AAc) and N-isopropylacrylamide (NIPAAm) have been synthesized with reactive OH groups at one end, using a chain transfer polymerization technique. The copolymer displays both pH and temperature sensitivity over a wide and useful range of pHs and temperatures, which permits both pH and temperature control of polymer conformation. This copolymer has been conjugated to a specific cysteine thiol site inserted by genetic engineering near the recognition site of streptavidin (SAv). In this paper, we demonstrate that this bioconjugate can provide pH control of biotin binding to and triggered release from the mutant SAv. These actions are relevant to affinity separations, biosensors, diagnostics, enzyme processes, and targeted delivery of drugs or chemical agents, labels, and other signals.

Smart and biofunctional streptavidin

The high affinity recognition of biotin and biotinylated molecules has made streptavidin one of the most important components in diagnostics and laboratory kits. While it is extremely useful as the native protein, there are many applications where its function can be improved re-engineering the subunits. We review here our efforts to construct streptavidin tetramers that have 'smart' recognition capabilities, and which display functional peptide sequences. These smart and biofunctional streptavidin derivatives can 'talk' to cells, and 'listen' to external signals which control capture and release of biotinylated molecules.

Thermoprecipitation of streptavidin via oligonucleotide-mediated self-assembly with poly(N-isopropylacrylamide)

A versatile strategy has been developed for selectively and sequentially isolating targets in a liquid-phase affinity separation environment. The strategy uses a recently developed approach for joining together molecules in linkages that are defined by the complementary pairing of oligonucleotides conjugated to the different molecules [Niemeyer, C. M., Sano, T., Smith, C. L., and Cantor, C. R. (1994) Nucleic Acids Res. 22, 5530-9]. In the work presented here, streptavidin was noncovalently coupled with the temperature-responsive poly(N-isopropylacrylamide) [poly(NIPAAM)] through the sequence-specific hybridization of oligonucleotides conjugated to the protein and polymer. A 20-mer oligonucleotide was covalently linked through a heterobifunctional linker to a genetically engineered streptavidin variant that contained a unique cysteine residue at the solvent-accessible site Glu 116. The complementary DNA sequence was conjugated to the end of a linear ester-activated poly(NIPAAM). The two conjugates were allowed to self-assemble in solution via hybridization of their complementary DNA sequences. The streptavidin-poly(NIPAAM) complex could be used to affinity-precipitate radiolabeled biotin or biotinylated alkaline phosphatase above 32 degrees C through the thermally induced phase separation activity of the poly(NIPAAM). The streptavidin-oligo species could then be reversibly separated from the precipitated polymer-oligo conjugate and recycled by lowering the salt concentration, which results in denaturation of the short double-stranded DNA connection. The use of oligonucleotides to couple polymer to streptavidin allows for selective precipitation of different polymers and streptavidin complexes based on the sequence-specific hybridization of their oligonucleotide appendages.

The design and synthesis of polymers for eukaryotic membrane disruption

The intracellular trafficking of drugs is critical to the efficacy of drugs that are susceptible to attack by lysosomal enzymes. It is therefore an important goal to design and synthesize molecules which can enhance the transport of endocytosed drugs from the endosomal compartments to the cytoplasm. The pH of an endosome is lower than that of the cytosol by one to two pH units, depending on the stage of endosomal development. This pH gradient is a key factor in the design of membrane-disruptive polymers which could enhance the endosomal release of drugs. Such polymers should disrupt lipid bilayer membranes at pH 6.5 and below, but should be non-lytic at pH 7.4. We have designed and synthesized pH-sensitive synthetic polymers which efficiently disrupt red blood cells within a sharply defined pH range. One of these polymers, poly(ethyl acrylic acid) (PEAAc) has been previously shown to disrupt synthetic vesicles in a pH-dependent fashion [6]. PEAAc hemolyzes red blood cells with an activity of 10(7) molecules per red blood cell, which is as efficient on a molar basis as the peptide melittin. The mechanism of RBC hemolysis by PEAAc is consistent with the colloid osmotic mechanism. PEAAc's hemolytic activity rises rapidly as the pH decreases from 6.3 to 5.0, and there is no hemolytic activity at pH 7.4. A related polymer, poly(propyl acrylic acid) (PPAAc), was synthesized to test whether making the pendant alkyl group more hydrophobic by adding one methylene group would increase the hemolytic activity. PPAAc was found to disrupt red blood cells 15 times more efficiently than PEAAc at pH 6.1. PPAAc was also not active at pH 7.4 and displayed a pH-dependent hemolysis that was shifted toward higher pH's. Random 1:1 copolymers of ethyl acrylate (EA) and acrylic acid (AAc) (which contain random -COOH and -C(2)H(5) groups that are present and regularly repeat in PEAAc) also displayed significant hemolytic activity, with an efficiency close to PEAAc. These results demonstrate that pH-sensitive synthetic polymers can be molecularly engineered to efficiently disrupt eukaryotic membranes within defined and narrow pH ranges. Thus, these polymers might serve as endosomal disruptive agents with specificities for early or late endosomes.

Hemolytic activity of pH-responsive polymer-streptavidin bioconjugates

Drug delivery systems that increase the rate and/or quantity of drug release to the cytoplasm are needed to enhance cytosolic delivery and to circumvent nonproductive cell trafficking routes. We have previously demonstrated that poly(2-ethylacrylic acid) (PEAAc) has pH-dependent hemolytic properties, and more recently, we have found that poly(2-propylacrylic acid) (PPAAc) displays even greater pH-responsive hemolytic activity than PEAAc at the acidic pHs of the early endosome. Thus, these polymers could potentially serve as endosomal releasing agents in immunotoxin therapies. In this paper, we have investigated whether the pH-dependent membrane disruptive activity of PPAAc is retained after binding to a protein. We did this by measuring the hemolytic activity of PPAAc-streptavidin model complexes with different protein to polymer stoichiometries. Biotin was conjugated to amine-terminated PPAAc, which was subsequently bound to streptavidin by biotin complexation. The ability of these samples to disrupt red blood cell membranes was investigated for a range of polymer concentrations, a range of pH values, and two polymer-to-streptavidin ratios of 3:1 and 1:1. The results demonstrate that (a) the PPAAc-streptavidin complex retains the ability to lyse the RBC lipid bilayers at low pHs, such as those existing in endosomes, and (b) the hemolytic ability of the PPAAc-streptavidin complex is similar to that of the free PPAAc.

Temperature control of biotin binding and release with A streptavidin-poly(N-isopropylacrylamide) site-specific conjugate

The many laboratory and diagnostic applications utilizing streptavidin as a molecular adaptor rely on its high affinity and essentially irreversible interaction with biotin. However, there are many situations where recovery of the biotinylated molecules is desirable. We have previously shown that poly(N-isopropylacrylamide) (PNIPAAm), a temperature-sensitive polymer, can reversibly block biotin association as the polymer's conformation changes at its lower critical solution temperature (LCST). Here, we have constructed a streptavidin-PNIPAAm conjugate which is able to bind biotin at room temperature or lower and release bound biotin at 37 degrees C. The conjugate can repeatedly bind and release biotin as temperature is cycled through the LCST. A genetically engineered streptavidin mutant, E116C, which has only one cysteine residue, was conjugated site specifically via the sulfhydryl groups with a PNIPAAm that has pendent sulfhydryl-reactive vinyl sulfone groups. The conjugation site is near the tryptophan 120 residue, which forms a van der Waals contact with biotin that is important in generating the large binding free energy. The temperature-induced conformational change of the polymer at position 116 may lead to structural changes in the region of tryptophan 120 that are responsible for the reversible binding between biotin and the conjugated streptavidin.

Mice that lack the angiogenesis inhibitor, thrombospondin 2, mount an altered foreign body reaction characterized by increased vascularity

Disruption of the thrombospondin 2 gene (Thbs2) in mice results in a complex phenotype characterized chiefly by abnormalities in fibroblasts, connective tissues, and blood vessels. Consideration of this phenotype suggested to us that the foreign body reaction (FBR) might be altered in thrombospondin 2 (TSP2)-null mice. To investigate the participation of TSP2 in the FBR, polydimethylsiloxane (PDMS) and oxidized PDMS (ox-PDMS) disks were implanted in TSP2-null and control mice. Growth of TSP2-null and control skin fibroblasts in vitro also was evaluated on both types of disks. Normal fibroblasts grew as a monolayer on both surfaces, but attachment of the cells to ox-PDMS was weak and sensitive to movement. TSP2-null fibroblasts grew as aggregates on both surfaces, and their attachment was further compromised on ox-PDMS. After a 4-week implantation period, both types of PDMS elicited a similar FBR with a collagenous capsule in both TSP2-null and control mice. However, strikingly, the collagenous capsule that formed in TSP2-null mice was highly vascularized and thicker than that formed in normal mice. In addition, abnormally shaped collagen fibers were observed in capsules from mutant mice. These observations indicate that the presence or absence of an extracellular matrix component, TSP2, can influence the nature of the FBR, in particular its vascularity. The expression of TSP2 therefore could represent a molecular target for local inhibitory measures when vascularization of the tissue surrounding an implanted device is desired.

Lysozyme loading and release from hydrogels carrying pendant phosphate groups

To develop a polymeric matrix for efficiently loading cationic biomolecules, polyelectrolyte hydrogels carrying pendant phosphate groups were synthesized by copolymerizing 2-methacryloyloxyethyl dihydrogen phosphate with N-isopropylacrylamide and N, N1-methylene-bis-acrylamide. The phosphate-carrying monomer yielded anionic hydrogels, which formed ionic complexes with the cationic protein, lysozyme. It was shown that the amount of complexed lysozyme reached 2.1 g g-1 dry gel, corresponding to 1.3 x 10(-3) mol phosphate group per gram lysozyme, when 40 mol% of phosphate-carrying monomer was incorporated in a hydrogel. When the hydrogel complexed with lysozyme was placed in deionized water and various KCl solutions, of varying concentrations of up to 0.5 M KCl, no lysozyme was released in deionized water, while increasing amounts of lysozyme were released as the KCl concentration increased. This confirmed that lysozyme was loaded in the hydrogel through electrostatic interactions. It was further found that the complexed lysozyme retained its enzymatic activity after being released from the hydrogel. These results suggest the use of this system for the controlled release of cationic protein drugs.

Unusual properties of thermally sensitive oligomer-enzyme conjugates of poly(N-isopropylacrylamide)-trypsin

Reversible soluble-insoluble oligomer-enzyme conjugates have been prepared by conjugating a thermally sensitive oligomer, poly(N-isopropylacrylamide) [poly(NIPAAm)] to trypsin. The conjugates can catalyze enzymatic reactions in solution and then may be separated from the solution by thermal precipitation. One special feature of the conjugates is that every poly(NIPAAm) chain has only one end attachment to the enzyme, so that the loss of enzymatic activity due to steric hindrance should be minimized. Conjugates with various numbers of oligomer chains per trypsin molecule were prepared. Surprisingly, the conjugates increased in enzymatic activity with increasing oligomer conjugation to the native trypsin. The trypsin active sites in the conjugates were accessible to large molecules, such as soybean trypsin inhibitor (MW = 21,500). The enzyme conjugates were more stable than native trypsin, both in solution and in the precipitated phase. On the other hand, the conjugates lost enzymatic activity faster than native trypsin when the temperature was repeatedly cycled through the lower critical solution temperature (LCST) of the poly(NIPAAm). The recovery of the conjugates by thermal precipitation in each cycle was over 95% even after 14 cycles through the LCST.

An AB block copolymer of oligo(methyl methacrylate) and poly(acrylic acid) for micellar delivery of hydrophobic drugs

An AB block copolymer of oligo(methyl methacrylate) (oMMA) and poly(acrylic acid) (PAAc) has been synthesized. The block copolymer forms micelles in an aqueous medium, as confirmed by a fluorescence probe technique using pyrene. Doxorubicin hydrochloride was incorporated into the micelle and the release profile of doxorubicin hydrochloride was investigated. Slow and prolonged release of doxorubicin hydrochloride from the micelle was observed. The AB block copolymer micelle can be useful for prolonged mucosal drug delivery of hydrophobic drugs.

Lysozyme loading and release from hydrogels carrying pendant phosphate groups

To develop a polymeric matrix for efficiently loading cationic biomolecules, polyelectrolyte hydrogels carrying pendant phosphate groups were synthesized by copolymerizing 2-methacryloyloxyethyl dihydrogen phosphate with N-isopropylacrylamide and N, N1-methylene-bis-acrylamide. The phosphate-carrying monomer yielded anionic hydrogels, which formed ionic complexes with the cationic protein, lysozyme. It was shown that the amount of complexed lysozyme reached 2.1 g g-1 dry gel, corresponding to 1.3 x 10(-3) mol phosphate group per gram lysozyme, when 40 mol% of phosphate-carrying monomer was incorporated in a hydrogel. When the hydrogel complexed with lysozyme was placed in deionized water and various KCl solutions, of varying concentrations of up to 0.5 M KCl, no lysozyme was released in deionized water, while increasing amounts of lysozyme were released as the KCl concentration increased. This confirmed that lysozyme was loaded in the hydrogel through electrostatic interactions. It was further found that the complexed lysozyme retained its enzymatic activity after being released from the hydrogel. These results suggest the use of this system for the controlled release of cationic protein drugs.

Synthesis and purification of thermally sensitive oligomer-enzyme conjugates of poly(N-isopropylacrylamide)-trypsin

Using chain-transfer polymerization, we have synthesized oligomers of poly(N-isopropylacrylamide) [poly(NIPAAm)] with one carboxyl group at the end of each oligomer chain. The lower critical solution temperature (LCST) of the oligomers is very close to that of homo-poly(NIPAAm) lacking the end carboxyl group. The carboxyl groups were activated in methylene chloride using N,N'-dicyclohexyl-carbodiimide (DCC) and N-hydroxysuccinimide (NHS). A conjugate of trypsin with the preactivated oligomer has been prepared. We studied the effect of oligomer to enzyme (O/E) ratio in the feed on the O/E ratio of the conjugate (the average number of oligomer chains conjugated to one trypsin molecule), assuming that only the primary amino groups of lysine residues and the amino terminal of trypsin would react. The O/E ratio of the conjugate was estimated by determination of the remaining primary amine groups on the trypsin molecule. More than 95% of the conjugate can be recovered by thermally induced precipitation.

Control of protein-ligand recognition using a stimuli-responsive polymer

Stimuli-responsive polymers exhibit reversible phase changes in response to changes in environmental factors such as pH or temperature. Conjugating such polymers to antibodies and proteins provides molecular systems for applications such as affinity separations, immunoassays and enzyme recovery and recycling. Here we show that conjugating a temperature-sensitive polymer to a genetically engineered site on a protein allows the protein's ligand binding affinity to be controlled. We synthesized a mutant of the protein streptavidin to enable site-specific conjugation of the responsive polymer near the protein's binding site. Normal binding of biotin to the modified protein occurs below 32 degrees C, whereas above this temperature the polymer collapses and blocks binding. The collapse of the polymer and thus the enabling and disabling of binding, is reversible. Such environmentally triggered control of binding may find many applications in biotechnology and biomedicine, such as the control of enzyme reaction rates and of biosensor activity, and the controlled release of drugs.

Platelet and monoclonal antibody binding to fibrinogen adsorbed on glow-discharge-deposited polymers

The state of fibrinogen adsorbed on untreated and glow-discharge-treated surfaces was examined by measuring platelet adhesion, monoclonal antibody (mAb) binding, the amount of fibrinogen adsorbed, and the amount of adsorbed fibrinogen which could be eluted with sodium dodecyl sulfate (SDS). Tetrafluoroethylene (TFE) glow-discharge-treated polymers have a lower surface free energy (in air) and retain a larger fraction of adsorbed fibrinogen than untreated surfaces after SDS elution. Platelet adhesion was lowest on the TFE-treated surfaces which retain the highest amounts of fibrinogen after SDS elution. Fibrinogen may undergo unfolding or spreading on the TFE-treated surfaces to minimize interfacial free energy (in water) and maximize protein-surface interactions. When it is adsorbed on the TFE-treated surfaces, fibrinogen evidently assumes a state which somehow prevents its recognition and binding by platelet receptors. Monoclonal antibodies that bind to the three regions in fibrinogen thought to be involved in platelet adhesion were therefore used to detect changes in adsorbed fibrinogen. These regions and the antibodies which bind to them are: the COOH-terminal of the gamma-chain, mAb M1; the RGD peptide sequence at A alpha 95-98, mAb R1; the RGD sequence at A alpha 572-575, mAb R2. For fibrinogen adsorbed on the untreated or TFE-treated surfaces, M1 and R2 binding was relatively high compared to background, while R1 binding was low. However, the amount of binding of each mAb to fibrinogen adsorbed on the TFE-treated surfaces was equal to or greater than fibrinogen adsorbed to the untreated surfaces. Therefore, antibody-detectable changes in the platelet binding regions of adsorbed fibrinogen that might have been caused by conformational or orientational rearrangements were not observed for the TFE-treated surfaces. The data suggest that the tight binding of fibrinogen on a surface may directly affect the ability of the fibrinogen to interact with the platelet receptors--i.e., that fibrinogen must be loosely held to facilitate maximal interaction with platelet receptors.

"Intelligent" polymers in medicine and biotechnology

One can define "intelligent" polymers as those polymers that respond with large property changes to small physical or chemical stimuli. These polymers may be in various forms, such as in solution, on surfaces, or as solids. One may also combine intelligent aqueous polymer systems with biomolecules to yield a large family of polymers that respond intelligently to physical, chemical, or biological stimuli. This article overviews such interesting and versatile polymer systems.

Graft copolymers that exhibit temperature-induced phase transitions over a wide range of pH

There are many potential applications of 'intelligent' aqueous polymer systems in medicine, biotechnology, industry and in environmental problems. Many of these polymer systems undergo reversible phase transitions--for example, abrupt changes in volume--in response to external stimuli such as temperature, pH or the nature of the solvent. Most of the polymers studied previously are responsive to only one kind of stimulus. But for some applications, independent responsiveness to several factors, such as temperature and pH, may be required. Here we describe a polymer that undergoes marked solubility changes in water in response to temperature and/or pH changes. The polymer is prepared by grafting temperature-sensitive side chains onto a pH-sensitive backbone. We also find that block copolymers, in which the temperature- and pH-sensitive units alternate along the chain, show similar behaviour.

Attempts to stabilize a monoclonal antibody with water soluble synthetic polymers of varying hydrophobicity

Proteins are subject to a variety of physical and chemical reactions that lead to a loss of activity. These reactions are a particular problem in controlled-release devices, where temperatures and protein concentrations are high. Current approaches to increasing protein stability include the addition of saccharides, amino acids, or polymers. New synthetic polymers may be promising protein stabilizers because properties such as molecular weight and side-chain composition can be controlled. In this study, the stability of a murine monoclonal antibody, BR96, was evaluated in solution at 37 degrees C. The antibody was incubated in the presence of a series of synthetic polymers that included poly(glucosylethyl methacrylate) (GEMA) and copolymers of N-vinylpyrrolidone (NVP) and methyl methacrylate (MMA). Samples were taken periodically up to 30 days. The formation of precipitated antibody in particulate aggregates was measured with a Coulter counter, and the molecular-weight distribution of soluble antibody was measured by size-exclusion chromatography. Two trends were evident. First, with poly(GEMA) and copolymers of NVP and MMA, protein aggregation increased at higher polymer concentrations. Second, higher molecular weights of the poly(NVP) homopolymer also led to increases in protein aggregation. Effects of polymer hydrophobicity were more complex. A copolymer containing 9 mol% MMA caused immediate protein precipitation, while a copolymer containing 21 mol% MMA did not. The effects of the copolymer containing 21% MMA were strongly concentration dependent. At 1 wt%, the polymer reduced aggregation, but aggregation increased strongly between concentrations of 2 and 3 wt%.