David Simpson | University of Portsmouth (original) (raw)

Papers by David Simpson

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2009

The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using st... more The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies. (J Am Soc Mass

Photosynthesis Research, 1993

We have compared the properties of a mutant of barley lacking Photosystem I (viridis-zb 63) with ... more We have compared the properties of a mutant of barley lacking Photosystem I (viridis-zb 63) with the corresponding wild type using modulated fluorescence measurements. The mutant showed two unexpected characteristics. Firstly, there was a slow decline in the fluorescence signal in the light which was dependent on the presence of 0 2 at concentrations similar to that in air; 2% 0 2 in N 2 had no effect. The observed decline was mainly due to an increase in the non-photochemical quenching. Secondly, in the absence of 02, saturating light pulses caused a pronounced transient decrease in the fluorescence signal; a similar effect could also be observed in wild type plants when neither CO 2 nor 0 2 was present.

Investigative Ophthalmology & Visual Science, 2006

PURPOSE. This study was conducted to evaluate whether regions of the retinal neuropile become hyp... more PURPOSE. This study was conducted to evaluate whether regions of the retinal neuropile become hypoxic during periods of high oxygen consumption and whether depletion of the outer retina reduces hypoxia and related changes in gene expression. METHODS. Retinas from rhodopsin knockout (Rho Ϫ/Ϫ ) mice were evaluated along with those of wild-type (WT) control animals. Retinas were also examined at the end of 12-hour dark or light periods, and a separate group was treated with L-cisdiltiazem at the beginning of a 12-hour dark period. Hypoxia was assessed by deposition of hypoxyprobe (HP) and HPprotein adducts were localized by immunohistochemistry and quantified using ELISA. Also, hypoxia-regulated gene expression and transcriptional activity were assessed alongside vascular density. RESULTS. Hypoxia was observed in the inner nuclear and ganglion cell layers in WT retina and was significantly reduced in Rho Ϫ/Ϫ mice (P Ͻ 0.05). Retinal hypoxia was significantly increased during dark adaptation in WT mice (P Ͻ 0.05), whereas no change was observed in Rho Ϫ/Ϫ or with L-cis-diltiazem-treated WT mice. Hypoxia-inducible factor (HIF)-1␣ DNA-binding and VEGF mRNA expression in Rho Ϫ/Ϫ retina was significantly reduced in unison with outer retinal depletion (P Ͻ 0.05). Retina from the Rho Ϫ/Ϫ mice displayed an extensive intraretinal vascular network after 6 months, although there was evidence that capillary density was depleted in comparison with that in WT retinas. CONCLUSIONS. Relative hypoxia occurs in the inner retina especially during dark adaptation. Photoreceptor loss reduces retinal oxygen usage and hypoxia which corresponds with attenuation of the retinal microvasculature. These studies suggest that in normal physiological conditions and diurnal cycles the adult retina exists in a state of borderline hypoxia, making this tissue particularly susceptible to even subtle reductions in perfusion. (Invest Ophthalmol Vis Sci. 2006;47:5553-5560)

Fems Microbiology Letters, 1989

Abstract A thermophilic strain of Synechococcus sp. was grown under light-limited conditions at i... more Abstract A thermophilic strain of Synechococcus sp. was grown under light-limited conditions at its optimum temperature of 58°C and at 38°C in order to investigate the effect of growth temperature on the composition of the photosynthetic apparatus. Cells grown at 38°C had a ratio of Photosystem I to Photosystem II of 2.2, close to that known to occur in unstressed mesophilic strains of Synechococcus. Growth at the higher temperature led to a doubling of the number of Photosystem I reaction centres per cell whilst Photosystem II remained essentially unchanged, causing the Photosystem I/Photosystem II ratio to rise to 4.1. These changes were correlated with an increase in the number of concentric layers of thylakoid membranes from four to nine. It is suggested that these changes result from a higher relative demand for energy (ATP) during growth at elevated temperatures.

… Record Part A: …, 2003

Several studies have shown that disruption of the normal expression patterns of platelet-derived ... more Several studies have shown that disruption of the normal expression patterns of platelet-derived growth factor (PDGF) ligands and receptors during development results in gross cardiac defects and embryonic or neonatal death. However, little is known about the specific role that PDGF plays in the differentiation of cardiac myocytes. In experiments complementing studies that utilized naturally-occurring Patch mice lacking the PDGFr ␣, or knockout animals lacking a PDGF ligand or receptor, we used rat and mouse whole-embryo culture (WEC) techniques to increase the exposure of embryos to the PDGF-AA or -BB ligands. Following a 48-hr culture period, we analyzed heart growth and cardiac myocyte differentiation. Exposure of rat embryos to 50 ng/ml of PDGF-AA resulted in a 42% increase in total protein levels in the heart, but did not result in a significant increase in heart growth, as determined by measurements of the atrioventricular length and the left ventricular length and width. Exposure of embryos to 50 ng/ml of PDGF-BB resulted in a 77% increase in total protein levels and a significant (P Ͻ 0.05) 8 -15% increase in the measured heart parameters. Although a comparison of control and PDGF-AA-treated embryos showed no increase in the overall size of the heart, confocal microscopy showed an increase in the size and number of myofibrillar bundles in the developing myocardium. In addition, transmission electron microscopy (TEM) revealed an increase in the presence of sarcomeres, indicating that myofibrils were more highly differentiated in these areas of the treated embryos. In PDGF-BB-treated embryos, the compact zone of the myocardium was thicker and, as shown by confocal microscopy and TEM, f-actin and well-developed sarcomeres were more prevalent, indicating that the myofibrils were more differentiated in the treated embryos than in the control embryos. These studies indicate that increased exposure of embryonic hearts to PDGF-AA or -BB increases the rate of myocardial development. Anat Rec Part A 272A: 424 -433, 2003.

Investigative Ophthalmology & Visual Science, 2007

AJP: Heart and Circulatory Physiology, 2006

Little is known about the molecular characteristics of the voltage-activated K(+) (K(v)) channels... more Little is known about the molecular characteristics of the voltage-activated K(+) (K(v)) channels that underlie the A-type K(+) current in vascular smooth muscle cells of the systemic circulation. We investigated the molecular identity of the A-type K(+) current in retinal arteriolar myocytes using patch-clamp techniques, RT-PCR, immunohistochemistry, and neutralizing antibody studies. The A-type K(+) current was resistant to the actions of specific inhibitors for K(v)3 and K(v)4 channels but was blocked by the K(v)1 antagonist correolide. No effects were observed with pharmacological agents against K(v)1.1/2/3/6 and 7 channels, but the current was partially blocked by riluzole, a K(v)1.4 and K(v)1.5 inhibitor. The current was not altered by the removal of extracellular K(+) but was abolished by flecainide, indicative of K(v)1.5 rather than K(v)1.4 channels. Transcripts encoding K(v)1.5 and not K(v)1.4 were identified in freshly isolated retinal arterioles. Immunofluorescence labeling confirmed a lack of K(v)1.4 expression and revealed K(v)1.5 to be localized to the plasma membrane of the arteriolar smooth muscle cells. Anti-K(v)1.5 antibody applied intracellularly inhibited the A-type K(+) current, whereas anti-K(v)1.4 antibody had no effect. Co-expression of K(v)1.5 with K(v)beta1 or K(v)beta3 accessory subunits is known to transform K(v)1.5 currents from delayed rectifers into A-type currents. K(v)beta1 mRNA expression was detected in retinal arterioles, but K(v)beta3 was not observed. K(v)beta1 immunofluorescence was detected on the plasma membrane of retinal arteriolar myocytes. The findings of this study suggest that K(v)1.5, most likely co-assembled with K(v)beta1 subunits, comprises a major component underlying the A-type K(+) current in retinal arteriolar smooth muscle cells.

Journal of proteome research, Feb 2, 2007

We investigated the combination of weak anion exchange (WAX) fractionation and on-line reversedph... more We investigated the combination of weak anion exchange (WAX) fractionation and on-line reversedphase liquid chromatography (RPLC) separation using a 12 T FTICR mass spectrometer for the detection of intact proteins from a Shewanella oneidensis MR-1 cell lysate. This work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification state. A total of 715 intact proteins were detected, and the combined results from the WAX fractions and the unfractionated cell lysate were aligned using LC-MS features to facilitate protein abundance measurements. Protein identifications and post-translational modifications were assigned for ∼10% of the detected proteins by comparing intact protein mass measurements to proteins identified in peptide MS/MS analysis of an aliquot of the same fraction. Intact proteins were also detected for S. oneidensis lysates obtained from cells grown on 13 C-, 15 N-depleted media under aerobic and sub-oxic conditions. The strategy can be readily applied for measuring differential protein abundances and provides a platform for high-throughput selection of biologically relevant targets for further characterization.