How can mathematical models advance tuberculosis control in high HIV prevalence settings?

Existing approaches to tuberculosis (TB) control have been no more than partially successful in areas with high human immunodeficiency virus (HIV) prevalence. In the context of increasingly constrained resources, mathematical modelling can augment understanding and support policy for implementing those strategies that are most likely to bring public health and economic benefits. In this paper, we present an overview of past and recent contributions of TB modelling in this key area, and suggest a way forward through a modelling research agenda that supports a more effective response to the TB-HIV epidemic, based on expert discussions at a meeting convened by the TB Modelling and Analysis Consortium. The research agenda identified high-priority areas for future modelling efforts, including 1) the difficult diagnosis and high mortality of TB-HIV; 2) the high risk of disease progression; 3) TB health systems in high HIV prevalence settings; 4) uncertainty in the natural progression of TB-HIV; and 5) combined interventions for TB-HIV. Efficient and rapid progress towards completion of this modelling agenda will require co-ordination between the modelling community and key stakeholders, including advocates, health policy makers, donors and national or regional finance officials. A continuing dialogue will ensure that new results are effectively communicated and new policy-relevant questions are addressed swiftly.

Weight loss effects from vegetable intake: a 12-month randomised controlled trial.

BACKGROUND/OBJECTIVES: Direct evidence for the effects of vegetable intake on weight loss is qualified. The study aimed to assess the effect of higher vegetable consumption on weight loss. SUBJECTS/METHODS: A single blind parallel controlled trial was conducted with 120 overweight adults (mean body mass index=29.98 kg/m(2)) randomised to two energy deficit healthy diet advice groups differing only by doubling the serving (portion) sizes of vegetables in the comparator group. Data were analysed as intention-to-treat using a linear mixed model. Spearmans rho bivariate was used to explore relationships between percentage energy from vegetables and weight loss. RESULTS: After 12 months, the study sample lost 6.5±5.2 kg (P<0.001 time) with no difference between groups (P>0.05 interaction). Both groups increased vegetable intake and lost weight in the first 3 months, and the change in weight was significantly correlated with higher proportions of energy consumed as vegetables (rho=-0.217, P=0.024). Fasting glucose, insulin and triglyceride levels decreased (P<0.001 time) and high-density lipoprotein cholesterol levels increased (P<0.001 time), with no difference between groups. Weight loss was sustained for 12 months by both groups, but the comparator group reported greater hunger satisfaction (P=0.005). CONCLUSIONS: Advice to consume a healthy low-energy diet leads to sustained weight loss, with reductions in cardiovascular disease risk factors regardless of an emphasis on more vegetables. In the short term, consuming a higher proportion of the dietary energy as vegetables may support a greater weight loss and the dietary pattern appears sustainable.

VEGF-induced choroidal damage in a murine model of retinal neovascularisation.

BACKGROUND/AIMS: Photoreceptor-specific upregulation of vascular endothelial growth factor (VEGF) in a transgenic mouse model (Kimba) of retinal neovascularisation induces retinal vascular damage which appears similar to that in diabetic retinopathy. Here we have determined whether the choroidal vasculature is also affected in Kimba. METHODS: Kimba mice were assessed with fundus fluorescein angiography for mild, moderate or severe retinal vascular leakage prior to preparation of choroidal corrosion casts for quantitative analysis using scanning electron microscopy. VEGF was located immunohistochemically. RESULTS: Choroidal abnormalities included microaneurysms, constriction, shrinkage and dropout in the capillaries and tortuosity and loops in the arteries and veins which were similar to those observed in corrosion casts of the human choroid in diabetes. Similar to human diabetes, choroidal neovascularisation was not observed. The severity of choroidal damage correlated with the extent of retinal vascular leakage. In addition to the expected presence of VEGF in photoreceptors, VEGF was also detected in the pigment epithelium and choroid in the transgenic mice. CONCLUSION: We show that elevated retinal VEGF levels trigger pathophysiological changes in the choroid. We suggest that therapies to prevent vascular damage in diabetes must target both the retinal and choroidal vasculatures.

Do chaperonins boost protein yields by accelerating folding or preventing aggregation?

The GroEL chaperonin has the ability to behave as an unfoldase, repeatedly denaturing proteins upon binding, which in turn can free them from kinetic traps and increase their folding rates. The complex formed by GroEL+GroES+ATP can also act as an infinite dilution cage, enclosing proteins within a protective container where they can fold without danger of aggregation. Controversy remains over which of these two properties is more critical to the GroEL/ES chaperonin's function. We probe the importance of the unfoldase nature of GroEL under conditions where aggregation is the predominant protein degradation pathway. We consider the effect of a hypothetical mutation to GroEL which increases the cycle frequency of GroEL/ES by increasing the rate of hydrolysis of GroEL-bound ATP. Using a simple kinetic model, we show that this modified chaperonin would be self-defeating: any potential reduction in folding time would be negated by an increase in time spent in the bulk, causing an increase in aggregation and a net decrease in protein folding yields.

Adaptations in cortical and trabecular bone in response to mechanical loading with and without weight bearing.

Exercise that imparts rapid, high-magnitude mechanical loading is considered to be advantageous to bone health. Previous rodent studies have suggested that swimming may also be beneficial to bone. We investigated the differential effects of exercise with and without weight bearing on cortical and trabecular bone. Forty female Sprague-Dawley rats (120 days) were weight-stratified and randomized into four groups: swim control (Cs, n = 10), swim (S, n = 10), treadmill control (Ct, n = 10), and treadmill (T, n = 10). Treadmill speed was adjusted to match the average limb loading frequency used for swimming, and all training progressed to 1 hour/day, 5 days/week, for 12 weeks. Femurs and humeri were assessed for cortical morphometry by peripheral quantitative computed tomography, areal bone mineral density (BMD) by peripheral dual-energy X-ray absorptiometry, mineral content by ashing, strength by three-point bending, and trabecular volume (BV/TV) by micro-computed tomography. Swimming was associated with increases in cortical thickness and BMD in the humerus midshaft and trabecular BV/TV in the distal femur and proximal humerus compared with age-matched controls. Compared to swimming, treadmill training was associated with increases in percent ash of the femur and humerus and Young's modulus of the femur. Swimming appears to engender novel bone strains and osteogenic adaptations in the humerus and femur, which are different from those induced by normal cage activity. In summary, our findings suggest that when limb loading frequency is matched, swimming may afford greater benefits to cortical and trabecular bone than uphill treadmill work in rats.

Folding on the chaperone: yield enhancement through loose binding.

A variety of small cageless chaperones have been discovered that can assist protein folding without the consumption of ATP. These include mini-chaperones (catalytically active fragments of larger chaperones), as well as small proteins such as alpha-casein and detergents acting as "artificial chaperones." These chaperones all possess exposed hydrophobic patches on their surface that act as recognition sites for misfolded proteins. They lack the complexity of chaperonins (that encapsulate proteins in their inner rings) and their study can offer insight into the minimal requirements for chaperone function. We use molecular dynamics simulations to investigate how a cageless chaperone, modeled as a sphere of tunable hydrophobicity, can assist folding of a substrate protein. We find that under steady-state (non-stress) conditions, cageless chaperones that bind to a single substrate protein increase folding yields by reducing the time the substrate spends in an aggregation-prone state in a dual manner: (a) by competing for aggregation-prone hydrophobic sites on the surface of a protein, hence reducing the time the protein spends unprotected in the bulk and (b) by accelerating folding rates of the protein. In both cases, the chaperone must bind to and hold the protein loosely enough to allow the protein to change its conformation and fold while bound. Loose binding may enable small cageless chaperones to help proteins fold and avoid aggregation under steady-state conditions, even at low concentrations, without the consumption of ATP.

Free energy landscapes for amyloidogenic tetrapeptides dimerization.

The oligomerization of four peptide sequences, KFFE, KVVE, KLLE, and KAAE is studied using replica-exchange molecular dynamics simulations with an atomically detailed peptide model. Previous experimental studies reported that of these four peptides, only those containing phenylalanine and valine residues form fibrils. We show that the fibrillogenic propensities of these peptides can be rationalized in terms of the equilibrium thermodynamics of their early oligomers. Thermodynamic stability of dimers, as measured by the temperature of monomer association, is seen to be higher for those peptides that are able to form fibrils. Although the relative high and low stabilities of the KFFE and KAAE dimers arise from their respective high and low interpeptide interaction energies, the higher stability of the KVVE dimer over the KLLE system results from the smaller loss of configurational entropy accompanying the dimerization of KVVE. Free energy landscapes for dimerization are found to be strongly sequence-dependent, with a high free energy barrier separating the monomeric and dimeric states for KVVE, KLLE, and KAAE sequences. In contrast, the most fibrillogenic peptide, KFFE, displayed downhill assembly, indicating enhanced kinetic accessibility of its dimeric states. The dimeric phase for all peptide sequences is found to be heterogeneous, containing both antiparallel beta-sheet structures that can grow into full fibrils as well as disordered dimers acting as on- or off-pathway intermediates for fibrillation.

Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway.

Recent experiments suggest that the folding of certain proteins can take place entirely within a chaperonin-like cavity. These substrate proteins experience folding rate enhancements without undergoing multiple rounds of ATP-induced binding and release from the chaperonin. Rather, they undergo only a single binding event, followed by sequestration into the chaperonin cage. The present work uses molecular dynamics simulations to investigate the folding of a highly frustrated protein within this chaperonin cavity. The chaperonin interior is modeled by a sphere with a lining of tunable degree of hydrophobicity. We demonstrate that a moderately hydrophobic environment, similar to the interior of the GroEL cavity upon complexion with ATP and GroES, is sufficient to accelerate the folding of a frustrated protein by more than an order of magnitude. Our simulations support a mechanism by which the moderately hydrophobic chaperonin environment provides an alternate pathway to the native state through a transiently bound intermediate state.

Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters.

A method is introduced to construct a better approximation for the reaction coordinate for protein folding from known order parameters. The folding of a two-state off-lattice alpha helical Go-type protein is studied using molecular dynamics simulations. Folding times are computed directly from simulation, as well as theoretically using an equation derived by considering Brownian-type dynamics for the putative reaction coordinate. Theoretical estimates of the folding time using the number of native contacts (Qn) as a reaction coordinate were seen to differ quite significantly from the true folding time of the protein. By considering the properties of the bimodal free energy surface of this protein as a function of Qn and another relevant coordinate for folding Q (the total number of contacts), we show that by introducing a rotation in the phase space of the order parameters Q and Qn, we can construct a new reaction coordinate q that leads to a fivefold improvement in the estimate of the folding rate. This new coordinate q, resulting from the rotation, lies along the line connecting the unfolded and folded ensemble minima of the free energy map plotted as a function of the original order parameters Q and Qn. Possible reasons for the remaining discrepancy between the folding time computed theoretically and from folding simulations are discussed.

EphA/ephrin-A interactions during optic nerve regeneration: restoration of topography and regulation of ephrin-A2 expression.

During visual system development, interactions between Eph tyrosine kinase receptors and their ligands, the ephrins, guide retinal ganglion cell (RGC) axons to their topographic targets in the optic tectum. Here we show that Eph/ephrin interactions are also involved in restoring topography during RGC axon regeneration in goldfish. Following optic nerve crush, EphA/ephrin-A interactions were blocked by intracranial injections of recombinant Eph receptor (EphA3-AP) or phospho-inositol phospholipase-C. Topographic errors with multiple inputs to some tectal loci were detected electrophysiologically and increased projections to caudal tectum demonstrated by RT-97 immunohistochemistry. In EphA3-AP-injected fish, ephrin-A2-expressing cells in the retino-recipient tectal layers were reduced in number compared to controls and their distribution was no longer graded. The findings, supported by in vitro studies, implicate EphA/ephrin-A interactions in restoring precise topography and in regulating ephrin-A2 expression during regeneration.

Kinetics of the coil-to-helix transition on a rough energy landscape.

The kinetics of folding of a fully atomic seven-residue polyalanine peptide in an implicit solvent are studied using molecular dynamics simulations. The use of an implicit solvent is found to dramatically increase the frustration of the energy landscape relative to simulations performed in an explicit solvent [Phys. Rev. Lett. 85, 2637 (2000)]. While the native state in both implicit and explicit solvent simulations is an alpha-helix, the kinetics of the coil-to-helix transition differ significantly. In contrast to the explicit solvent simulations, the native state in the implicit solvent simulations is not kinetically accessible at temperatures where it is thermodynamically stable and could not be brought into equilibrium with other conformational states. At temperatures where statistical equilibrium was achieved, the conformational diffusion folding mechanism, found earlier to be adequate for this peptide in an explicit solvent [Phys. Rev. Lett. 85, 2637 (2000)], is met with only limited success. Issues relating to the evaluation of the quality of implicit solvent models on the basis of thermodynamic criteria only are reexamined.

Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape.

Chaperonins, such as the GroE complex of the bacteria Escherichia coli, assist the folding of proteins under non-permissive folding conditions by providing a cavity in which the newly translated or translocated protein can be encapsulated. Whether the chaperonin cage plays a passive role in protecting the protein from aggregation, or an active role in accelerating folding rates, remains a matter of debate. Here, we investigate the role of confinement in chaperonin mediated folding through molecular dynamics simulations. We designed a substrate protein with an alpha/beta sandwich fold, a common structural motif found in GroE substrate proteins and confined it to a spherical hydrophilic cage which mimicked the interior of the GroEL/ES cavity. The thermodynamics and kinetics of folding were studied over a wide range of temperature and cage radii. Confinement was seen to significantly raise the collapse temperature, T(c), as a result of the associated entropy loss of the unfolded state. The folding temperature, T(f), on the other hand, remained unaffected by encapsulation, a consequence of the folding mechanism of this protein that involves an initial collapse to a compact misfolded state prior to rearranging to the native state. Folding rates were observed to be either accelerated or retarded compared to bulk folding rates, depending on the temperature of the simulation. Rate enhancements due to confinement were observed only at temperatures above the temperature T(m), which corresponds to the temperature at which the protein folds fastest. For this protein, T(m) lies above the folding temperature, T(f), implying that encapsulation alone will not lead to a rate enhancement under conditions where the native state is stable (T

The cardiac innervation of a marsupial heterotherm, the fat-tailed dunnart (Sminthopsis crassicaudata).

This study investigated the pattern of autonomic innervation of the heart of the fat-tailed dunnart (Sminthopsis crassicaudata) using isolated cardiac preparations. While the pattern of autonomic innervation of the atria was consistent with that found in other mammals, the ventricles displayed an unusual pattern of mammalian cardiac innervation. Transmural stimulation of the intramural nerves of isolated right ventricular preparations caused a decrease in the force of contraction of 46.8+/-3.2% followed by a rebound increase in the force of contraction beyond basal levels of 40.9+/-6.9%. These responses could be blocked independently by the application of the muscarinic receptor antagonist hyoscine and beta-adrenoreceptor antagonist propranolol respectively and could also be mimicked by the application of the agonists acetylcholine (Ach) and noradrenaline (NA). These findings indicated the presence of a functional cholinergic innervation of the ventricles that was capable of reducing the force of contraction below basal levels. This pattern of innervation has only been found previously in one other mammal, the bent-winged bat (Miniopterus schreibersii). Given that both of these species are heterotherms, it is possible that such a pattern of innervation may relate to the control of cardiac output during torpor. These findings are the first that demonstrate the homogeneity of a physiological control mechanism in a so-called 'shallow, daily torpidator' (S. crassicaudata) and a 'deep hibernator' (M. schreibersii) that is absent in mammalian homeotherms. These findings are consistent with recent work suggesting that there may be little difference between these types of heterothermy.

Glass transition in an off-lattice protein model studied by molecular dynamics simulations.

In this paper we report the results of a numerical investigation of the glass transition phenomenon in a minimalist protein model. The inherent structure theory of Stillinger and Weber was applied to an off-lattice protein model with a native state beta-sheet motif. By using molecular dynamics simulations and the steepest descent method, sets of local potential energy minima were generated for the model over a range of temperatures. The mean potential energy of the inherent structures allowed to make rough estimates of the glass-transition temperature T(K). More accurately T(K) was computed by direct evaluations of the total and vibrational entropies. It is found that for the present model the thermodynamic ratio of the folding and glass-transition temperatures is 1.7 which is in good agreement with experimental observations.

Alterations in skeletal and mineral metabolism following thermal injuries.

Severe burns and other chronic inflammatory diseases are associated with altered skeletal metabolism that result in an increased incidence of osteopenia. In thermally injured children and adults there is a dramatic decrease in bone formation accompanied with an increase or maintenance of bone resorption. Children also exhibit a growth delay and subsequently fail to reach a predicted stature. Animal models, including the thermal injury mouse model, are being used to understand the mechanisms behind the uncoupling of bone formation and resorption that occurs following a major burn. The model has numerous commonalities with the human condition such as reduced bone formation, increased bone resorption, and decreased endochondral growth. The mechanisms that modulate calcium and skeletal metabolism following a thermal injury are complex and likely involve a number of endocrine, cytokine, and immune factors. Specifically, the potential roles of glucocorticoids, growth hormone, insulin-like growth factor-1, parathyroid hormone, interleukin-1 and -6, and tumor necrosis factor alpha are addressed. Subsequent to the increased survival rate of burn victims, there has been a heightened focus on therapeutic interventions that prevent or decrease the impact of thermal injuries on the skeletal system. These include exercise programs, exogenous recombinant human growth hormone, insulin, and oxandrolone.

The microanatomy of the rectal salt gland of the Port Jackson Shark, Heterodontus portusjacksoni (Meyer) (Heterodontidae): suggestions for a counter-current exchange system.

A comprehensive anatomical study was undertaken to examine the rectal salt gland in the Port Jackson shark, Heterodontus portusjacksoni, a shark known to invade estuarine environments. The microstructure and vascular organisation of the rectal salt gland was investigated using histological observation and scanning electron microscopy of vascular corrosion casts. Cellular specialisation was observed in the lining of the central lumen of this gland. This may indicate that there is some modification of the principal product of the gland prior to its secretion. The rectal salt gland has a complex structure related to its function. Contrary to previous reports, the flow in secretory tubules is in the opposite direction to that of the capillaries and thus constitutes a counter-current arrangement. The similarity in the organisation of the counter-current and lobulate arrangement of salt-secreting glands through phylogenetically diverse organisms, such as sharks and birds, suggests that this arrangement is important in achieving efficient salt secretion.

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding.

Beginning with simplified lattice and continuum "minimalist" models and progressing to detailed atomic models, simulation studies have augmented and directed development of the modern landscape perspective of protein folding. In this review we discuss aspects of detailed atomic simulation methods applied to studies of protein folding free energy surfaces, using biased-sampling free energy methods and temperature-induced protein unfolding. We review studies from each on systems of particular experimental interest and assess the strengths and weaknesses of each approach in the context of "exact" results for both free energies and kinetics of a minimalist model for a beta-barrel protein. We illustrate in detail how each approach is implemented and discuss analysis methods that have been developed as components of these studies. We describe key insights into the relationship between protein topology and the folding mechanism emerging from folding free energy surface calculations. We further describe the determination of detailed "pathways" and models of folding transition states that have resulted from unfolding studies. Our assessment of the two methods suggests that both can provide, often complementary, details of folding mechanism and thermodynamics, but this success relies on (a) adequate sampling of diverse conformational regions for the biased-sampling free energy approach and (b) many trajectories at multiple temperatures for unfolding studies. Furthermore, we find that temperature-induced unfolding provides representatives of folding trajectories only when the topology and sequence (energy) provide a relatively funneled landscape and "off-pathway" intermediates do not exist.

Evidence of a hypermineralised calcified fibrocartilage on the human femoral neck and lesser trochanter.

Femoral neck fractures are a major cause of morbidity and mortality in elderly humans. In addition to the age-related loss of cancellous bone, changes to the microstructure and morphology of the metaphyseal cortex may be a contributing factor in osteoporotic hip fractures. Recent investigations have identified a hypermineralised tissue on the neck of the femur and trochanteric region that increases in fractional area with advancing age in both males (Boyce & Bloebaum, 1993) and females (Vajda & Bloebaum, 1999). The aim of this study was to determine if the hypermineralised tissue previously observed on the proximal femur is calcified fibrocartilage. Regional variations in the fractional area of hypermineralised tissue, cortical bone, and porosity of the cortical bone along the neck of the femur and lesser trochanter were also quantified. Comparison of back scattered electron and light microscope images of the same area show that regions of hypermineralised tissue correlate with the regions of calcified fibrocartilage from tendon and capsular insertions. The hypermineralised tissue and calcified fibrocartilage had similar morphological features such as the interdigitations of the calcified fibrocartilage into the bone, lacunar spaces, and distinctly shaped pores adjacent to the 2 tissues. Regions of the neck that did not contain insertions were covered with periosteum. There were no regional differences (P > 0.05) on the superior and inferior femoral neck in terms of the percentage area of hypermineralised calcified fibrocartilage, cortical bone, or cortical bone porosity. The lesser trochanter exhibited regional differences in the fractional area of hypermineralised calcified fibrocartilage (P = 0.007) and cortical bone (P = 0.007) but not porosity of the cortical bone (P > 0.05). The effects of calcified fibrocartilage on femoral neck periosteal expansion, repair, and mechanics are unknown, but may play a role in osteoporotic fractures and intracapsular fracture healing.

Combating Gram-positive pathogens: emerging techniques to identify relevant virulence targets.

Recent progress in microbial genome sequencing, along with functional genomics technologies based on gene expression, proteomics and genetics have facilitated the identification of significant numbers of Gram-positive virulence genes. These genes represent a novel and heterogeneous class of targets for antimicrobial drug development. This review will concentrate of the contribution of two functional genomics technologies, in vivo expression technology (IVET) based on gene expression and signature-tagged mutagenesis (STM), a genetics based technology to the identification of virulence genes in Gram-positive pathogens.

Signature-tagged mutagenesis in the identification of virulence genes in pathogens.

Signature-tagged mutagenesis is a functional genomics technique that identifies microbial genes required for infection within an animal host, or within host cells. The application of this technique to a range of microbial pathogens has resulted in the identification of novel virulence determinants in each screen performed to date, so that cumulatively several hundred genes have been ascribed a role in virulence.