Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection

ABSTRACT: Background: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming. Nonetheless, few in silico assessments of the effect of nutritional conditions on Mtb’s vulnerability and metabolic adaptation have been carried out. Results: A genome-scale model (GEM) of Mtb, modified from the H37Rv iOSDD890, was used to explore the metabolic reprogramming of two Mtb knockout mutants (pfkA- and icl-mutants), lacking key enzymes of central carbon metabolism, while exposed to changing nutritional conditions (oxygen, and carbon and nitrogen sources). A combination of shadow pricing, sensitivity analysis, and flux distributions patterns allowed us to identify metabolic behaviors that are in agreement with phenotypes reported in the literature. During hypoxia, at high glucose consumption, the Mtb pfkA-mutant showed a detrimental growth effect derived from the accumulation of toxic sugar phosphate intermediates (glucose-6-phosphate and fructose-6-phosphate) along with an increment of carbon fluxes towards the reductive direction of the tricarboxylic acid cycle (TCA). Furthermore, metabolic reprogramming of the icl-mutant (icl1&icl2) showed the importance of the methylmalonyl pathway for the detoxification of propionyl-CoA, during growth at high fatty acid consumption rates and aerobic conditions. At elevated levels of fatty acid uptake and hypoxia, we found a drop in TCA cycle intermediate accumulation that might create redox imbalance. Finally, findings regarding Mtb-mutant metabolic adaptation associated with asparagine consumption and acetate, succinate and alanine production, were in agreement with literature reports. Conclusions: This study demonstrates the potential application of genome-scale modeling, flux balance analysis (FBA), phenotypic phase plane (PhPP) analysis and shadow pricing to generate valuable insights about Mtb metabolic reprogramming in the context of human granulomas

Recent progress in understanding and projecting regional and global mean sea-level change

Considerable progress has been made in understanding the present and future regional and global sea level in the 2 years since the publication of the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. Here, we evaluate how the new results affect the AR5’s assessment of (i) historical sea level rise, including attribution of that rise and implications for the sea level budget, (ii) projections of the components and of total global mean sea level (GMSL), and (iii) projections of regional variability and emergence of the anthropogenic signal. In each of these cases, new work largely provides additional evidence in support of the AR5 assessment, providing greater confidence in those findings. Recent analyses confirm the twentieth century sea level rise, with some analyses showing a slightly smaller rate before 1990 and some a slightly larger value than reported in the AR5. There is now more evidence of an acceleration in the rate of rise. Ongoing ocean heat uptake and associated thermal expansion have continued since 2000, and are consistent with ocean thermal expansion reported in the AR5. A significant amount of heat is being stored deeper in the water column, with a larger rate of heat uptake since 2000 compared to the previous decades and with the largest storage in the Southern Ocean. The first formal detection studies for ocean thermal expansion and glacier mass loss since the AR5 have confirmed the AR5 finding of a significant anthropogenic contribution to sea level rise over the last 50 years. New projections of glacier loss from two regions suggest smaller contributions to GMSL rise from these regions than in studies assessed by the AR5; additional regional studies are required to further assess whether there are broader implications of these results. Mass loss from the Greenland Ice Sheet, primarily as a result of increased surface melting, and from the Antarctic Ice Sheet, primarily as a result of increased ice discharge, has accelerated. The largest estimates of acceleration in mass loss from the two ice sheets for 2003–2013 equal or exceed the acceleration of GMSL rise calculated from the satellite altimeter sea level record over the longer period of 1993–2014. However, when increased mass gain in land water storage and parts of East Antarctica, and decreased mass loss from glaciers in Alaska and some other regions are taken into account, the net acceleration in the ocean mass gain is consistent with the satellite altimeter record. New studies suggest that a marine ice sheet instability (MISI) may have been initiated in parts of the West Antarctic Ice Sheet (WAIS), but that it will affect only a limited number of ice streams in the twenty-first century. New projections of mass loss from the Greenland and Antarctic Ice Sheets by 2100, including a contribution from parts of WAIS undergoing unstable retreat, suggest a contribution that falls largely within the likely range (i.e., two thirds probability) of the AR5. These new results increase confidence in the AR5 likely range, indicating that there is a greater probability that sea level rise by 2100 will lie in this range with a corresponding decrease in the likelihood of an additional contribution of several tens of centimeters above the likely range. In view of the comparatively limited state of knowledge and understanding of rapid ice sheet dynamics, we continue to think that it is not yet possible to make reliable quantitative estimates of future GMSL rise outside the likely range. Projections of twenty-first century GMSL rise published since the AR5 depend on results from expert elicitation, but we have low confidence in conclusions based on these approaches. New work on regional projections and emergence of the anthropogenic signal suggests that the two commonly predicted features of future regional sea level change (the increasing tilt across the Antarctic Circumpolar Current and the dipole in the North Atlantic) are related to regional changes in wind stress and surface heat flux. Moreover, it is expected that sea level change in response to anthropogenic forcing, particularly in regions of relatively low unforced variability such as the low-latitude Atlantic, will be detectable over most of the ocean by 2040. The east-west contrast of sea level trends in the Pacific observed since the early 1990s cannot be satisfactorily accounted for by climate models, nor yet definitively attributed either to unforced variability or forced climate change

Gut microbiota functions: metabolism of nutrients and other food components

The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays

The fabrication of a high performance enzymatic hybrid membrane reactor (EHMR) containing immobilized Candida rugosa lipase (CRL) onto graphene oxide nanosheets-blended polyethersulfone membrane

© 2020 Elsevier B.V. Recently, membrane-immobilized enzyme as an affordable bioreactor has been explored in various fields such as biodiesel production and biosensing because of the reusability of the biocatalyst, increasing its stability and being a low-cost separating unit for producing pure products. Usually, membrane modification could affect the surface morphology and hydrophilicity to make them appropriate for enzyme immobilization. In this context, the modified nanocomposite membranes of polyethersulfone (PES) with various percentages (x: 0.00, 0.25, 0.50, 1.00, 2.00, 3.00) of the graphene oxide nanosheets (GON) named (PGx) are synthesized through the phase inversion technique. The enzymatic hybrid membrane reactors (EHMRs) are provided through the Candida rugosa lipase (CRL) immobilization on the synthesized hybrid membranes. The structure and surface functionalities of the synthesized GON and hybrid membrane are characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and attenuated total reflection (ATR), respectively. The effect of the GON incorporation and CRL immobilization on the morphology of the membrane are explored through field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), contact angle goniometry, and surface free energy analysis. After measuring the porosity of the hybrid membranes with different amounts of GON, their performance, before and after CRL immobilization, are studied through pure water flux. The effective parameters on the activity and performance of EHMR such as GON percentages, CRL initial concentration, immobilization time, and storage condition are accurately optimized. The examination of the relative activity, reusability, and product permeability display that EHMR with 1.00% of GON (EHMR1) is the most efficient between EHMRs with different percentages of GON. Moreover, EHMR1 exhibits the enhancement in pH and thermal stability compared with free CRL and even the immobilized CRL on GON. While the storage stability of the wet- EHMR1 is higher than that of the dry-EHMR1, the stored wet- EHMR1 at 4 °C is more stable than room temperature. Because of these advantages, it is recommended that this bioactive membrane could be a passable candidate for application in the environmental, analytical, and industrial processes

Enzymatic biodiesel production from crude Eruca sativa oil using Candida rugosa lipase in a solvent-free system using response surface methodology

© 2017, © 2017 Informa UK Limited, trading as Taylor & Francis Group. In the present study, enzymatic biodiesel production from low-cost, non-edible crude Eruca sativa oil was investigated. Candida rugosa lipase (CRL), a commercially promising biocatalyst in different industries, was used. Although this source of lipase has been reported as unsuitable for biodiesel production from non-edible oil, in this study, it was attempted to use this enzyme for production of fatty acid methyl esters (FAME) from Eruca sativa oil in a solvent-free system. For the first time, the effects of pre-hydrolysis and pH on the yield of biodiesel were evaluated. Afterward, the four most commonly reported influential parameters were analyzed with the use of response surface methodology (RSM). It was observed that pre-hydrolysis had a significant effect on biodiesel conversion due to the mechanism of enzymatic biodiesel production. Deionized water was more efficient in comparison with phosphate buffer with different pH values. According to the RSM analysis, water content and temperature have a highly significant effect on biodiesel production. Methanol-to-oil ratio and enzyme amounts were also significant factors in FAME production. The optimum methanol-to-oil ratio, enzyme amount, water content, and temperature for achieving high conversion was found to be 3:1, 5 mg, 40%, and 21 °C, respectively

Spectroscopic study on the interaction of ct-DNA with manganese Salen complex containing triphenyl phosphonium groups

The DNA binding properties of a bulky and hydrophobic Schiff base complex of manganese(III) [N,N'-bis(5-(triphenyl phosphonium methyl)salicylidene)-1,2-ethylene diamine chloride Mn(III) acetate] was examined by spectroscopic techniques. UV-vis titration data indicate both hypo and hyperchromic effect with addition of DNA to complex. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding Mn Salen complex. This finding indicates that Mn Salen complex displaces EB from its binding site in DNA. Helix melting studies indicate improvement in the helix stability, and an increase in the melting temperature. The analysis of CD spectra represents the structural changes in DNA due to the binding of Mn Salen complex. The binding constant has been calculated using absorbance and fluorescence data. The results also represent that the binding process proceeds by strong electrostatic and hydrophobic interactions