Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation

Viral replication relies on host metabolic machinery and precursors to produce large numbers of progeny - often very rapidly. A fundamental example is the infection of Escherichia coli by bacteriophage T7. The resource draw imposed by viral replication represents a significant and complex perturbation to the extensive and interconnected network of host metabolic pathways. To better understand this system, we have integrated a set of structured ordinary differential equations quantifying T7 replication and an E. coli flux balance analysis metabolic model. Further, we present here an integrated simulation algorithm enforcing mutual constraint by the models across the entire duration of phage replication. This method enables quantitative dynamic prediction of virion production given only specification of host nutritional environment, and predictions compare favorably to experimental measurements of phage replication in multiple environments. The level of detail of our computational predictions facilitates exploration of the dynamic changes in host metabolic fluxes that result from viral resource consumption, as well as analysis of the limiting processes dictating maximum viral progeny production. For example, although it is commonly assumed that viral infection dynamics are predominantly limited by the amount of protein synthesis machinery in the host, our results suggest that in many cases metabolic limitation is at least as strict. Taken together, these results emphasize the importance of considering viral infections in the context of host metabolism.     

The Uptake of Carnitine by Slices of Rat Cerebral Cortex

Abstract: The properties of carnitine transport were studied in rat brain slices. A rapid uptake system for carnitine was observed, with tissue-medium gradients of 38 ± 3 for L-[¹⁴CH₃]carnitine and 27 ± 3 for D-[¹⁴CH₃]carnitine after 180 min incubation at 37°C in 0.64 mM substrate. Uptake of L- and D-carnitine showed saturability. The estimated values of K _m for L- and D-carnitine were 2.85 mM and 10.0 mM, respectively; but values of V _max (1 μmol/min/ml in-tracellular fluid) were the same for the two isomers. The transport system showed stereospecificity for L-carnitine. Carnitine uptake was inhibited by structurally related compounds with a four-carbon backbone containing a terminal carboxyl group. L-Carnitine uptake was competitively inhibited by γ-butyrobetaine ( K _i= 3.22 mM), acetylcarnitine ( K _i= 6.36 mM), and γ-aminobutyric acid ( K _i= 0.63 mM). The data suggest that carnitine and γ-aminobutyric acid interact at a common carrier site. Transport was not significantly reduced by choline or lysine. Carnitine uptake was inhibited by an N₂ atmosphere, 2,4-dinitrophenol, carbonylcyanide- N -chlorophenylhydrazone, potassium cyanide, n-ethylmaleimide, and ouabain. Transport was abolished by low temperature (4°C) and absence of glucose from the medium. Carnitine uptake was Na⁺-dependent, but did not require K⁺ or Ca²⁺.     

The perspective of GABA replenishment therapy in the epilepsies: A critical evaluation of hopes and concerns

Impaired GABA-mediated inhibition is probably one of the cellular abnormalities leading to Focal Epilepsy. The role of GABA in generalized seizures, particularly of Petit Mal type, is unknown. Various approaches are available to potentiate GABA function. Merits and flaws of each one of them are critically evaluated. In some forms of epilepsy, GABA agonists may replenish depleted pools, and in some others may nonspecifically raise the general excitability threshold of the brain, yet in other forms they may exert a glutamate/aspartate antagonistic effect. The available experimental evidence suggests that in bilaterally synchronous spike and wave epilepsies, GABA agonists are either ineffective or pejorative.     

Evolution of Sirenian Pachyosteosclerosis,a Model-case for the Study of Bone Structure in Aquatic Tetrapods

Osteosclerosis, or inner bone compaction, and pachyostosis, or outer hyperplasy of bone cortices (swollen bones), are typical features of tetrapods secondarily adapted to life in water. These peculiarities are spectacularly exemplified by the ribs of extant and extinct Sirenia. Sea cows are thus the best model for studying this kind of bone structural specializations. In order to document how these features differentiated during sirenian evolution, the ribs of 15 species, from the most basal form (Pezosiren portelli) up to extant taxa, were studied, and compared to those of other mammalian species from both morphometric and histological points of view. Pachyostosis was the first of these two specializations to occur, by the middle of the Eocene, and is a basal feature of the Sirenia. However, it subsequently regressed in some taxa that do not exhibit hyperplasic rib cortices. Osteosclerosis was only incipient in P. portelli. Its full development occurred later, by the end of the Eocene. These two structural specializations of bone are variably pronounced in extinct and extant sirenians, and relatively independent from each other, although frequently associated. They are possibly due to similar heterochronic mechanisms bearing on the timing of osteoblast activity. These results are discussed with respect to the functional constraints of locomotion in water.     

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.     

Systemic acetyl-L-carnitine elevates nigral levels of glutathione and GABA

Amino acid and reduced glutathione (GSH) levels in substantia nigra (SN) as well as striatal monoamine levels were measured in acetyl-L-carnitine (ALCar) treated and control Swiss-Webster mice. ALCar, L carnitine, or saline were administered i.p. to mice for 5 days and mice were decapitated 24 hours following the last injection. Substantia nigra and striata were isolated within 2.5 and 3 min., respectively, and frozen immediately on dry ice. A significant dose-dependent increase of nigral GABA was observed following ALCar treatment; GABA levels were also increased by administration of carnitine. Nigral GSH levels were also increased. Striatal levels of dopamine and metabolites were not significantly affected by ALCar or carnitine. These results, suggest that ALCar may be useful in treating symptoms of neuronal dysfunction related to accumulation of metabolic waste.     

Effect of ill-fitting dentures on the swallowing duration in patients using polygraphy

doi: 10.1111/j.1741‐2358.2011.00536.x Effect of ill‐fitting dentures on the swallowing duration in patients using polygraphy Background: Surface electromyography (SEMG) has been widely used in the recent years to study swallowing physiology, offering a valid and reliable tool for identifying normal swallowing. The goal of our study was to assess the contribution of denture fitness in the age‐related increase of swallowing duration. Methods: Twenty denture wearers and 20 dentate individuals were analysed using SEMG and a computerised kinesiography of mandibular movement. Three spontaneous saliva swallowings were recorded for each patient with both their old and new prostheses. Three spontaneous saliva swallowings were recorded for each dentate person in two different recording sessions. Results: Old prosthesis mean swallowing time was 1.84 (SD ± 0.85) seconds while the new well‐fitting prostheses needed a 1.28 (SD ± 0.55) (p = 0.0009) swallowing time. The difference in swallowing time was significant (p = 0.01) between dentate subjects and individuals wearing an old prosthesis. No significant difference was found between dentate subjects and the same prosthesis wearers when a new well‐fitting prosthesis was worn. Conclusion: Data presented in this work suggest that part of the increased duration of swallowing showed by elderly and healthy people is because of incorrect an dental prosthesis. Prolongation of swallowing duration in the elderly population could be reconsidered in the light of the quality of dental device worn by the aged population.