Retroviral gene transfer is inhibited by chondroitin sulfate proteoglycans/glycosaminoglycans in malignant pleural effusions

Gene therapy may be an important adjuvant for treating cancer in the pleural space. The initial results of retroviral gene transfer to cancer cells in malignant pleural effusions revealed that transduction was markedly inhibited, and studies to characterize the inhibitory factor(s) were performed. The inhibition was contained within the soluble, rather than cellular, components of the effusions and was demonstrated with amphotropic, gibbon ape leukemia virus, and vesicular stomatitis virus-glycoprotein pseudotyped retroviral vectors. After excluding complement proteins, a series of studies identified chondroitin sulfates (CSs) as the inhibitory substances. First, treatment of the effusions with mammalian hyaluronidase or chondroitinases, but not Streptomyces hyaluronidase, abolished the inhibitory activity. Second, addition of exogenous CS glycosaminoglycans mimicked the inhibition observed with pleural effusions. Third, immunoassays and biochemical analyses of malignant pleural effusion specimens revealed CS in relevant concentrations within pleural fluid. Fourth, proteoglycans/glycosaminoglycans isolated from the effusions inhibited retroviral gene transfer. Analyses of the mechanism of inhibition indicate that the chondroitin sulfates interact with vector in solution rather than at the target cell surface. These results suggest that drainage of the malignant pleural effusion, and perhaps enzymatic pretreatment of the pleural cavity, will be necessary for efficient retroviral vector mediated gene delivery to pleural metastases.     

Mapping Parallel Application Communication Topology to Rhombic Overlapping-Cluster Multiprocessors

This paper extends research into rhombic overlapping-connectivity interconnection networks into the area of parallel applications. As a foundation for a shared-memory non-uniform access bus-based multiprocessor, these interconnection networks create overlapping groups of processors, buses, and memories, forming a clustered computer architecture where the clusters overlap. This overlapping-membership characteristic is shown to be useful for matching parallel application communication topology to the architecture's bandwidth characteristics. Many parallel applications can be mapped to the architecture topology so that most or all communication is localized within an overlapping cluster, at the low latency of processor direct to cache (or memory) over a bus. The latency of communication between parallel threads does not degrade parallel performance or limit the graininess of applications. Parallel applications can execute with good speedup and scaling on a proposed architecture which is designed to obtain maximum advantage from the overlapping-cluster characteristic, and also allows dynamic workload migration without moving the instructions or data. Scalability limitations of bus-based shared-memory multiprocessors are overcome by judicious workload allocation schemes, that take advantage of the overlapping-cluster memberships. Bus-based rhombic shared-memory multiprocessors are examined in terms of parallel speedup models to explain their advantages and justify their use as a foundation for the proposed computer architecture. Interconnection bandwidth is maximized with bi-directional circular and segmented overlapping buses. Strategies for mapping parallel application communication topologies to rhombic architectures are developed. Analytical models of enhanced rhombic multiprocessor performance are developed with a unique bandwidth modeling technique, and are compared with the results of simulation.     

Toxin gene-mediated growth inhibition of lung adenocarcinoma in an animal model of pleural malignancy

Transduction of malignant cells with toxin genes provides a novel strategy by which to promote tumor cell destruction. Whereas the capacity of the toxin gene/prodrug combination cytosine deaminase/fluorocytosine to inhibit growth of human metastatic pulmonary adenocarcinoma cell lines in vitro is established, the in vivo efficacy of this binary system has not yet been determined. For the development of toxin gene therapy for the treatment of lung adenocarcinoma metastatic to the pleural space, a reliable, disease-specific model is required. The serosa of the rat small intestine resembles the basal lamina of the pleura and provides the basis for a more convenient model than direct injection of tumor into the pleural space. Adenocarcinoma cells are inoculated into everted denuded rat intestine configured as a sac. Immunocytochemical and histological analyses show rapid cell growth with characteristics that mimic nodular metastatic intrapleural disease. In the context of this model, systemically delivered fluorocytosine significantly inhibits the growth of cytosine deaminase-expressing human lung adenocarcinoma cells. The dosing schedule required 30 days; neither addition of an enzyme inhibitor that increases the half-life of fluorocytosine nor intralumenal drug delivery is effective in shortening (to 15 days) the protocol. We conclude that CD continues to hold promise as a toxin gene for lung adenocarcinoma gene therapy, and that prolonged prodrug administration may be required for maximum efficacy.     

From water to oxygen and back again: mechanistic similarities in the enzymatic redox conversions between water and dioxygen

We propose that the interconversions of water and oxygen are catalyzed by the transition metal ions of Photosystem II and cytochrome c oxidase in remarkably similar ways. Oxygen-oxygen bond formation and cleavage occurs between two oxygen atoms that are bound as terminal ligands to two redox-active metal ions. Hydrogen atom transfer to or from a tyrosine residue is an essential component of the processes in both enzymes.     

Targeted delivery of DNA encoding cytotoxic proteins through high-affinity fibroblast growth factor receptors

Nonviral DNA delivery strategies for gene therapy have generally been limited by a lack of specificity and efficacy. However, ligand-mediated endocytosis can specifically deliver DNA in vitro to cells bearing the appropriate cognate receptors. Similarly, in order to circumvent problems related to efficacy, DNA must encode proteins with high intrinsic activities. We show here that the ligand basic fibroblast growth factor (FGF2) can target FGF receptor-bearing cells with DNA encoding therapeutic proteins. Delivery of genes encoding saporin, a highly potent ribosomal inactivating protein, or the conditionally cytotoxic herpes simplex virus thymidine kinase, a protein that can kill cells by activating the prodrug ganciclovir, is demonstrated. The saporin gene was codon optimized for mammalian expression and demonstrated to express functional protein in a cell-free assay. FGF2-mediated delivery of saporin DNA or thymidine kinase DNA followed by ganciclovir treatment resulted in a 60 and 75% decrease in cell number, respectively. Specificity of gene delivery was demonstrated in competition assays with free FGF2 or with recombinant soluble FGF receptor. Alternatively, when histone H1, a ligand that binds to cell surface heparan sulfate proteoglycans ("low-affinity" FGF receptors), was used to deliver DNA encoding thymidine kinase, no ganciclovir sensitivity was observed. These findings establish the feasibility of using ligands such as FGF2 to specifically deliver genes encoding molecular chemotherapeutic agents to cells.     

Aspartate-407 in Rhodobacter sphaeroides cytochrome c oxidase is not required for proton pumping or manganese binding

Several pathways for proton transport in cytochrome c oxidase have been proposed on the basis of mutational analysis and X-ray structure: at least one for moving "pumped" protons from the interior to exterior of the membrane and a separate route for transporting "substrate" protons from the interior to the binuclear metal center to combine with oxygen to make H2O. According to the crystal structures of cytochrome c oxidase, Asp407 (Rhodobacter sphaeroides numbering) is at the interface of subunit I and subunit II of the oxidase, in a negative patch proposed to be the proton exit site in a pumping pathway, as well as a possible ligand to Mg [Iwata et al. (1995) Nature 376, 660-669]. Three mutants at the Asp407 position of R. sphaeroides cytochrome oxidase, Asp407Ala, Asp407Asn, and Asp407Cys, have been purified and characterized. All showed electron transfer activity, and pH dependence of activity, similar to that of the wild type enzyme and no major structural changes, as evidenced by visible, EPR, and resonance Raman spectroscopy. When reconstituted into artificial vesicles, the purified mutants pumped protons with normal efficiency and responded to the membrane pH and electrical gradients in a manner similar to that of wild type. Furthermore, the EPR spectra and Mn quantitation analysis of mutants grown in high Mn indicated no significant alteration in the Mn/Mg site. These results suggest that Asp407 does not play a critical role in proton translocation or in Mn/Mg binding.     

Guidelines for harvesting forest biomass for energy: A synthesis of environmental considerations

Interest in the utilization of forest biomass for energy is growing. A search into existing forest biomass harvesting and regeneration guidelines was carried out to identify how biomass energy can be environmentally sustainable. Findings have shown that there are only a few guidelines that specifically address harvesting and regenerating biomass for bioenergy or other bio-based products. Of these few, there are guidelines developed for dedicated energy plantations such as the Scottish Agricultural College guidelines, as well as some Finnish and Swedish guidelines recommending management practices for both timber and biomass extraction. Most of the existing small woody material guidelines emphasize the retention, disposal, redistribution, burning and mulching of biomass material on-site in a more detailed manner than forest and timber management guidelines. This study synthesizes and classifies existing biomass-related guidelines based on an in-depth literature review of existing guidelines in Europe and North America involved with biomass energy harvesting. Biomass guidelines are classified according to those applicable to systems producing biomass commercially for energy versus those that are applicable to systems managing this material for non-commercial purposes. Biomass guidelines are analyzed with respect to how they address issues of sustainability related to soil, water and habitat. Recommendations are offered for developing guidelines for biomass harvesting.     

Solvent-free surface modification by initiated chemical vapor deposition to render plasma bonding capabilities to surfaces

A versatile solvent-free method for surface modification of various materials including both metals and polymers is described. Strong irreversible bonds were formed when substrates modified by initiated chemical vapor deposition (iCVD) of poly(1,3,5-trivinyltrimethylcyclotrisiloxane) or poly(V3D3) and exposed to an oxygen plasma were brought into contact with plasma-treated poly(dimethylsiloxane) (PDMS). The strength of these bonds was quantified by burst pressure testing microfluidic channels in the PDMS. The burst pressures of PDMS bonded to various coated substrates were in some cases comparable to that of PDMS bonded directly to PDMS. In addition, porous PTFE membrane coated with poly(V3D3) was successfully bonded to a PDMS microfluidic device and withstood pressures of over 300 mmHg. Bond strength was shown to correlate with surface roughness and quality of the bond between the coating and substrate. This work paves a methodology to fabricate microfluidic devices that include a specifically tailored membrane. Furthermore, the bonded devices exhibited hydrolytic stability; no dramatic change was observed even after immersion in water at room temperature over a period of 10 days.     

Bacterial sporulation and regulation of dihydrodipicolinate synthase in ribonucleic acid polymerase mutants of Bacillus subtilis

The activity of dihydrodipicolinate synthase increased late in sporulation in Bacillus subtilis. Mutants blocked at several stages of sporulation due to having an altered ribonucleic acid polymerase failed to exhibit this increase.