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1.
J Strength Cond Res ; 38(6): e310-e319, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38781474

ABSTRACT

ABSTRACT: Morgan, RM, Wheeler, TD, Poolman, MA, Haugen, ENJ, LeMire, SD, and Fitzgerald, JS. Effects of photobiomodulation on pain and return to play of injured athletes: A systematic review and meta-analysis. J Strength Cond Res 38(6): e310-e319, 2024-The aims of this systematic review and meta-analysis were to evaluate the effect of photobiomodulation (PBM) on musculoskeletal pain in injured athletes and to determine if the effects of PBM allowed injured athletes to return to play faster. Electronic databases (MEDLINE Complete, CINAHL, and SPORTDiscus, PubMed, Web of Science, and Embase) were systematically searched (up to and including November 7, 2023) for peer-reviewed randomized controlled trials (RCTs) meeting criteria. Six RCTs, representing 205 competitive and recreational athletes with a mean age of 24 years, were included in the analysis. There were 6 intervention groups using standard physical therapy (n = 1), placebo PBM (n = 4), and aloe gel (n = 1) lasting between 10 minutes and 8 weeks in duration. The level of significance set for the study was p < 0.05. Overall, the use of PBM indicated a positive effect on pain reduction for PBM vs. control groups, standardized mean differences = 1.03, SE = 0.22, 95% confidence intervals = [0.43-1.63], p = 0.0089, but the 2 RCTs found evaluating the effect of PBM on time to return to play after injury in athletes do not support a benefit. Allied healthcare professionals may use PBM to reduce pain, thus allowing an athlete to return to their normal biomechanical movement faster; however, limited evidence suggests that PBM does not reduce time to return to play after an injury.


Subject(s)
Athletic Injuries , Low-Level Light Therapy , Musculoskeletal Pain , Return to Sport , Humans , Athletic Injuries/radiotherapy , Athletic Injuries/physiopathology , Athletic Injuries/rehabilitation , Low-Level Light Therapy/methods , Musculoskeletal Pain/radiotherapy , Athletes , Randomized Controlled Trials as Topic
2.
Microorganisms ; 10(7)2022 Jul 05.
Article in English | MEDLINE | ID: mdl-35889074

ABSTRACT

Campylobacter jejuni, the major cause of bacterial foodborne illness, is also a fastidious organism that requires strict growth requirements in the laboratory. Our aim was to study substrate utilisation and energy metabolism in non-growing C. jejuni to investigate the ability of these bacteria to survive so effectively in the food chain. We integrated phenotypic microarrays and genome-scale metabolic modelling (GSM) to investigate the survival of C. jejuni on 95 substrates. We further investigated the underlying metabolic re-adjustment associated with varying energy demands on each substrate. We identified amino acids, organic acids and H2, as single substrates supporting survival without growth. We identified several different mechanisms, which were used alone or in combination, for ATP production: substrate-level phosphorylation via acetate kinase, the TCA cycle, and oxidative phosphorylation via the electron transport chain that utilised alternative electron donors and acceptors. The benefit of ATP production through each of these mechanisms was associated with the cost of enzyme investment, nutrient availability and/or O2 utilisation. C. jejuni can utilise a wide range of substrates as energy sources, including organic acids commonly used for marination or preservation of ingredients, which might contribute to the success of their survival in changing environments.

3.
PLoS Comput Biol ; 18(5): e1010106, 2022 05.
Article in English | MEDLINE | ID: mdl-35604933

ABSTRACT

Exploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including the waste gas carbon dioxide, whilst also naturally producing large quantities of polyhydroxybutyrate (PHB) during nutrient-limited conditions. Understanding the complex metabolic behaviour of this bacterium is a prerequisite for the design of successful engineering strategies for optimising product yields. We present a genome-scale metabolic model (GSM) of C. necator H16 (denoted iCN1361), which is directly constructed from the BioCyc database to improve the readability and reusability of the model. After the initial automated construction, we have performed extensive curation and both theoretical and experimental validation. By carrying out a genome-wide essentiality screening using a Transposon-directed Insertion site Sequencing (TraDIS) approach, we showed that the model could predict gene knockout phenotypes with a high level of accuracy. Importantly, we indicate how experimental and computational predictions can be used to improve model structure and, thus, model accuracy as well as to evaluate potential false positives identified in the experiments. Finally, by integrating transcriptomics data with iCN1361 we create a condition-specific model, which, importantly, better reflects PHB production in C. necator H16. Observed changes in the omics data and in-silico-estimated alterations in fluxes were then used to predict the regulatory control of key cellular processes. The results presented demonstrate that iCN1361 is a valuable tool for unravelling the system-level metabolic behaviour of C. necator H16 and can provide useful insights for designing metabolic engineering strategies.


Subject(s)
Cupriavidus necator , Biotechnology , Carbon Dioxide/metabolism , Cupriavidus necator/genetics , Cupriavidus necator/metabolism , Metabolic Engineering , Transcriptome
4.
Metabolites ; 12(2)2022 Feb 02.
Article in English | MEDLINE | ID: mdl-35208211

ABSTRACT

Staphylococcus epidermidis is a common commensal of collagen-rich regions of the body, such as the skin, but also represents a threat to patients with medical implants (joints and heart), and to preterm babies. Far less studied than Staphylococcus aureus, the mechanisms behind this increasingly recognised pathogenicity are yet to be fully understood. Improving our knowledge of the metabolic processes that allow S. epidermidis to colonise different body sites is key to defining its pathogenic potential. Thus, we have constructed a fully curated, genome-scale metabolic model for S. epidermidis RP62A, and investigated its metabolic properties with a focus on substrate auxotrophies and its utilisation for energy and biomass production. Our results show that, although glucose is available in the medium, only a small portion of it enters the glycolytic pathways, whils most is utilised for the production of biofilm, storage and the structural components of biomass. Amino acids, proline, valine, alanine, glutamate and arginine, are preferred sources of energy and biomass production. In contrast to previous studies, we have shown that this strain has no real substrate auxotrophies, although removal of proline from the media has the highest impact on the model and the experimental growth characteristics. Further study is needed to determine the significance of proline, an abundant amino acid in collagen, in S. epidermidis colonisation.

5.
Front Plant Sci ; 12: 642199, 2021.
Article in English | MEDLINE | ID: mdl-33897733

ABSTRACT

Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower cell density. Thus, alternative ways need to be explored to enhance the lipid production as well as biomass density to make them sustainable at industrial scale. In this study, we have used experimental and metabolic modeling approaches to optimize the media composition, in terms of elemental composition, organic and inorganic carbon sources, and light intensity, that boost both biomass quality and quantity of P. tricornutum. Eventually, the optimized conditions were scaled-up to 2 L photobioreactors, where a better system control (temperature, pH, light, aeration/mixing) allowed a further improvement of the biomass capacity of P. tricornutum to 12 g/L.

6.
Front Microbiol ; 11: 1072, 2020.
Article in English | MEDLINE | ID: mdl-32636809

ABSTRACT

Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis, is a fastidious organism when grown in the laboratory. Oxygen is required for growth, despite the presence of the metabolic mechanism for anaerobic respiration. Amino acid auxotrophies are variably reported and energy metabolism can occur through several electron donor/acceptor combinations. Overall, the picture is one of a flexible, but vulnerable metabolism. To understand Campylobacter metabolism, we have constructed a fully curated, metabolic model for the reference organism M1 (our variant is M1cam) and validated it through laboratory experiments. Our results show that M1cam is auxotrophic for methionine, niacinamide, and pantothenate. There are complete biosynthesis pathways for all amino acids except methionine and it can produce energy, but not biomass, in the absence of oxygen. M1cam will grow in DMEM/F-12 defined media but not in the previously published Campylobacter specific defined media tested. Using the model, we identified potential auxotrophies and substrates that may improve growth. With this information, we designed simple defined media containing inorganic salts, the auxotrophic substrates, L-methionine, niacinamide, and pantothenate, pyruvate and additional amino acids L-cysteine, L-serine, and L-glutamine for growth enhancement. Our defined media supports a 1.75-fold higher growth rate than Brucella broth after 48 h at 37°C and sustains the growth of other Campylobacter jejuni strains. This media can be used to design reproducible assays that can help in better understanding the adaptation, stress resistance, and the virulence mechanisms of this pathogen. We have shown that with a well-curated metabolic model it is possible to design a media to grow this fastidious organism. This has implications for the investigation of new Campylobacter species defined through metagenomics, such as C. infans.

7.
Sci Rep ; 10(1): 8438, 2020 05 21.
Article in English | MEDLINE | ID: mdl-32439837

ABSTRACT

We characterized the global transcriptome of Escherichia coli MG1655:: tetA grown in the presence of ½ MIC (14 mg/L) of OTC, and for comparison WT MG1655 strain grown with 1//2 MIC of OTC (0.25 mg/L OTC). 1646 genes changed expression significantly (FDR > 0.05) in the resistant strain, the majority of which (1246) were also regulated in WT strain. Genes involved in purine synthesis and ribosome structure and function were top-enriched among up-regulated genes, and anaerobic respiration, nitrate metabolism and aromatic amino acid biosynthesis genes among down-regulated genes. Blocking of the purine-synthesis- did not affect resistance phenotypes (MIC and growth rate with OTC), while blocking of protein synthesis using low concentrations of chloramphenicol or gentamicin, lowered MIC towards OTC. Metabolic-modeling, using a novel model for MG1655 and continuous weighing factor that reflected the degree of up or down regulation of genes encoding a reaction, identified 102 metabolic reactions with significant change in flux in MG1655:: tetA when grown in the presence of OTC compared to growth without OTC. These pathways could not have been predicted by simply analyzing functions of the up and down regulated genes, and thus this work has provided a novel method for identification of reactions which are essential in the adaptation to growth in the presence of antimicrobials.


Subject(s)
Anti-Bacterial Agents/pharmacology , Escherichia coli Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Metabolome/drug effects , Oxytetracycline/pharmacology , Tetracycline Resistance/genetics , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Proteins/genetics , Gene Expression Profiling , Gene Expression Regulation, Bacterial
8.
Plant J ; 96(6): 1228-1241, 2018 12.
Article in English | MEDLINE | ID: mdl-30257035

ABSTRACT

Analysis of the impact of photorespiration on plant metabolism is usually based on manual inspection of small network diagrams. Here we create a structural metabolic model that contains the reactions that participate in photorespiration in the plastid, peroxisome, mitochondrion and cytosol, and the metabolite exchanges between them. This model was subjected to elementary flux modes analysis, a technique that enumerates all the component, minimal pathways of a network. Any feasible photorespiratory metabolism in the plant will be some combination of the elementary flux modes (EFMs) that contain the Rubisco oxygenase reaction. Amongst the EFMs we obtained was the classic photorespiratory cycle, but there were also modes that involve photorespiration coupled with mitochondrial metabolism and ATP production, the glutathione-ascorbate cycle and nitrate reduction to ammonia. The modes analysis demonstrated the underlying basis of the metabolic linkages with photorespiration that have been inferred experimentally. The set of reactions common to all the elementary modes showed good agreement with the gene products of mutants that have been reported to have a defective phenotype in photorespiratory conditions. Finally, the set of modes provided a formal demonstration that photorespiration itself does not impact on the CO2 :O2 ratio (assimilation quotient), except in those modes associated with concomitant nitrate reduction.


Subject(s)
Energy Metabolism , Photosynthesis , Plants/metabolism , Adenosine Triphosphate/metabolism , Chloroplasts/metabolism , Glycolates/metabolism , Metabolic Networks and Pathways , Mitochondria/metabolism , Peroxisomes/metabolism
9.
Sci Rep ; 8(1): 12504, 2018 08 21.
Article in English | MEDLINE | ID: mdl-30131500

ABSTRACT

Genome-scale metabolic network models can be used for various analyses including the prediction of metabolic responses to changes in the environment. Legumes are well known for their rhizobial symbiosis that introduces nitrogen into the global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model of the clover Medicago truncatula, which has been adopted as a model organism for legumes. We employed flux balance analysis to demonstrate that the network is capable of producing biomass components in experimentally observed proportions, during day and night. By connecting the plant model to a model of its rhizobial symbiont, Sinorhizobium meliloti, we were able to investigate the effects of the symbiosis on metabolic fluxes and plant growth and could demonstrate how oxygen availability influences metabolic exchanges between plant and symbiont, thus elucidating potential benefits of inter organism amino acid cycling. We thus provide a modelling framework, in which the interlinked metabolism of plants and nodules can be studied from a theoretical perspective.


Subject(s)
Medicago truncatula/growth & development , Metabolic Networks and Pathways , Nitrogen Fixation , Sinorhizobium meliloti/physiology , Biomass , Medicago truncatula/genetics , Medicago truncatula/microbiology , Models, Genetic , Molecular Sequence Annotation , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Roots/genetics , Plant Roots/growth & development , Plant Roots/microbiology , Symbiosis
10.
Metab Eng ; 46: 1-12, 2018 03.
Article in English | MEDLINE | ID: mdl-29408291

ABSTRACT

Biologically-derived hydrocarbons are considered to have great potential as next-generation biofuels owing to the similarity of their chemical properties to contemporary diesel and jet fuels. However, the low yield of these hydrocarbons in biotechnological production is a major obstacle for commercialization. Several genetic and process engineering approaches have been adopted to increase the yield of hydrocarbon, but a model driven approach has not been implemented so far. Here, we applied a constraint-based metabolic modeling approach in which a variable demand for alkane biosynthesis was imposed, and co-varying reactions were considered as potential targets for further engineering of an E. coli strain already expressing cyanobacterial enzymes towards higher chain alkane production. The reactions that co-varied with the imposed alkane production were found to be mainly associated with the pentose phosphate pathway (PPP) and the lower half of glycolysis. An optimal modeling solution was achieved by imposing increased flux through the reaction catalyzed by glucose-6-phosphate dehydrogenase (zwf) and iteratively removing 7 reactions from the network, leading to an alkane yield of 94.2% of the theoretical maximum conversion determined by in silico analysis at a given biomass rate. To validate the in silico findings, we first performed pathway optimization of the cyanobacterial enzymes in E. coli via different dosages of genes, promoting substrate channelling through protein fusion and inducing substantial equivalent protein expression, which led to a 36-fold increase in alka(e)ne production from 2.8 mg/L to 102 mg/L. Further, engineering of E. coli based on in silico findings, including biomass constraint, led to an increase in the alka(e)ne titer to 425 mg/L (major components being 249 mg/L pentadecane and 160 mg/L heptadecene), a 148.6-fold improvement over the initial strain, respectively; with a yield of 34.2% of the theoretical maximum. The impact of model-assisted engineering was also tested for the production of long chain fatty alcohol, another commercially important molecule sharing the same pathway while differing only at the terminal reaction, and a titer of 1506 mg/L was achieved with a yield of 86.4% of the theoretical maximum. Moreover, the model assisted engineered strains had produced 2.54 g/L and 12.5 g/L of long chain alkane and fatty alcohol, respectively, in the bioreactor under fed-batch cultivation condition. Our study demonstrated successful implementation of a combined in silico modeling approach along with the pathway and process optimization in achieving the highest reported titers of long chain hydrocarbons in E. coli.


Subject(s)
Alkanes/metabolism , Escherichia coli , Fatty Alcohols/metabolism , Metabolic Engineering/methods , Models, Biological , Escherichia coli/genetics , Escherichia coli/metabolism , Glycolysis/genetics , Pentose Phosphate Pathway/genetics
11.
J Exp Bot ; 68(11): 2667-2681, 2017 05 17.
Article in English | MEDLINE | ID: mdl-28830099

ABSTRACT

The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drastically different timescales from picoseconds to hours. Efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes, including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project, AccliPhot, placing the results in a wider context. The review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It intends to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.


Subject(s)
Acclimatization , Photosynthesis/physiology , Plants , Chlorophyta , Models, Biological , Systems Biology
12.
Philos Trans R Soc Lond B Biol Sci ; 372(1728)2017 Sep 05.
Article in English | MEDLINE | ID: mdl-28717014

ABSTRACT

Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use in biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the sole energy source. Some diatoms, however, can also grow in a mixotrophic mode, wherein both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as the source of reduced carbon. Transcriptomics, metabolomics, metabolic modelling and physiological data combine to indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, provision of glycerol mimics typical responses of nitrogen limitation on lipid metabolism at the level of triacylglycerol accumulation and fatty acid composition. The presence of glycerol, despite provoking features reminiscent of nutrient limitation, neither diminishes photosynthetic activity nor cell growth, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.


Subject(s)
Carbon/metabolism , Diatoms/growth & development , Diatoms/metabolism , Light , Biomass , Glycerol/metabolism
13.
J Biotechnol ; 251: 30-37, 2017 Jun 10.
Article in English | MEDLINE | ID: mdl-28385593

ABSTRACT

Rice straw is a major crop residue which is burnt in many countries, creating significant air pollution. Thus, alternative routes for disposal of rice straw are needed. Biotechnological treatment of rice straw hydrolysate has potential to convert this agriculture waste into valuable biofuel(s) and platform chemicals. Geobacillus thermoglucosidasius is a thermophile with properties specially suited for use as a biocatalyst in lignocellulosic bioprocesses, such as high optimal temperature and tolerance to high levels of ethanol. However, the capabilities of G. thermoglucosidasius to utilise sugars in rice straw hydrolysate for making bioethanol and other platform chemicals have not been fully explored. In this work, we have created a genome scale metabolic model (denoted iGT736) of the organism containing 736 gene products, 1159 reactions and 1163 metabolites. The model was validated both by purely theoretical approaches and by comparing the behaviour of the model to previously published experimental results. The model was then used to determine the yields of a variety of platform chemicals from glucose and xylose - two primary sugars in rice straw hydrolysate. A comparison with results from a model of Escherichia coli shows that G. thermoglucosidasius is capable of producing a wider range of products, and that for the products also produced by E. coli, the yields are comparable. We also discuss strategies to utilise arabinose, a minor component of rice straw hydrolysate, and propose additional reactions to lead to the synthesis of xylitol, not currently produced by G. thermoglucosidasius. Our results provide additional motivation for the current exploration of the industrial potential of G. thermoglucosidasius and we make our model publicly available to aid the development of metabolic engineering strategies for this organism.


Subject(s)
Geobacillus/metabolism , Models, Biological , Genome, Bacterial , Geobacillus/genetics , Glucose/metabolism , Lignin/metabolism , Metabolic Engineering , Oryza , Waste Products , Xylose/metabolism
14.
Plant J ; 85(2): 289-304, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26576489

ABSTRACT

Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.


Subject(s)
Droughts , Photosynthesis/genetics , Solanum lycopersicum/metabolism , Gene Expression Regulation, Plant/physiology , Solanum lycopersicum/physiology , Metabolic Networks and Pathways/genetics , Metabolic Networks and Pathways/physiology , Plant Leaves/metabolism , Plant Leaves/physiology
15.
Biochem Soc Trans ; 43(6): 1182-6, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26614658

ABSTRACT

Marine diatoms have potential as a biotechnological production platform, especially for lipid-derived products, including biofuels. Here we introduce some features of diatom metabolism, particularly with respect to photosynthesis, photorespiration and lipid synthesis and their differences relative to other photosynthetic eukaryotes. Since structural metabolic modelling of other photosynthetic organisms has been shown to be capable of representing their metabolic capabilities realistically, we briefly review the main approaches to this type of modelling. We then propose that genome-scale modelling of the diatom Phaeodactylum tricornutum, in response to varying light intensity, could uncover the novel aspects of the metabolic potential of this organism.


Subject(s)
Diatoms/metabolism , Lipid Metabolism/physiology , Oxygen Consumption/physiology , Photosynthesis/physiology , Algorithms , Computer Simulation , Diatoms/genetics , Glycolysis/genetics , Glycolysis/physiology , Lipid Metabolism/genetics , Metabolic Networks and Pathways/genetics , Metabolic Networks and Pathways/physiology , Models, Biological , Oxygen Consumption/genetics , Photosynthesis/genetics
16.
Front Plant Sci ; 5: 656, 2014.
Article in English | MEDLINE | ID: mdl-25506349

ABSTRACT

Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequately represented, in the model, the scenario was not that of the typical function of the leaf-to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.

17.
PLoS One ; 9(7): e101869, 2014.
Article in English | MEDLINE | ID: mdl-24992475

ABSTRACT

Bacterial infections remain a threat to human and animal health worldwide, and there is an urgent need to find novel targets for intervention. In the current study we used a computer model of the metabolic network of Salmonella enterica serovar Typhimurium and identified pairs of reactions (cut sets) predicted to be required for growth in vivo. We termed such cut sets synthetic auxotrophic pairs. We tested whether these would reveal possible combined targets for new antibiotics by analyzing the performance of selected single and double mutants in systemic mouse infections. One hundred and two cut sets were identified. Sixty-three of these included only pathways encoded by fully annotated genes, and from this sub-set we selected five cut sets involved in amino acid or polyamine biosynthesis. One cut set (asnA/asnB) demonstrated redundancy in vitro and in vivo and showed that asparagine is essential for S. Typhimurium during infection. trpB/trpA as well as single mutants were attenuated for growth in vitro, while only the double mutant was a cut set in vivo, underlining previous observations that tryptophan is essential for successful outcome of infection. speB/speF,speC was not affected in vitro but was attenuated during infection showing that polyamines are essential for virulence apparently in a growth independent manner. The serA/glyA cut-set was found to be growth attenuated as predicted by the model. However, not only the double mutant, but also the glyA mutant, were found to be attenuated for virulence. This adds glycine production or conversion of glycine to THF to the list of essential reactions during infection. One pair (thrC/kbl) showed true redundancy in vitro but not in vivo demonstrating that threonine is available to the bacterium during infection. These data add to the existing knowledge of available nutrients in the intra-host environment, and have identified possible new targets for antibiotics.


Subject(s)
Bacterial Proteins/genetics , Metabolic Networks and Pathways , Salmonella typhimurium/growth & development , Salmonella typhimurium/pathogenicity , Virulence Factors/genetics , Animals , Asparagine/metabolism , Bacterial Proteins/metabolism , Computer Simulation , Female , Genetic Fitness , Humans , Mice , Mice, Inbred C57BL , Salmonella Infections, Animal/microbiology , Salmonella typhimurium/genetics , Salmonella typhimurium/metabolism , Tryptophan/metabolism , Virulence Factors/metabolism
18.
Microbiology (Reading) ; 160(Pt 6): 1252-1266, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24777662

ABSTRACT

Salmonella enterica sv. Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of S. Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in the energy demand while growing in glucose minimal medium. By grouping reactions with similar flux responses, a subnetwork of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions that when removed from the genome-scale model interfered with energy and biomass generation. Eleven such sets were found to be essential for the production of biomass precursors. Experimental investigation of seven of these showed that knockouts of the associated genes resulted in attenuated growth for four pairs of reactions, whilst three single reactions were shown to be essential for growth.


Subject(s)
Metabolic Networks and Pathways/genetics , Salmonella typhimurium/genetics , Anti-Bacterial Agents/pharmacology , Biomass , Computer Simulation , Culture Media/chemistry , Gene Knockout Techniques , Genomics , Glucose/metabolism , Salmonella typhimurium/drug effects , Salmonella typhimurium/growth & development
19.
Plant Physiol ; 165(2): 917-929, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24596328

ABSTRACT

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis.

20.
Am J Alzheimers Dis Other Demen ; 29(3): 201-4, 2014 May.
Article in English | MEDLINE | ID: mdl-24370620

ABSTRACT

We analyzed data from 74 male collegiate hockey players. Each athlete's season began with a baseline administration of the Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) neuropsychology test battery. Fourteen athletes sustained a sport-related head injury and were readministered the test to assess the impact of the injury. A significant decrease in performance (compared to baseline) on immediate and delayed word recall and designs followed the first concussion. Following a second sport-related concussion, the 4 affected athletes showed significant decrease in visual motor speed. Performance improved on 2 response speed measures (Ps < .01). More errors occurred during a visual processing/discrimination task and immediate recall of designs declined (Ps < .05). We discuss the results in light of recent work related to the impact of early-life concussions and head injury on late-life consequences, such as chronic traumatic encephalopathy, and more immediate issues such as return-to-play decisions for athletes.


Subject(s)
Athletic Injuries/complications , Brain Concussion/complications , Cognition Disorders/diagnosis , Hockey , Psychomotor Performance/physiology , Adult , Cognition Disorders/etiology , Humans , Male , Neuropsychological Tests , Universities , Young Adult
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