Polyelectrolyte multilayer films as substrates for photoreceptor cells

Reconstruction of extracellular matrix substrates for delivery of functional photoreceptors is crucial in pathologies such as retinal degeneration and age-related macular degeneration. In this study, we assembled polyelectrolyte films using the layer-by-layer deposition method. The buildup of three different films composed of poly(L-lysine)/chondroitin sulfate (PLL/CSA), poly(L-lysine)/poly(styrenesulfonate) (PLL/PSS), or poly(L-lysine)/hyaluronic acid (PLL/HA) was followed by means of quartz crystal microbalance measurements, optical waveguide light mode spectroscopy, confocal microscopy, and atomic force microscopy. The exponential growth regime and the diffusion of PLL chains from the bulk through the PLL/CSA, PLL/PSS, and PLL/HA films was examined. Evaluation of photoreceptor cell viability was optimal on one layer of PLL (PLL(1)), followed by 10 bilayers of PLL/HA [(PLL/HA)(10)] and 10 bilayers of PLL/CSA [(PLL/CSA)(10)]. The number of bilayers and the type of terminating layer also had a significant influence on the number of photoreceptor cells attached. Functionalized polyelectrolyte multilayer films were obtained by adsorbing basic fibroblastic factor (bFGF) or the insoluble fraction of interphotoreceptor matrix (IPM) on or within polyelectrolyte multilayers. bFGF and IPM adsorption on top of the (PLL/CSA)(10)/PLL polyelectrolyte films increased the number of photoreceptor cells attached and maintained the differentiation of rod and cone cells.     

Novel polymer substrates for SFM investigations of living cells, biological membranes, and proteins.

Extended studies were performed to prepare substrates for scanning force microscopy of biological samples with a surface roughness below 1 nm rms over an area of 500 x 500 nm2. The substrate smoothness and the lack of tip obscuring material are indispensable in order to visualize detailed structures of membrane surfaces, particularly when scanning the lamellipodia of mechanically sensitive goldfish glial cells where peripheral lamellipodia are only 20-30 nm in thickness. Appropriate substrates are poly(vinyl phenyl ketone) or furan polymers with corrugations of 0.3 and 0.15 nm rms, respectively, to which the growth-promoting protein laminin adsorbs directly with an acceptably increased roughness. Cells show normal growth behavior on these substrates and stick to the substrates in a stable fashion during several scans. Thus details of the membrane's surface may be resolved and are not obscured by the substrate texture. The uncoated furan polymer substrates are suitable for immobilization of membrane preparations such as purified membrane fragments containing bacteriorhodopsin or Na, K-ATPase and protein preparations such as antibodies.     

N-hydroxy peptides as substrates for alpha-chymotrypsin.

An N-hydroxylated peptide bond was found to be cleaved faster by an endopeptidase than the corresponding peptide bond. This preferred enzymatic cleavage was detected during proteolytic studies of the N-hydroxy peptide SIINFpsi[CO-N(OH)]GKL in the presence of the serine protease alpha-chymotrypsin in comparison with the natural SIINFEKL epitope and related analogs. For the first time, the replacement of the peptide bond by another motif afforded an oligomer which is degraded faster than the natural peptide. The N-hydroxy peptide is also more sensitive to the enzymatic degradation than the Gly-containing analog SIINFGKL. A tentative explanation for the unexpected higher cleavage rate of the CO-N(OH) bond is given on the basis of the N-OH intramolecular H-bonding capacity as indicated by NMR experiments. This property of the hydroxamate group may be of particular advantage for the introduction of a specific cleavage site within peptidomimetics or in prodrugs.     

A highly parallel strategy for storage of digital information in living cells

Background

Encoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and reading the data (biases and systematic error arising from synthesis and sequencing), and overall scalability.

Results

To this end, we have developed and implemented an encoding scheme that is suitable for detecting and correcting errors that may arise during storage, writing, and reading, such as those arising from nucleotide substitutions, insertions, and deletions. We propose a scheme for parallelized long term storage of encoded sequences that relies on overlaps rather than the address blocks found in previously published work. Using computer simulations, we illustrate the encoding, sequencing, decoding, and recovery of encoded information, ultimately demonstrating the possibility of a successful round-trip read/write. These demonstrations show that in theory a precise control over error tolerance is possible. Even after simulated degradation of DNA, recovery of original data is possible owing to the error correction capabilities built into the encoding strategy. A secondary advantage of our method is that the statistical characteristics (such as repetitiveness and GC-composition) of encoded sequences can also be tailored without sacrificing the overall ability to store large amounts of data. Finally, the combination of the overlap-based partitioning of data with the LZMA compression that is integral to encoding means that the entire sequence must be present for successful decoding. This feature enables inordinately strong encryptions. As a potential application, an encrypted pathogen genome could be distributed and carried by cells without danger of being expressed, and could not even be read out in the absence of the entire DNA consortium.

Conclusions

We have developed a method for DNA encoding, using a significantly different fundamental approach from existing work, which often performs better than alternatives and allows for a great deal of freedom and flexibility of application.

     

Models for 1/f noise in nerve membranes.

A recently proposed model for 1/f(w-1) noise in nerve membrane (Clay and Schlesinger, 1976; Lundström and McQueen, 1974) is shown to be mathematically inconsistent in several respects. A self-consistent model based on similar membranes lipid orientation fluctuation effects is proposed.     

RNA tetraloops as minimalist substrates for aminoacylation.

Previous work established that seven-base-pair hairpin microhelices with sequences based on the acceptor stems of alanine, glycine, methionine, and histidine tRNAs can be aminoacylated specifically with their cognate amino acids. To obtain "minimalist" substrates with fewer base pairs, we took advantage of the high thermodynamic stability of RNA tetraloop motifs that are found in ribosomal RNAs. We show here that rationally designed RNA tetraloops with as few as four base pairs are substrates for aminoacylation. Major nucleotide determinants for recognition by the class II synthetases were incorporated into each of the respective tetraloop substrates, resulting in specific aminoacylation by the alanine, glycine, and histidine tRNA synthetases. An analysis of the kinetics of aminoacylation shows that, for the alanine system, the majority of the transition-state stabilization provided by the synthetase-tRNA interaction is reproduced by the interaction of the synthetase with nucleotides in its minimalist tetraloop substrate. In an extension of this work, we also observed specific aminoacylation with the class I methionine tRNA synthetase of RNA tetraloops based on sequences in the acceptor stem of methionine tRNA. Thus, the results demonstrate four different examples where specific aminoacylation is directed by sequences/structures contained in less than half of a turn of an RNA helix.     

Cattle wastes as substrates for bioelectricity production via microbial fuel cells

A new 2 l scale microbial fuel cell (MFC) configuration was developed to generate bioelectricity from particulate substrates. Voltage and power densities generated in this MFC fed with sucrose, particulate cattle manure, and manure wash-water as the substrates were evaluated in batch mode, with and without external mediators. Voltages averaged 0.5 V in open circuit, and 0.4 V under a resistive load of 470 Ω. Power densities (67 to 215 mW/m²) were comparable to previous work that had used liquid wastes as substrates. Based on the energy yield per unit mass of feedstock (~10 kJ/kg wet manure), cattle manure has limited potential to serve as a feedstock for electricity production via MFCs.     

Glutamine and glucose as energy substrates for Ehrlich ascites tumour cells

Energy metabolism of freshly harvested Ehrlich ascites tumour cells in the presence of 5 mM glucose and/or 0.5 mM glutamine was studied. The rate of oxygen utilization was not altered by the addition of 0.5 mM glutamine; 5 mM glucose induced an inhibition of respiration. In the presence of both glucose and glutamine, the Crabtree effect decreased. In these conditions, the rates of oxygen uptake, the CO2 evolution and the changes in the redox states of cytochromes indicate that glucose is preferred by Ehrlich ascites tumour cells as energy substrate. Glucose decreased the rate of glutamine utilization by 34%. On the other hand, glutaminolysis did not inhibit glycolysis.     

Thiols as myeloperoxidase-oxidase substrates.

Nine low-Mr thiols were compared with regard to their ability to function as myeloperoxidase-oxidase substrates under conditions where no auto-oxidation of the thiols could be observed. The methyl and ethyl esters of cysteine were found to be about twice as active as cysteamine at pH 7.0, in terms of increased O2 consumption. Cysteine itself was poorly active, whereas glutathione, N-acetylcysteine and penicillamine were completely inactive as myeloperoxidase-oxidase substrates under these conditions. The structure-activity relationships indicated that both a free thiol and free amino group were required for peroxidase-oxidase activity, and also that a free carboxy group abolished activity. In analogy with cysteamine, the activities of both cysteine esters were inhibited by superoxide dismutase (less than 5 micrograms/ml) and by catalase and not by the hydroxyl-radical scavenger mannitol. In contrast with cysteamine, the activities of both cysteine esters were stimulated more than 2-fold by high concentrations (greater than 5 micrograms/ml) of superoxide dismutase. The activities of both cysteine esters exhibited broad pH optima at pH 7. A mechanism for the myeloperoxidase-oxidase oxidation of the cysteine esters is proposed, which is partly different from that previously proposed for cysteamine.     

Spin labels as enzyme substrates Heterogeneous lipid distribution in liver microsomal membranes

Phenobarbital-stimulated microsomal membranes of rabbit liver, containing the cytochrome P450- cytochrome P450 reductase hydroxylating enzyme system in high concentration, have been studied with a version of the spin label technique which uses nitroxide radicals as enzyme substrates. The reduction kinetics of a phosphate ester of tetramethylpiperidine nitroxide (TEMPO-phosphate) and of stearic acid nitroxide by the cytochrome P450 reductase has been studied as a function of the temperature. The Arrhenius plot of the reduction rate constants reveals a striking difference in the behaviour of the water-soluble TEMPO-phosphate label and the lipid-soluble fatty acid label: The activation energy of the fatty acid reduction decreases abruptly at about 32°C from a value of 30.8 kcal/mole to a value of 8.7 kcal/mole, whereas no such break is observed in the Arrhenius plot of the TEMPO-phosphate reduction which yields a value of the activation energy of $\text{ΔW = 13.8}$ kcal/mole in the whole temperature range investigated. Our results clearly indicate the existence of a mosaic-like structure of the membrane with the whole enzyme system being enclosed by a rather rigid phospholipid halo which is in a quasicrystalline structure below 32 °C and undergoes a crystalline-liquid crystalline phase transition at 32 °C, while the bulk lipid of the membrane is in a rather fluid state as reflected by the measured high diffusion coefficient of $\text{D}{}_{\mathrm{<mtext>diff</mtext>}}\text{= 11.0·10}{}^{\mathrm{?8}}\text{cm}{}^2\text{/s}$ at 30 °C and low activation energy of diffusion of $\text{ΔW = 3.85}\text{kcal/mole}$ of a fatty acid spin label incorporated in the membrane.     

Actin associated with membranes of monoamine storage organelles.

A histo-immunofluorescence technique using anti-actin antibodies has been applied to various subcellular fractions of bovine adrenal medulla and rabbit blood platelets. In the adrenal medulla only the membranes of the chromaffin granules, but not the fractions containing other subcellular particles (microsomes, mitochondria) showed marked immunofluorescence was present in the membranes of the 5-hydroxy-tryptamine organelles as well as in other subcellular particles. It is concluded that in the adrenal medulla, actin is specifically associated with the membranes of the amine storage organelles, whereas in platelets the protein shows a rather general subcellular distribution.     

Mechanisms for the facilitated diffusion of substrates across cell membranes

Two classes of theoretical mechanisms for protein-mediated, passive, transmembrane substrate transport (facilitated diffusion) are compared. The simple carrier describes a carrier protein that exposes substrate influx and efflux sites alternately but never both sites simultaneously. Two-site models for substrate transport describe carrier proteins containing influx and efflux sites simultaneously. Velocity equations describing transport by these mechanisms are derived. These equations take the same general form, being characterized by five experimental constants. Simple carrier-mediated transport is restricted to hyperbolic kinetics under all conditions. Two-site carrier-mediated transport may deviate from hyperbolic kinetics only under equilibrium exchange conditions. When both simple- and two-site carriers display hyperbolic kinetics under equilibrium exchange conditions, these models are indistinguishable by using steady-state transport data alone. Seven sugar transport systems are analyzed. Five of these systems are consistent with both models for sugar transport. Uridine, leucine, and cAMP transport by human red cells are consistent with both simple- and two-site models for transport. Human erythrocyte sugar transport can be modeled by simple- and two-site carrier mechanisms, allowing for compartmentalization of intracellular sugars. In this instance, resolution of the intrinsic properties of the human red cell sugar carrier at 20 degrees C requires the use of submillisecond transport measurements.     

Ultrafiltration membranes as carriers for lipase immobilization.

The feasibility of directly incorporating lipase from Rhizopus in the interior of poly(vinyl chloride) ultrafiltration membranes during the phase inversion process for their manufacturing has been demonstrated. The obtained membranes used for plant oil hydrolysis have shown better time stability as compared with those of lipase immobilized by adsorption. The specific activity of entrapped lipase achieves values higher than those of the soluble one. The activity of immobilized lipase is strongly affected by the rate of removing fatty acids from the interior of the membrane.