Genome-scale metabolic models have proven to be valuable for predicting organism phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with genome sequencing. To ...address this problem, we introduce the Model SEED, a web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic models. The Model SEED integrates existing methods and introduces techniques to automate nearly every step of this process, taking approximately 48 h to reconstruct a metabolic model from an assembled genome sequence. We apply this resource to generate 130 genome-scale metabolic models representing a taxonomically diverse set of bacteria. Twenty-two of the models were validated against available gene essentiality and Biolog data, with the average model accuracy determined to be 66% before optimization and 87% after optimization.
Theoretical models of the evolution of parasites and their hosts have shaped our understanding of infectious disease dynamics for over 40 years. Many theoretical models assume that the underlying ...ecological dynamics are at equilibrium or constant, yet we know that in a great many systems there are fluctuations in the ecological dynamics owing to a variety of intrinsic or extrinsic factors. Here, we discuss the challenges presented when modelling evolution in systems with fluctuating ecological dynamics and summarize the main approaches that have been developed to study host-parasite evolution in such systems. We provide an in-depth guide to one of the methods by applying it to two worked examples of host evolution that have not previously been studied in the literature: when cycles occur owing to seasonal forcing in competition, and when the presence of a free-living parasite causes cycles, with accompanying interactive Python code provided. We review the findings of studies that have explored host-parasite evolution when ecological dynamics fluctuate, and point to areas of future research. Throughout we stress the importance of feedbacks between the ecological and evolutionary dynamics in driving the outcomes of infectious disease systems. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
Tissue engineered vascular grafts (TEVGs) have the potential to overcome the issues faced by existing small diameter prosthetic grafts by providing a biodegradable scaffold where the patient's own ...cells can engraft and form functional neotissue. However, applying classical approaches to create arterial TEVGs using slow degrading materials with supraphysiological mechanical properties, typically results in limited host cell infiltration, poor remodeling, stenosis, and calcification. The purpose of this study is to evaluate the feasibility of novel small diameter arterial TEVGs created using fast degrading material. A 1.0mm and 5.0mm diameter TEVGs were fabricated with electrospun polycaprolactone (PCL) and chitosan (CS) blend nanofibers. The 1.0mm TEVGs were implanted in mice (n = 3) as an unseeded infrarenal abdominal aorta interposition conduit., The 5.0mm TEVGs were implanted in sheep (n = 6) as an unseeded carotid artery (CA) interposition conduit. Mice were followed with ultrasound and sacrificed at 6 months. All 1.0mm TEVGs remained patent without evidence of thrombosis or aneurysm formation. Based on small animal outcomes, sheep were followed with ultrasound and sacrificed at 6 months for histological and mechanical analysis. There was no aneurysm formation or calcification in the TEVGs. 4 out of 6 grafts (67%) were patent. After 6 months in vivo, 9.1 ± 5.4% remained of the original scaffold. Histological analysis of patent grafts demonstrated deposition of extracellular matrix constituents including elastin and collagen production, as well as endothelialization and organized contractile smooth muscle cells, similar to that of native CA. The mechanical properties of TEVGs were comparable to native CA. There was a significant positive correlation between TEVG wall thickness and CD68+ macrophage infiltration into the scaffold (R2 = 0.95, p = 0.001). The fast degradation of CS in our novel TEVG promoted excellent cellular infiltration and neotissue formation without calcification or aneurysm. Modulating host macrophage infiltration into the scaffold is a key to reducing excessive neotissue formation and stenosis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Metabolic rate reduction has been considered the mechanism by which sleep conserves energy, similar to torpor or hibernation. This mechanism of energy savings is in conflict with the known ...upregulation (compared to wake) of diverse functions during sleep and neglects a potential role in energy conservation for partitioning of biological operations by behavioral state. Indeed, energy savings as derived from state-dependent resource allocations have yet to be examined. A mathematical model is presented based on relative rates of energy deployment for biological processes upregulated during either wake or sleep. Using this model, energy savings from sleep-wake cycling over constant wakefulness is computed by comparing stable limit cycles for systems of differential equations. A primary objective is to compare potential energy savings derived from state-dependent metabolic partitioning versus metabolic rate reduction. Additionally, energy conservation from sleep quota and the circadian system are also quantified in relation to a continuous wake condition. As a function of metabolic partitioning, our calculations show that coupling of metabolic operations with behavioral state may provide comparatively greater energy savings than the measured decrease in metabolic rate, suggesting that actual energy savings derived from sleep may be more than 4-fold greater than previous estimates. A combination of state-dependent metabolic partitioning and modest metabolic rate reduction during sleep may enhance energy savings beyond what is achievable through metabolic partitioning alone; however, the relative contribution from metabolic partitioning diminishes as metabolic rate is decreased during the rest phase. Sleep quota and the circadian system further augment energy savings in the model. Finally, we propose that state-dependent resource allocation underpins both sleep homeostasis and the optimization of daily energy conservation across species. This new paradigm identifies an evolutionary selective advantage for the upregulation of central and peripheral biological processes during sleep, presenting a unifying construct to understand sleep function.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract Background Tissue-engineered vascular grafts (TEVGs) offer potential to overcome limitations of current approaches for reconstruction in congenital heart disease by providing biodegradable ...scaffolds on which autologous cells proliferate and provide physiologic functionality. However, current TEVGs do not address the diverse anatomic requirements of individual patients. This study explores the feasibility of creating patient-specific TEVGs by combining 3-dimensional (3D) printing and electrospinning technology. Methods An electrospinning mandrel was 3D-printed after computer-aided design based on preoperative imaging of the ovine thoracic inferior vena cava (IVC). TEVG scaffolds were then electrospun around the 3D-printed mandrel. Six patient-specific TEVGs were implanted as cell-free IVC interposition conduits in a sheep model and explanted after 6 months for histologic, biochemical, and biomechanical evaluation. Results All sheep survived without complications, and all grafts were patent without aneurysm formation or ectopic calcification. Serial angiography revealed significant decreases in TEVG pressure gradients between 3 and 6 months as the grafts remodeled. At explant, the nanofiber scaffold was nearly completely resorbed and the TEVG showed similar mechanical properties to that of native IVC. Histological analysis demonstrated an organized smooth muscle cell layer, extracellular matrix deposition, and endothelialization. No significant difference in elastin and collagen content between the TEVG and native IVC was identified. There was a significant positive correlation between wall thickness and CD68+ macrophage infiltration into the TEVG. Conclusions Creation of patient-specific nanofiber TEVGs by combining electrospinning and 3D printing is a feasible technology as future clinical option. Further preclinical studies involving more complex anatomical shapes are warranted.
Tolerance and resistance provide hosts with two distinct defense strategies against parasitism. In resistance the hosts "fight" the parasite directly, whereas in tolerance the hosts fight the disease ...by ameliorating the damage that infection causes. There is increasing recognition that the two mechanisms may exhibit very different evolutionary behaviors. Although empirical work has often noted considerable variance in tolerance within hosts, theory has predicted the fixation of tolerance due to positive frequency dependence through a feedback with disease prevalence. Here we reconcile these findings through a series of dynamic game theoretical models. We emphasize that there is a crucial distinction between tolerance to the effects of disease-induced mortality and tolerance to the effect of the disease-induced reductions in fecundity. Only mortality tolerance has a positive effect on parasite fitness, whereas sterility tolerance is neutral and may therefore result in polymorphisms. The nature of the costs to defense and their relationship to trade-offs between resistance and tolerance are crucial in determining the likelihood of variation, whereas the co-evolution of the parasite will not affect diversity. Our findings stress that it is important to measure the effects of different mechanisms on characteristics that affect the epidemiology of the parasite to completely understand the evolutionary dynamics of defense.
A number of theoretical models have been developed in recent years modelling epidemic spread in educational settings such as universities, often as part of efforts to inform re-opening strategies ...during the COVID-19 pandemic. However, these studies have had differing conclusions as to the most effective non-pharmaceutical interventions. They also largely assumed permanent acquired immunity, meaning we have less understanding of how disease dynamics will play out when immunity wanes. Here, we complement these studies by developing and analysing a general stochastic simulation model of disease spread on a university campus where we allow immunity to wane, exploring the effectiveness of different interventions. We find that the two most effective interventions to limit the severity of a disease outbreak are reducing extra-household mixing and surveillance testing backed-up by a moderate isolation period. We find that contact tracing only has a limited effect, while reducing class sizes only has much effect if extra-household mixing is already low. We identify a range of measures that can not only limit an outbreak but prevent it entirely, and also comment on the variation in measures of severity that emerge from our stochastic simulations. We hope that our model may help in designing effective strategies for universities in future disease outbreaks.
•Painful diabetic peripheral sensorimotor polyneuropathy affects at least 20% of individuals with diabetes mellitus.•In this condition good glycemic control and available treatments are not effective ...in all individuals.•Surgical decompression of lower limb nerves decreases pain in painful diabetic peripheral sensorimotor polyneuropathy.
To assess the efficacy of surgical decompression of lower extremity nerves for the treatment of painful diabetic peripheral sensorimotor polyneuropathy (DPN).
People with painful diabetic neuropathy were randomized single-blind to a lower extremity decompression surgery (n = 12) or observation (n = 10) for 1 year.
Pain was the primary outcome assessed with 2 measures. The McGill pain visual analogue scores over time changed within the groups (p for time < 0.0001), and changed differently over time within the groups (p for group × time = 0.0138). The NeuroQoL pain sensitivity analysis significantly changed from baseline to 12 months comparing intervention to control (p = 0.0079), and the joint effect of group and time on pain scores was statistically significant (p for group × time = 0.0009). At the study end-point of 12 months, intervention group participants had over 3 times the odds of rating their pain as “better” compared to “unchanged” or “worse” in the control group (p = 0.0177).
Surgical decompression of lower limb nerves was an effective treatment for decreasing pain in patients with DPN and superimposed nerve compressions.
The human red blood cell (RBC) membrane, a fluid lipid bilayer tethered to an elastic 2D spectrin network, provides the principal control of the cell's morphology and mechanics. These properties, in ...turn, influence the ability of RBCs to transport oxygen in circulation. Current mechanical measurements of RBCs rely on external loads. Here we apply a noncontact optical interferometric technique to quantify the thermal fluctuations of RBC membranes with 3 nm accuracy over a broad range of spatial and temporal frequencies. Combining this technique with a new mathematical model describing RBC membrane undulations, we measure the mechanical changes of RBCs as they undergo a transition from the normal discoid shape to the abnormal echinocyte and spherical shapes. These measurements indicate that, coincident with this morphological transition, there is a significant increase in the membrane's shear, area, and bending moduli. This mechanical transition can alter cell circulation and impede oxygen delivery.
The remarkable deformability of the human red blood cell (RBC) results from the coupled dynamic response of the phospholipid bilayer and the spectrin molecular network. Here we present quantitative ...connections between spectrin morphology and membrane fluctuations of human RBCs by using dynamic full-field laser interferometry techniques. We present conclusive evidence that the presence of adenosine 5'-triphosphate (ATP) facilitates non-equilibrium dynamic fluctuations in the RBC membrane that are highly correlated with the biconcave shape of RBCs. Spatial analysis of the fluctuations reveals that these non-equilibrium membrane vibrations are enhanced at the scale of spectrin mesh size. Our results indicate that the dynamic remodeling of the coupled membranes powered by ATP results in non-equilibrium membrane fluctuations manifesting from both metabolic and thermal energies and also maintains the biconcave shape of RBCs.
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