On the controversy over "fast" and "slow" helix-coil transition rates in polypeptides

The controversy over “fast” and “slow” helix-coil transition rates in polypeptides is discussed. The “slow” results are derived from the assumption that multiple NMR spectra of α-CH and NH groups arise from chemical exchange. In this paper it is shown that such spectra may be obtained without invoking chemical exchange. The multiplicity arises from the difference in helicity of amino acid residues near the ends of the chain by comparison with amino acid residues nearer the middle, and from a polydispersity in molecular weight. As a consequence of this analysis, support is given to the “fast” transition rates.     

Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

Genetic demonstration of bidirectionality in the high affinity purine base transporter of mutant mouse S49 cells

A mutant cell line was selected from wild type S49 lymphoblasts that expressed a novel high affinity purine base transport system not found in parental cells or any other mammalian cell line (Aronow, B., Toll, D., Patrick, J., Hollingsworth, P., McCartan, K., and Ullman, B. (1986) Mol. Cell. Biol. 6, 2957-2962). In order to determine whether this nucleobase transport system was bidirectional, mutant cell lines possessing this high affinity base transport capability were derived from a nucleoside transport-deficient derivative of an adenylosuccinate synthetase-deficient S49 cell line. The resulting progeny excreted significantly greater amounts of purine into the cell culture medium than parental cells. This purine was identified as hypoxanthine. These results demonstrate genetically that the high affinity purine base transport system can mediate both the influx and efflux of hypoxanthine.     

Nutrient release rates from the sediments of Saginaw Bay,Lake Huron

Direct measurements of net production rates and pore water profiles of solutes in the fine-grained sediments of Saginaw Bay, imply corresponding steady-state fluxes to the overlying water of 1.1–1.3 (I), 450–1010 (NH₄ ⁺), 1250–2650 (Si(OH)₄), 3000–3400 (Ca²⁺), 440–1330 (Mg²⁺), 1.5–728 (Fe²⁺), and 179–281 (Mn²⁺) moles/m²/day and 11.0–11.8 (alkalinity) meq/m²/day at 17.5 °C. Silica production rates in sediments apparently follow first order kinetics with a rate coefficient of 0.09/day and a steady-state silica concentration of 1.2 mM at 23.5°C. The remaining solutes follow kinetics approximately independent of solute concentration over the range of concentrations observed. Measured solute production rates are consistent with observed solute profiles only if lateral diffusion gradients are maintained in the sediments by the burrowing and irrigation activity of benthic organisms such asChironomous, the dominant burrower in Saginaw Bay. Assuming that solute fluxes from Saginaw Bay are representative of all of the post-glacial sediments of Lake Huron, the iodine flux from sediments is comparable to the total fluvial input of iodine. The extrapolated silica fluxes from Lake Huron sediments balance the estimated biogenic silica flux to the sediments.     

Platelet-neutrophil interactions. (12S)-hydroxyeicosatetraen-1,20-dioic acid: a new eicosanoid synthesized by unstimulated neutrophils from (12S)-20-dihydroxyeicosatetraenoic acid

In the course of a cell-cell interaction, 12-HETE (12-hydroxy-5,8,10,14-eicosatetraenoic acid), the arachidonic acid lipoxygenase product released from stimulated platelets, is metabolized by a cytochrome P-450 enzyme system in unstimulated neutrophils to 12,20-DiHETE (12,20-dihydroxy-5,8,10,14-eicosatetraenoic acid). This report describes time-dependent formation of a new eicosanoid by unstimulated neutrophils exposed to 12-HETE, which is more polar than 12,20-DiHETE (reversed-phase high performance liquid chromatography). Time course studies indicated that the precursor compound of this new eicosanoid was 12,20-DiHETE. This was determined by incubation of purified 12,20-DiHETE with neutrophils, which resulted in a progressive decrease in 12,20-DiHETE as formation of the polar metabolite increased. In the absence of neutrophils, 12,20-DiHETE was quantitatively unchanged. The new metabolite of 12,20-DiHETE was identified as 12-hydroxyeicosatetraen-1,20-dioic acid, based upon its UV spectrum, co-chromatography with a chemically synthesized standard in both high performance liquid chromatography and thin layer chromatography systems, and gas chromatography-mass spectrometry. Formation of 12-HETE-1,20-dioic acid was partially inhibited by 20-hydroxy-LTB4. This indicated that the neutrophil dehydrogenase responsible for further metabolism of 12,20-DiHETE may also be involved in conversion of 20-hydroxy-LTB4 to 20-carboxy-LTB4. The 12,20-DiHETE dehydrogenase enzyme system specifically requires NAD as cofactor and has subcellular components in both cytosolic and microsomal fractions which are synergistic in their activity. These results provide additional evidence for the occurrence of multicellular metabolic events during hemostasis, thrombosis, and the inflammatory response.     

Non-linearities in cortical simple cells and the possible detection of zero crossings

A theory of early visual information processing proposed by Marr and co-workers suggests that simple cortical cells may be involved in the detection of zero crossing in the retinal output. We have tested this theory by using pairs of adjacent edges (staircases stimuli) and recording from edge-specific simple cells in cat striate cortex. The zero crossing hypothesis gives rise for such stimuli to non-obvious predictions that were generally confirmed by the experiment.     

Identification and reconstitution of the nucleoside transporter of CEM human leukemia cells

The major nucleoside transporter of the human T leukemia cell line CEM has been identified by photoaffinity labeling with the transport inhibitor nitrobenzylmercaptopurine riboside (NBMPR). The photolabeled protein migrates on SDS-PAGE gels as a broad band with a mean apparent molecular weight (75,000 +/- 3000) significantly higher than that reported for the nucleoside transporter in human erythrocytes (55,000) (Young et al. (1983) J. Biol. Chem. 258, 2202-2208). However, after treatment with endoglycosidase F to remove carbohydrate, the NBMPR-binding protein in CEM cells migrates as a sharp peak with an apparent molecular weight (47,000 +/- 3000) identical to that reported for the deglycosylated protein in human erythrocytes (Kwong et al. (1986) Biochem. J. 240, 349-356). It therefore appears that the difference in the apparent molecular weight of the NBMPR-sensitive nucleoside transporter between the CEM cell line and human erythrocytes is a result of differences in glycosylation. The NBMPR-binding protein from CEM cells has been solubilized with 1% octyl glucoside and reconstituted into phospholipid vesicles by a freeze-thaw sonication technique. Optimal reconstitution of uridine transport activity was achieved using a sonication interval of 5 to 10 s and lipid to protein ratios of 60:1 or greater. Under these conditions transport activity in the reconstituted vesicles was proportional to the protein concentration and was inhibited by NBMPR. Omission of lipid or protein, or substitution of a protein extract prepared from a nucleoside transport deficient mutant of the CEM cell line resulted in vesicles with no uridine transport activity. The initial rate of uridine transport, in the vesicles prepared with CEM protein, was saturable with a Km of 103 +/- 11 microM and was inhibited by adenosine, thymidine and cytidine. The Km for uridine and the potency of the other nucleosides as inhibitors of uridine transport (adenosine greater than thymidine greater than cytidine) were similar to intact cells. Thus, although the nucleoside transporter of CEM cells has a higher molecular weight than the human erythrocyte transporter, it exhibits typical NBMPR-sensitive nucleoside transport activity both in the intact cell and when reconstituted into phospholipid vesicles.     

A model for the temporal organization of X- and Y-type receptive fields in the primate retina

A model is proposed for the temporal characteristics of X-and Y-type responses of ganglion cells in the primate retina. The main suggestions of the model are: (I) The X-type temporal response is determined primarily by the delay between center and surround contributions. (II) The Y-type response is generated in the inner plexiform layer by a derivativelike operation on the bipolar cell's input, followed by a rectification in the convergence of these inputs onto the Y-ganglion-cell. (III) The derivative-like operation is obtained by recurrent inhibition in the dyad synaptic structure.The X-and Y-type responses predicted by the model, for a variety of stimuli, were examined and compared with available electrophysiological recordings. Finally, certain predictions derived from the model are discussed.     

In vitro methods for peptide display and their applications

The presentation of recombinant peptide libraries linked to their coding sequence can be referred to as 'peptide display'. Phage display is the most widely practiced peptide display technology but more recent alternatives such as CIS display, ribosome display and mRNA display offer advantages over phage for speed, library size and the display of unnatural amino acids. These have provided researchers with tools to address some of the failings of peptides such as their low affinity, low stability and inability to cross biological membranes. In this review, we assess some of the recent advances in peptide display and its application.