A novel algorithm to calculate elementary modes: Analysis of Campylobacter jejuni metabolism.

We describe a novel algorithm, 'LPEM', that given a steady-state flux vector from a (possibly genome-scale) metabolic model, decomposes that vector into a set of weighted elementary modes such that the sum of these elementary modes is equal to the original flux vector. We apply the algorithm to a genome scale metabolic model of the human pathogen Campylobacter jejuni. This organism is unusual in that it has an absolute growth requirement for oxygen, despite being able to operate the electron transport chain anaerobically.

Impedance Spectroscopy Measures of Whole and Segmental Skeletal Muscle Quantity Associated With Strength and Power in Collegiate Ice Hockey Players.

Otremba, JR, Heesch, AJ, Morgan, RM, Poolman, MA, Schindler, GD, and Fitzgerald, JS. Bioelectrical impedance spectroscopy measures of whole and segmental skeletal muscle quantity associated with strength and power in collegiate ice hockey players. J Strength Cond Res XX(X): 000-000, 2024-Bioelectrical impedance spectroscopy (BIS) is a promising monitoring tool for body water compartment assessment, particularly intracellular water (ICW), in which acute decreases are associated with increased muscle damage and reduced function, and chronic changes are associated with muscle quantity.

Effects of Photobiomodulation on Pain and Return to Play of Injured Athletes: A Systematic Review and Meta-analysis.

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.

Substrate Utilisation and Energy Metabolism in Non-Growing M1cam.

, 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 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 on 95 substrates.

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications.

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.

Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen RP62A.

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 , the mechanisms behind this increasingly recognised pathogenicity are yet to be fully understood. Improving our knowledge of the metabolic processes that allow to colonise different body sites is key to defining its pathogenic potential.

Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom .

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.

Genome-Scale Metabolic Model Driven Design of a Defined Medium for M1cam.

, 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.

Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli.

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.

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Stoichiometric analysis of the energetics and metabolic impact of photorespiration in C3 plants.

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.

The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling.

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.

Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production.

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.

A systems-wide understanding of photosynthetic acclimation in algae and higher plants.

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.

Investigating mixotrophic metabolism in the model diatom .

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.

A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate.

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.

Modelling metabolism of the diatom Phaeodactylum tricornutum.

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.

A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism.

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.

Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome-scale metabolic model of rice.

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.

Identification of metabolic pathways essential for fitness of Salmonella Typhimurium in vivo.

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.

Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation.

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.

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.

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.

Neuropsychological factors related to college ice hockey concussions.

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.

Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses.

Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability.