Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation)

Copyright @ 2007 Gu et al; licensee BioMed Central LtdBiochemists often conduct experiments in-vivo in order to explore observable behaviours and understand the dynamics of many intercellular and intracellular processes. However an intuitive understanding of their dynamics is hard to obtain because most pathways of interest involve components connected via interlocking loops. Formal methods for modelling and analysis of biochemical pathways are therefore indispensable. To this end, ODEs (ordinary differential equations) have been widely adopted as a method to model biochemical pathways because they have an unambiguous mathematical format and are amenable to rigorous quantitative analysis. BioNessie http://www.bionessie.com webcite is a workbench for the composition, simulation and analysis of biochemical networks which is being developed in by the Systems Biology team at the Bioinformatics Research Centre as a part of a large DTI funded project 'BPS: A Software Tool for the Simulation and Analysis of Biochemical Networks' http://www.brc.dcs.gla.ac.uk/projects/dti_beacon webcite. BioNessie is written in Java using NetBeans Platform libraries that makes it platform independent. The software employs specialised differential equations solvers for stiff and non-stiff systems to produce model simulation traces. BioNessie provides a user-friendly interfact that comes up with an intuitive tree-based graphical layout, an edition function to SBML-compatible models and feature of data output

Mating opportunities and energetic constraints drive variation in age-dependent sexual signalling

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Online Version of Record published before inclusion in an issue: 11 October 2016When males repeatedly produce energetically expensive sexual signals, trade-offs between current and future investment can cause plasticity in age-dependent signalling. Such variation is often interpreted as alternate adaptive strategies: live fast and die young vs. slow and steady. An alternative (yet rarely tested) explanation is that condition-dependent constraints on allocation cause variation in signalling with age (‘late bloomers’ do not have early investment options). Testing this hypothesis is challenging because resource acquisition and allocation are difficult to measure, and energetic reserves both affect and are affected by reproductive effort. We simultaneously manipulated acquisition (through dietary nutrition) and access to potential mates (as a proxy for manipulating sexual trait allocation) in male decorated crickets (Gryllodes sigillatus), while measuring age- and signalling effort-mediated changes in energy storage components. Increased diet quality caused increased signalling effort and energy storage, while access to females increased both the likelihood of and time spent signalling. Males with lower resource budgets signalled less, but still suffered energetic storage loss and viability costs. Our results suggest that energetic constraints, rather than strategic resource accumulation, reduced signalling levels in males with lower resource acquisition ability. Our findings imply a non-adaptive explanation for age-dependent variation in sexual signalling, and an important role for energetic constraints in maintaining the honesty of costly behavioural displays.T.M.H. and L.F.B. were supported by the University of Stirling. J.H. was funded by a University Royal Society Fellowship. J.R. was funded by a NERC studentship (awarded to J.H)

Causes of adaptive differences in age-dependent reproductive effort

Sexually selected ornaments are among the most spectacular traits in nature. Indeed, the extreme costs associated with producing sexual traits seem to play a crucial role in their evolution by enforcing honest levels of advertisement: only males with high levels of acquired resources (or high ‘condition’, as it is known in the literature) can afford to produce extravagant signals, a phenomenon which maintains signal reliability in a constant environment. In my thesis I examine many implications of this condition-dependent model of ornament and preference evolution for variation in age-dependent allocation to sexual signals and other life history traits. In Chapter 1, I review theoretical implications of condition-dependent signalling for life history and sexual selection theory. I note that a universal cost of expenditure in sexual advertisement is metabolic in nature: metabolites used to fund ornament expression are by definition unavailable to other life history traits that compete for a limited resource pool. This universal constraint on expenditure does more than maintain honesty (as noted above), however: the reliance of sexual displays on high levels of nutrient acquisition may help maintain genetic variation in sexual signals that would otherwise be eroded by strong mate choice, and without which the selective basis for good-genes choice would disappear. Three mechanisms in particular probably help to maintain genetic variation in acquisition. 1) Because acquiring resources and converting them efficiently to useful forms depends on the high function of many biochemical pathways, condition is undoubtedly highly polygenic, which slows the erosion of genetic variation under strong directional selection by females (especially in the presence of epistatic interactions). 2) The highly polygenic nature of condition also presents a large target for mutation, which continually restores variation at the loci under selection. 3) The many loci underlying condition may also be particularly sensitive to environmental heterogeneity in time or space. By favouring the most ornate males, females acquire high performing genes for their offspring, regardless of the precise allele combinations that have conferred the ability to acquire resources. Selection on specific alleles is liable to fluctuate over time or space whenever allelic performance is strongly context-specific. I close by noting the considerable challenges in advancing research on sexual selection and life history allocation, including the fact that two key processes central to life history (acquisition and allocation) are latent variables that interact in complexways and are intrinsically difficult to measure empirically. In the remainder of my thesis I conduct a series of experiments involving decorated crickets, Gryllodes sigillatus, which are useful models for studying life history because they enable precise measurement of male reproductive effort. Male G. sigillatus face important allocation decisions owing to the highly polyandrous nature of females, and the substantial costs involved in signalling and mating. Chapter 2 examines sex differences in age-dependent reproductive effort as a function of diet and development stage. I reared outbred crickets using four combinations of diet nutritional quality, and studied the effects of these combinations on male and female reproductive effort (calling effort in males and fecundity in females) and longevity. While I expected males to be more sensitive than females to variation in diet and developmental changes in its quality, I actually observed the opposite: males in all treatments increased calling effort over time, exhibiting consistently positive covariance between calling effort and longevity across treatments. By contrast, the relationships between female reproductive effort and longevity changed dramatically across treatments, and females who lived to intermediate ages had the highest fecundity. Although my results support sex-specific selection on life history allocation over time, a compelling additional explanation for my findings relates to the strategic role of calling for achieving male fitness. In the absence of positive feedback from potential mates, perhaps male allocation to sexual advertisement is careful and only increases gradually as a function of accumulating metabolic resources and increasing risk of intrinsic mortality. Alleles underlying condition are expected to be particularly sensitive to environmental heterogeneity. While this sensitivity may help maintain additive variation in male quality (which is essential for the sustenance of adaptive good-genes mate choice, as noted in Chapter 1), too much environmental sensitivity could also underiii mine the signal value of the male trait. For example, if there are strong genotypeby- environment interactions (GEIs) for sexual advertisement, in a rapidly changing environment females risk favouring a male whose alleles are no longer best suited to current conditions. This problem is particularly pressing for animals like crickets where males exhibit a behaviourally plastic sexual display (such as calling), and so may dynamically adjust signalling effort over time. In Chapter 3, I used inbred lines of decorated crickets to quantify age and diet dependent genetic variation in male signalling. I demonstrate that while genetic correlations across diets were quite strong for morphological traits, correlations between measures of the male sexual trait rapidly approached zero as I increased the distance in time (i.e., across widely spaced ages) or diet (i.e., comparing more dissimilar dietary histories) between samples. While extrapolating from my laboratory experiments to nature is difficult, my findings nevertheless cast doubt on the value of behaviourally dynamic signals (such as cricket calls) for reliably indicating genetic quality in realistically complex environments. In Chapter 4 I used physiological assays to evaluate factors affecting metabolite storage and use over time in decorated crickets. I manipulated the acquisition ability of all males using artificial diets that varied linearly in nutrient quality, and manipulated access to female mates over the course of the second week of adult life. By sacrificing crickets at key stages before and after manipulating the diet and social environment, I was able to estimate changes in stored metabolites, and relate these changes to calling effort and longevity. During the first week of adulthood (in the absence of females), higher diet quality significantly increased calling effort and storage of lipid, glycogen, and carbohydrate (but not protein). The presence of females increased both the probability of calling and the amount of calling during the second week, whereas diet quality only improved calling effort. By the end of the second week, calling effort had decreased, even by high quality males in the presence of females, suggesting a depletion of resources. Furthermore, the loss of condition during week 2 covaried with calling effort during the previous week irrespective of diet. Males who started the second week in high condition lost more glycogen and carbohydrate than rivals; meanwhile, lipid accumulation covaried positively with calling effort during week 2. The contrasting patterns of storage and use for lipids compared to the ‘quick-release’ metabolites (glycogen and carbohydrates) affirms starkly distinct functions for the different storage components, and underlines the importance of specific physiological measures in life history research. Finally, in the general discussion, I attempt to synthesise my thesis’s contributions to the study of life history trade-offs involving behavioural sexual displays. I argue that my work may have strong implications for the general honesty of male advertisements, and invite further research focused on quantifying interactions between the genotype, age, and environment in natural systems. I also question the prevalence of adaptive age-dependent plasticity in sexual advertisement, arguing for the parsimony of a more mechanistic and non-adaptive explanation for variation among populations and taxa in age-dependent signalling: males vary in signalling effort primarily as a function of constraints on energy expenditure, rather than because they are carefully saving resources for future use

Role of computed tomography and magnetic resonance imaging in patients with cardiovascular disease

Background: Although there have been recent advances, cardiovascular disease remains the commonest cause of premature death in the United Kingdom. There is a need to develop safe non-invasive techniques to aid the diagnosis and treatment of patients with cardiovascular disease.Objectives: The aims of this thesis are: (i) to establish whether coronary artery calcification can be measured reproducibly by helical computed tomography; (ii) to establish the effect of lipid lowering therapy on the progression of coronary calcification; (iii) to determine whether multidetector computed tomography can predict graft patency in patients who have undergone coronary artery bypass grafting; and (iv), to investigate the role of magnetic resonance imaging to assess plaque characteristics following acute carotid plaque rupture.Methods: In 16 patients, coronary artery calcification was assessed twice within 4 weeks by helical computed tomography. As part of a randomised controlled trial, patients received atorvastatin 80 mg daily or matching placebo, and had coronary calcification assessed annually. Fifty patients with previous coronary artery bypass surgery who were listed for diagnostic coronary angiography underwent contrast enhanced computed tomography angiography using a 16-slice multidetector computed tomography scanner. Finally, 15 patients with recent symptoms and signs of an acute transient ischaemic attack, amaurosis fugax or stroke underwent magnetic resonance angiography of the carotid arteries using dedicated surface coils. Plaque volume, regional plaque densities and neovascularisation were determined before and after gadolinium enhancement.Results: Quantification of coronary artery calcification demonstrated good reproducibility in patients with scores > 100 AU. Despite reducing systemic inflammation and halving serum low-density lipoprotein cholesterol concentrations, atorvastatin therapy did not affect the rate of progression of coronary artery calcification. Computed tomography angiography was found to be highly specific for the detection of graft patency. Assessment of plaque characteristics by magnetic resonance scanning in patients with recent acute carotid plaque was feasible and reproducible.Conclusions: Coronary artery calcium scores can be determined in a reproducible manner. Although they correlate well with the presence of atherosclerosis and predict future coronary risk. there is little role for monitoring progression of coronary artery calcification in order to assess the response to lipid lowering therapy. Computed tomography can be used reliably to predict graft patency in patients who have undergone coronary artery bypass grafting, and is an acceptable non-invasive alternative to invasive coronary angiography. Magnetic resonance imaging techniques ' can be employed in a feasible, timely and reproducible manner to detect plaque characteristics associated with acute atherothrombotic disease

Delineation of RAID1, the RACK1 interaction domain located within the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5

Background The cyclic AMP specific phosphodiesterase, PDE4D5 interacts with the β-propeller protein RACK1 to form a signaling scaffold complex in cells. Two-hybrid analysis of truncation and mutant constructs of the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5 were used to define a domain conferring interaction with the signaling scaffold protein, RACK1. Results Truncation and mutagenesis approaches showed that the RACK1-interacting domain on PDE4D5 comprised a cluster of residues provided by Asn-22/Pro-23/Trp-24/Asn-26 together with a series of hydrophobic amino acids, namely Leu-29, Val-30, Leu-33, Leu-37 and Leu-38 in a 'Leu-Xaa-Xaa-Xaa-Leu' repeat. This was done by 2-hybrid analyses and then confirmed in biochemical pull down analyses using GST-RACK1 and mutant PDE4D5 forms expressed in COS cells. Mutation of Arg-34, to alanine, in PDE4D5 attenuated its interaction with RACK1 both in 2-hybrid screens and in pull down analyses. A 38-mer peptide, whose sequence reflected residues 12 through 49 of PDE4D5, bound to RACK1 with similar affinity to native PDE4D5 itself (Ka circa 6 nM). Conclusions The RACK1 Interaction Domain on PDE4D5, that we here call RAID1, is proposed to form an amphipathic helical structure that we suggest may interact with the C-terminal β-propeller blades of RACK1 in a manner akin to the interaction of the helical G-γ signal transducing protein with the β-propeller protein, G-β

Epac and the high affinity rolipram binding conformer of PDE4 modulate neurite outgrowth and myelination using an in vitro spinal cord injury model

<b>Background and Purpose</b><p></p> cAMP and pharmacological inhibition of PDE4, which degrades it, are promising therapeutic targets for the treatment of spinal cord injury (SCI). Using our previously described in vitro SCI model, we studied the mechanisms by which cAMP modulators promote neurite outgrowth and myelination using enantiomers of the PDE4-specific inhibitor rolipram and other modulators of downstream signalling effectors.<p></p> <b>Experimental Approach</b><p></p> Rat mixed neural cell myelinating cultures were cut with a scalpel and treated with enantiomers of the PDE4-specific inhibitor rolipram, Epac agonists and PKA antagonists. Neurite outgrowth, density and myelination were assessed by immunocytochemistry and cytokine levels analysed by qPCR.<p></p> <b>Key Results</b><p></p> Inhibition of the high-affinity rolipram-binding state (HARBS), rather than the low-affinity rolipram binding state (LARBS) PDE4 conformer promoted neurite outgrowth and myelination. These effects were mediated through the activation of Epac and not through PKA. Expression of the chemokine CXCL10, known to inhibit myelination, was markedly elevated in astrocytes after Rho inhibition and this was blocked by inhibition of Rho kinase or PDE4.<p></p> <b>Conclusions and Implications</b><p></p> PDE4 inhibitors targeted at the HARBS conformer or Epac agonists may provide promising novel targets for the treatment of SCI. Our study demonstrates the differential mechanisms of action of these compounds, as well as the benefit of a combined pharmacological approach and highlighting potential promising targets for the treatment of SCI. These findings need to be confirmed in vivo

Avoiding the misuse of BLUP in behavioral ecology

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Having recognized that variation around the population-level “Golden Mean” of labile traits contains biologically meaningful information, behavioural ecologists have focused increasingly on exploring the causes and consequences of individual variation in behaviour. These are exciting new directions for the field, assisted in no small part by the adoption of mixed-effects modelling techniques that enable the partitioning of among- and within-individual behavioural variation. It has become commonplace to extract predictions of individual random effects from such models for use in subsequent analyses (for example, between a personality trait and other individual traits such as cognition, physiology, or fitness-related measures). However, these predictions are made with large amounts of error that is not carried forward, rendering further tests susceptible to spurious P values from these individual-level point estimates. We briefly summarize the problems with such statistical methods that are used regularly by behavioural ecologists, and highlight the robust solutions that exist within the mixed model framework, providing tutorials to aid in their implementation.This work was supported by a Biotechnology and Biological Sciences Research Council grant (BB/L022656/1

The activity of cAMP-Phosphodiesterase 4D7 (PDE4D7) is regulated by protein kinase A-dependent phosphorylation within its unique N-terminus

The cyclic AMP phosphodiesterases type 4 (PDE4s) are expressed in a cell specific manner, with intracellular targeting directed by unique N-terminal anchor domains. All long form PDE4s are phosphorylated and activated by PKA phosphorylation within their upstream conserved region 1 (UCR1). Here, we identify and characterise a novel PKA site (serine 42) within the N-terminal region of PDE4D7, an isoform whose activity is known to be important in prostate cancer progression and ischemic stroke. In contrast to the UCR1 site, PKA phosphorylation of the PDE4D7 N-terminus appears to occur constitutively and inhibits PDE4 activity to allow cAMP signalling under basal conditions

Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)

PDE4 is one of eleven known cyclic nucleotide phosphodiesterase families and plays a pivotal role in mediating hydrolytic degradation of the important cyclic nucleotide second messenger, cyclic 3′5′ adenosine monophosphate (cAMP). PDE4 inhibitors are known to have anti-inflammatory properties, but their use in the clinic has been hampered by mechanism-associated side effects that limit maximally tolerated doses. In an attempt to initiate the development of better-tolerated PDE4 inhibitors we have surveyed existing approved drugs for PDE4-inhibitory activity. With this objective, we utilised a high-throughput computational approach that identified moexipril, a well tolerated and safe angiotensin-converting enzyme (ACE) inhibitor, as a PDE4 inhibitor. Experimentally we showed that moexipril and two structurally related analogues acted in the micro molar range to inhibit PDE4 activity. Employing a FRET-based biosensor constructed from the nucleotide binding domain of the type 1 exchange protein activated by cAMP, EPAC1, we demonstrated that moexipril markedly potentiated the ability of forskolin to increase intracellular cAMP levels. Finally, we demonstrated that the PDE4 inhibitory effect of moexipril is functionally able to induce phosphorylation of the Hsp20 by cAMP dependent protein kinase A. Our data suggest that moexipril is a bona fide PDE4 inhibitor that may provide the starting point for development of novel PDE4 inhibitors with an improved therapeutic window

Phosphorylation of PDE4A5 by MAPKAPK2 attenuates fibrin degradation via p75 signalling

Phosphodiesterases (PDEs) shape local cAMP gradients to underpin the specificity of receptor function. Key to this process is the highly defined nature of the intra-cellular location of PDEs in the cell. PDE4A5 is a PDE isoform that specifically degrades cAMP and is known to associate with the p75 neurotrophin receptor (p75NTR) where it modulates cAMP signalling cascades that regulate extracellular matrix remodelling in the lungs. Here we map and validate novel protein–protein interaction sites that are important for formation of the PDE4A5–p75NTR complex and show, for the first time, that phosphorylation of PDE4A5 by MAPKAPK2 enhances PDE4A5 interaction with p75NTR and that this, in turn, serves to attenuate fibrin degradation