Biomedical subjects

John Ross

Publications and source records attributed to John Ross.

At least 19 recordsLinked to original sources

PubMed2006

Transition event statistics in genetics and disordered kinetics. Theoretical approaches for extracting rate distributions from experimental data.

We study the analogies between the theory of rate processes in disordered systems and the overdispersed molecular clocks in evolutionary biology. A biological "molecular clock" expresses the statistics of the number of amino acid or nucleotide substitutions during evolution. Random variations of the evolution rates lead to statistical (overdispersed) molecular clocks which are described by random point processes with random substitution rates. We find that the models for overdispersed molecular clocks are equivalent to those of the random-rate or random channel models used in disordered kinetics. The number of transport (reaction) events in disordered kinetics plays the same role as the number of substitution events in molecular biology. We study the connections between the (observed) statistics of the transition events and the statistics of random rate coefficients and random channels; a unified approach is developed which is valid both in molecular biology and in disordered kinetics. We develop methods for extracting statistical information about the variations of rate coefficients from experimental or observed data regarding the fluctuations of the numbers of substitution, reaction, or transport events. For systems with static disorder, the observed statistics of the number of reaction events, expressed in terms of probabilities at a given time or by the cumulants of the number of transition events at a given time, contains the information necessary for evaluating the cumulants or the probability density of the rate coefficients or the density of states for random channel kinetics. For dynamic disorder this is not possible; further information about multitime probability distributions of the reaction events is needed.

Amino Acid Substitution↗

PubMed2006

Cell bank characterization and fermentation optimization for production of recombinant heavy chain C-terminal fragment of botulinum neurotoxin serotype E (rBoNTE(H(c)): antigen E) by Pichia pastoris.

A process was developed for production of a candidate vaccine antigen, recombinant C-terminal heavy chain fragment of the botulinum neurotoxin serotype E, rBoNTE(H(c)) in Pichia pastoris. P. pastoris strain GS115 was transformed with the rBoNTE(H(c)) gene inserted into pHILD4 Escherichia coli-P. pastoris shuttle plasmid. The clone was characterized for genetic stability, copy number, and BoNTE(H(c)) sequence. Expression of rBoNTE(H(c)) from the Mut(+) HIS4 clone was confirmed in the shake-flask, prior to developing a fed-batch fermentation process at 5 and 19 L scale. The fermentation process consists of a glycerol growth phase in batch and fed-batch mode using a defined medium followed by a glycerol/methanol transition phase for adaptation to growth on methanol and a methanol induction phase resulting in the production of rBoNTE(H(c)). Specific growth rate, ratio of growth to induction phase, and time of induction were critical for optimal rBoNTE(H(c)) production and minimal proteolytic degradation. A computer-controlled exponential growth model was used for process automation and off-gas analysis was used for process monitoring. The optimized process had an induction time of 9 h on methanol and produced up to 3 mg of rBoNTE(H(c)) per gram wet cell mass as determined by HPLC and Western blot analysis.

Bacterial Vaccines↗

PubMed2006

SGK1-dependent cardiac CTGF formation and fibrosis following DOCA treatment.

The mineralocorticoids aldosterone and deoxycorticosterone acetate (DOCA) stimulate renal tubular salt reabsorption, increase salt appetite, induce extracellular volume expansion, and elevate blood pressure. Cardiac effects of mineralocorticoids include stimulation of matrix protein deposition leading to cardiac fibrosis, which is at least partially due to the direct action of the hormones on cardiac cells. The signaling mechanisms mediating mineralocorticoid-induced cardiac fibrosis have so far remained elusive. Mineralocorticoids have been shown to upregulate the serum- and glucocorticoid-inducible kinase 1 (SGK1), which participates in the effects of mineralocorticoids on renal tubular Na+ reabsorption and salt appetite. To explore the involvement of SGK1 in the pathogenesis of mineralocorticoid-induced cardiac fibrosis, SGK1 knockout mice (sgk1-/-) and wild-type littermates (sgk1+/+) were implanted a 21-day-release 50-mg DOCA pellet and supplied with 1% NaCl in drinking water for 18 days. This DOCA/high-salt treatment increased blood pressure in both genotypes but led to significant cardiac fibrosis only in sgk1+/+ but not in sgk1-/- mice. According to real-time polymerase chain reaction and Western blotting, DOCA/high-salt treatment enhanced transcript levels and protein expression of cardiac connective tissue growth factor (CTGF) only in sgk1+/+ but not in sgk1-/- mice. Furthermore, DOCA (10 microM) upregulated CTGF expression and enhanced CTGF promoter activity in lung fibroblasts isolated from sgk1+/+ but not from sgk1-/- mice, an effect involving spironolactone-sensitive mineralocorticoid receptors and activation of nuclear factor-kappaB (NFkappaB). Our results suggest that SGK1 plays a decisive role in mineralocorticoid-induced CTGF expression and cardiac fibrosis.

Angiotensins↗

PubMed2006

Energy transfer from adenosine triphosphate.

We suggest a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP) in hydrolysis and phosphorylation reactions, from chemical energy into mechanical energy. Upon hydrolysis of ATP, say bound to a protein, the electrostatic energy of Coulombic repulsion of the ions adenosine diphosphate and phosphate is available to assert a force on a neighboring molecular group in the protein and can do work on that group, or as the ions recede from each without asserting such a force, they gain relative kinetic energy, which, in the absence of dissipative collisions that turn this kinetic energy into heat, can be converted into any other form of energy and work by an impulse, a collision with a neighboring group, without restrictions. Either possibility can be used as a source of activation energy for reactions, as a source of energy to surmount energy barriers in conformational changes, and as a source of work to be done, as in muscle. In some systems where the Gibbs free energy change is fully utilized, all of this energy is turned into mechanical energy, and we suggest a similar mechanism. From the literature we cite some experimental evidence and several quotations indicative of the possibility of our suggestion.

Actins↗

PubMed2005

Exact solutions for the entropy production rate of several irreversible processes.

We investigate thermal conduction described by Newton's law of cooling and by Fourier's transport equation and chemical reactions based on mass action kinetics where we detail a simple example of a reaction mechanism with one intermediate. In these cases we derive exact expressions for the entropy production rate and its differential. We show that at a stationary state the entropy production rate is an extremum if and only if the stationary state is a state of thermodynamic equilibrium. These results are exact and independent of any expansions of the entropy production rate. In the case of thermal conduction we compare our exact approach with the conventional approach based on the expansion of the entropy production rate near equilibrium. If we expand the entropy production rate in a series and keep terms up to the third order in the deviation variables and then differentiate, we find out that the entropy production rate is not an extremum at a nonequilibrium steady state. If there is a strict proportionality between fluxes and forces, then the entropy production rate is an extremum at the stationary state even if the stationary state is far away from equilibrium.

Journal Article↗

PubMed2005

Random activation energy model and disordered kinetics, from static to dynamic disorder.

We suggest a unified path integral approach for random rate processes with random energy barriers, which includes systems with static and dynamic disorder as particular cases. We assume that the random component of the activation energy barrier can be described by a generalized Zubarev-McLennan nonequilibrum statistical ensemble that can be derived from the maximum information entropy approach by assuming that the time history of the fluctuations of the random components of the energy barrier are known. We show that the average survival function, which is an experimental observable in disorderd kinetics, can be computed exactly in terms of the characteristic functional of this generalized Zubarev-McLennan nonequilibrium statistical ensemble. We investigate different types of disorder described by our approach, ranging from static disorder with infinite memory to random processes with long or short memory, and finally to rapidly fluctuating independent random processes with no memory. We derive expressions of the average survival function for all these types of disorder and discuss their implications in the evaluation of kinetic parameters from experimental data. We illustrate our approach by studying a simple model of dynamic disorder of the renewal type. Finally we discuss briefly the implications of our approach in molecular biology and genetics.

Entropy↗

PubMed2005

Seeing and ballistic pointing at perisaccadic targets.

We studied the effects of visual references and the level of illumination on the localization of stimuli flashed briefly near the start of saccades. A translucent shutter made it possible to remove visual references, but admit light, at different times after saccadic onset. The results show that post-saccadic visual references are not necessary for compression: a consistent compression of verbally reported relative stimulus distances is found at all shutter latencies and at all post-shutter levels of illumination. They also show that positions indicated by blind pointing show no compression except when visual references remain in view for a substantial time after saccades. These results confirm that the visual system uses multiple representations of space and suggest that it weights them differently for different tasks and different viewing conditions. No single map is used exclusively for conscious perception or for motor action, and conscious perception is always subject to compression at the time of saccades.

Darkness↗

PubMed2005

The effects of opposite-polarity dipoles on the detection of Glass patterns.

Glass patterns--randomly positioned coherently orientated dipoles--create a strong sensation of oriented spatial structure. On the other hand, coherently oriented dipoles comprising dots of opposite polarity ("anti-Glass" patterns) have no distinct spatial structure and are very hard to distinguish from random noise. Although anti-Glass patterns have no obvious spatial structure themselves, their presence can destroy the structure created by Glass patterns. We measured the strength of this effect for both static and dynamic Glass patterns, and showed that anti-Glass patterns can raise thresholds for Glass patterns by a factor of 2-4, increasing with density. The dependence on density suggests that the interactions occur at a local level. When the Glass and anti-Glass dipoles were confined to alternate strips (in translational and circular Glass patterns), the detrimental effect occurred for stripe widths less than about 1.5 degrees, but had little effect for larger stripe widths, reinforcing the suggestion that the interaction occurred over a limited spatial extent. The extent of spatial interaction was much less than that for spatial summation of these patterns, at least 30 degrees under matched experimental conditions. The results suggest two stages of analysis for Glass patterns, an early stage of limited spatial extent where orientation is extracted, and a later stage that sums these orientation signals.

Humans↗

PubMed2005

Cardiomyopathy associated with microcirculation dysfunction in laminin alpha4 chain-deficient mice.

Laminin alpha4 chain is a component of extracellular matrix (ECM) laminin-8 and -9 and serves dual roles as a structure protein and as a signaling molecule. The abundance of laminin alpha4 chain transcripts in the heart suggests an important role of this protein in cardiovascular development and function. In this study, we demonstrate that laminin alpha4 deficient mice gradually develop cardiac hypertrophy with impaired function. We show that depletion of laminin alpha4 chain did not alter the levels of dystrophin-glycoprotein complex (DGC) components or affect cell membrane integrity. No alteration in integrin beta 1D protein was observed in terms of expression level or distribution pattern, indicating that the postnatal development of cardiac hypertrophy and cardiomyopathy in these mice is unlikely associated with the stability of sarcolemmal DGC and integrin complexes. Moreover, cardiomyocytes isolated from Lama4-/- mutant hearts maintained their contractility in vitro. In contrast, elevated levels of hypoxia-inducible factor 1alpha (Hif1alpha) and vascular endothelial growth factor A (Vegfa) transcripts, along with multiple foci of cardiomyocyte degeneration and fibrosis suggested sustained cardiac ischemia. Electron microscopy confirmed malformed blood vessels and wide pericapillary ECM spaces, suggesting the presence of microcirculation abnormalities in Lama4-/- mutant hearts. We thus conclude that mutation in the laminin alpha4 chain leads to abnormal cardiovascular ECM structure that cause insufficient oxygen supply to the heart and the subsequent ischemic cardiac phenotype observed. Our study links the genetic deficiency of an ECM protein to cardiomyopathy and implies a novel pathway of idiopathic cardiomyopathy in human.

Animals↗

PubMed2005

Gene transfer of a phospholamban-targeted antibody improves calcium handling and cardiac function in heart failure.

BACKGROUND: Abnormalities of intracellular calcium handling are widely recognized as a common hallmark of heart failure in animal models and humans. Modifying the interaction of phospholamban (PLB) with the sarcoplasmic reticulum ATPase (SERCA) by PLB mutants improves cardiac function but may also lead to heart failure. In this study we describe the in vivo effects of a new approach to modify the PLB-SERCA interaction using a recombinant, intracellularly expressed chicken-antibody derived protein (PLADP) targeting the cytoplasmic domain of PLB in the cardiomyopathic BIO 14.6 hamster. METHODS AND RESULTS: In vivo gene transfer was performed in 12-14-week-old BIO 14.6 cardiomyopathic hamsters using intracoronary delivery of adenovirus containing the PLADP or the beta-galactosidase (LacZ) gene (8 x 10(9) PFU per animal). A third group was injected with saline (Sham). Echocardiography was performed before and, together with hemodynamic measurements, repeated 4-5 days after gene transfer. Indo-1 calcium transients and myocyte contractility were measured in isolated cardiomyocytes from the BIO 14.6 hamster transfected with the PLADP. Gene expression (LacZ) was found in 54+/-15% of cells throughout the heart without any signs of myocardial inflammation. Echocardiographic and hemodynamic indices of left ventricular function were significantly increased after gene transfer with the PLADP, compared to controls. Measurements of myocyte contractility and calcium transients in isolated cardiac myocytes from BIO 14.6 hamsters revealed improved intracellular calcium handling and contractility. CONCLUSION: In vivo adenoviral gene transfer with the PLADP resulted in short-term intracellular expression of a PLADP, improving LV function and enhancing myocardial contractility in the failing cardiomyopathic hamster heart. The PLADP enhanced contractility and cardiac function by improving intracellular calcium handling. Expression of antibody-derived protein represents a new approach to modify protein-protein interactions at the cellular level.

Adenoviridae↗

PubMed2005

NOC/oFQ activates ERK and JNK but not p38 MAPK to impair prostaglandin cerebrovasodilation after brain injury.

Fluid percussion brain injury (FPI) elevates the CSF concentration of the opioid nociceptin/orphanin FQ (NOC/oFQ), which contributes to impairment of pial artery dilation to the prostaglandins (PG) PGE2 and PGI2. This study investigated the role of the ERK, p38, and JNK isoforms of mitogen-activated protein kinase (MAPK) in impaired PG cerebrovasodilation after FPI, and the relationship of brain injury induced release of NOC/oFQ to MAPK in such vascular impairment in newborn pigs equipped with a closed cranial window. FPI blunted PGE2 pial artery dilation, but U 0126 and SP 600125 (10(-6) M) (ERK and JNK MAPK inhibitors, respectively) partially prevented such impairment (7 +/- 1, 12 +/- 1, and 17 +/- 1 vs. 2 +/- 1, 3 +/- 1, and 5 +/- 1 vs. 4 +/- 1, 7 +/- 1, and 12 +/- 1% for 1, 10, and 100 ng/ml PGE2 in control, FPI, and FPI + U 0126 pretreated animals, respectively). In contrast, administration of SB 203580 (10(-5) M) (p38 MAPK inhibitor) did not prevent FPI impairment of PGE2 dilation. Co-administration of NOC/oFQ at the dose of 10(-10) M, the cerebrospinal fluid concentration observed after FPI, with PGE2 under non-brain injury conditions blunted PG dilation, but U 0126 or SP 600125 partially prevented such impairment (7 +/- 1, 11 +/- 1, and 16 +/- 2 vs. 0 +/- 1, 1 +/- 1, and 2 +/- 1, vs. 5 +/- 1, 9 +/- 1, and 13 +/- 2 for responses to PGE2 in control, NOC/oFQ, and NOC/oFQ + U 0126 treated animals, respectively). Administration of SB 203580 did not prevent impairment of PG pial artery dilation by NOC/oFQ. These data show that activation of ERK and JNK but not p38 MAPK contributes to impairment of PG cerebrovasodilation after FPI. These data suggest that NOC/oFQ induced ERK and JNK but not p38 MAPK activation contributes to impaired cerebrovasodilation to PG after FPI.

Animals↗

PubMed2005

Fisher's theorems for multivariable, time- and space-dependent systems, with applications in population genetics and chemical kinetics.

We study different physical, chemical, or biological processes involving replication, transformation, and disappearance processes, as well as transport processes, and assume that the time and space dependence of the species densities are known. We derive two types of Fisher equations. The first type relates the average value of the time derivative of the relative time-specific rates of growth of the different species to the variance of the relative, time-specific rates of growth. A second type relates the average value of the gradient or the divergence of the relative, space-specific rates of growth to the space correlation matrix of the relative, space-specific rates of growth. These Fisher equations are exact results, which are independent of the detailed kinetics of the process: they are valid whether the evolution equations are linear or nonlinear, local or nonlocal in space and/or time and can be applied for the study of a large class of physical, chemical, and biological systems described in terms of time- and/or space-dependent density fields. We examine the implications of our generalized Fisher relations in population genetics, biochemistry, and chemical kinetics (reaction-diffusion systems). We show that there is a connection between the enhanced (hydrodynamic) transport of mutations induced by population growth and space-specific rate vectors: the velocity of enhanced transport is proportional to the product of the diffusion coefficient of the species and the space rate vector; this relation is similar to a fluctuation-dissipation relation in statistical mechanics.

Analysis of Variance↗

PubMed2005

What happens to British veterans when they leave the armed forces?

BACKGROUND: Little is known about the factors associated with leaving the armed forces, or what predicts subsequent employment success for veterans. It is likely that there is a complex interaction of adverse social outcomes and mental health status in this group. METHOD: Analysis of existing data from the King's Military Cohort, a large, randomly selected, longitudinal cohort of service personnel, many of whom have now left the armed forces. The sample consisted of 8195 service personnel who served in the armed forces in 1991; a third deployed to the Gulf (1990-91), a third deployed to Bosnia (1992-97) and the final third an 'Era' control group in the Armed Forces in 1991 but not deployed. RESULTS: The majority of service leavers do well after leaving and are in full-time employment. Those with poor mental health during service were more likely to leave and had a greater chance of becoming unemployed after leaving. Mental health problems appear to remain static for veterans after leaving. Veterans of the Gulf War enjoyed more favourable employment outcomes, provided that they came home well. CONCLUSIONS: Only a minority of veterans fare badly after service, even amongst those with active tours of duty behind them. Veterans with mental health problems during service seem to be at higher risk of social exclusion after leaving and therefore these individuals represent an especially vulnerable group of the veteran population.

Adult↗

PubMed2005

Multiple rate-determining steps for nonideal and fractal kinetics.

We show that the kinetic model of a single rate-determining step in a reaction mechanism can be extended to systems with multiple overall reactions for which the elementary reactions obey nonideal or fractal kinetics. The following assumptions are necessary: (1) The system studied is either closed or open, but no constraints exist preventing the evolution toward equilibrium. (2) Elementary reactions occur in pairs of forward and backward steps. (3) The kinetics of the elementary steps are either nonideal or fractal and are compatible with equilibrium thermodynamics. (4) The number of reaction routes is identical with the number of rate-determining steps. If these hypotheses are valid, then the overall reaction rates can be explicitly evaluated: they have a form similar to the kinetic equations for the elementary reactions and the apparent reaction orders and fractal coefficients can be expressed analytically in terms of the kinetic parameters of the elementary reactions. We derive a set of relationships which connect the equilibrium constants of the reaction routes, the corresponding overall rate coefficients, and the stoichiometric numbers of the rate-determining steps. We also derive a set of generalized Boreskov relations among the apparent activation energies of the forward and backward overall processes, the corresponding reaction enthalpies, and the stoichiometric coefficients of the rate-determining steps. If the elementary reactions obey fractal kinetics, the same is true for the rate-determining steps. The fractal exponents of the forward and backward overall reactions are linear combinations of the fractal exponents of the fractal elementary reactions. Similar to the theory of single rate-determining steps, our approach can be used for selecting suitable reaction mechanisms from experimental data.

Journal Article↗

PubMed2005

ASF/SF2-regulated CaMKIIdelta alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle.

The transition from juvenile to adult life is accompanied by programmed remodeling in many tissues and organs, which is key for organisms to adapt to the demand of the environment. Here we report a novel regulated alternative splicing program that is crucial for postnatnal heart remodeling in the mouse. We identify the essential splicing factor ASF/SF2 as a key component of the program, regulating a restricted set of tissue-specific alternative splicing events during heart remodeling. Cardiomyocytes deficient in ASF/SF2 display an unexpected hypercontraction phenotype due to a defect in postnatal splicing switch of the Ca(2+)/calmodulin-dependent kinase IIdelta (CaMKIIdelta) transcript. This failure results in mistargeting of the kinase to sarcolemmal membranes, causing severe excitation-contraction coupling defects. Our results validate ASF/SF2 as a fundamental splicing regulator in the reprogramming pathway and reveal the central contribution of ASF/SF2-regulated CaMKIIdelta alternative splicing to functional remodeling in developing heart.

Alternative Splicing↗

PubMed2005

A role for decorin in the remodeling of myocardial infarction.

Because the small leucine-rich proteoglycan decorin has been implicated in regulation of collagen fibrillogenesis leading to proper extracellular matrix assembly, we hypothesized it could play a key role in cardiac fibrosis following myocardial infarction. In this study we ligated the left anterior descending coronary artery in wildtype and decorin-null mice to produce large infarcts in the anterior wall of the left ventricle. At early stages post-coronary occlusion the myocardial infarction size did not appreciably differ between the two genotypes. However, we found a wider distribution of collagen fibril sizes with less organization and loose packing in mature scar from decorin-null mice. Thus, we tested the hypothesis that these abnormal collagen fibrils would adversely affect post-infarction mechanics and ventricular remodeling. Indeed, scar size, right ventricular remote hypertrophy, and left ventricular dilatation were greater in decorin-null animals compared with wildtype littermates 14 days after acute myocardial infarction. Echocardiography revealed depressed left ventricular systolic function between 4 and 8 weeks post-ischemia in the decorin-null animals. These changes indicate that decorin is required for the proper fibrotic evolution of myocardial infarctions, and that its absence leads to abnormal scar tissue formation. This might contribute to aneurysmal ventricular dilatation, remote hypertrophy, and depressed ventricular function.

Animals↗

PubMed2005

Saccadic eye movements cause compression of time as well as space.

There is now considerable evidence that space is compressed when stimuli are flashed shortly before or after the onset of a saccadic eye movement. Here we report that short intervals of time between two successive perisaccadic visual (but not auditory) stimuli are also underestimated, indicating a compression of perceived time. We were even more surprised that in a critical interval before saccades, perceived temporal order is consistently reversed. The very similar time courses of spatial and temporal compression suggest that both are mediated by a common neural mechanism, probably related to the predictive shifts that occur in receptive fields of many visual areas at the time of saccades.

Humans↗

PubMed2005

PINCH1 plays an essential role in early murine embryonic development but is dispensable in ventricular cardiomyocytes.

PINCH1, an adaptor protein composed of five LIM domains, mediates protein-protein interactions and functions as a component of the integrin-integrin-linked kinase (ILK) complex. The integrin-ILK signaling complex plays a pivotal role in cell motility, proliferation, and survival during embryonic development of many animal species. To elucidate the physiological function of PINCH1 in mouse embryonic development, we have deleted the mouse PINCH1 gene by homologous recombination. Mice heterozygous for PINCH1 are viable and indistinguishable from wild-type littermates. However, no viable homozygous offspring were observed from PINCH1+/- intercrosses. Histological analysis of homozygous mutant embryos revealed that they had a disorganized egg cylinder by E5.5, which degenerated by E6.5. Furthermore, E5.5 PINCH1-/- embryos exhibited decreased cell proliferation and excessive cell death. We have also generated and analyzed mice in which PINCH1 has been specifically deleted in ventricular cardiomyocytes. These mice exhibit no basal phenotype, with respect to mouse survival, cardiac histology, or cardiac function as measured by echocardiography. Altogether, these data indicate that PINCH1 plays an essential role in early murine embryonic development but is dispensable in ventricular cardiomyocytes.

Adaptor Proteins, Signal Transducing↗