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.