Biochemical assessment of phosphate homeostasis.

Phosphate homeostasis is a requirement for normal life. Phosphate is involved in the synthesis of membrane lipids, DNA, RNA, and energy-rich molecules (ATP and GTP), and the regulation of protein activity by phosphorylation/dephosphorylation. Moreover, phosphate is a component of apatite crystals, which provide stability to the bone, and is essential for normal growth. Phosphate balance in the body is the difference between net phosphate absorption through the intestine and phosphate excretion through the kidney. Numerous disorders, both genetic and acquired, may alter phosphate homeostasis. In affected individuals, it is crucial to identify the underlying mechanism(s) to provide adequate treatment; however, phosphate homeostasis assessment remains challenging. Besides the measurement of key hormones involved in the control of phosphate homeostasis (parathyroid hormone, vitamin D and metabolites, fibroblast growth factor 23), assessing the magnitude of phosphate reabsorption by the kidney is a crucial step. It makes it possible to distinguish between a primary disorder of renal phosphate reabsorption, associated with an intrinsic defect or endocrine disturbance, and a nutritional cause of phosphate deficiency. This strategy is described, and the potential consequences for therapeutic decisions are discussed.

Metabolic limits on classical information processing by biological cells.

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

Algorithmic extraction of smartphone accelerometer-derived mechano-biological descriptors of resistance exercise is robust to changes in intensity and velocity.

BACKGROUND: It was shown that single repetition, contraction-phase specific and total time-under-tension (TUT) can be extracted reliably and validly from smartphone accelerometer-derived data of resistance exercise machines using user-determined resistance exercise velocities at 60% one repetition maximum (1-RM). However, it remained unclear how robust the extraction of these mechano-biological descriptors is over a wide range of movement velocities (slow- versus fast-movement velocity) and intensities (30% 1-RM versus 80% 1-RM) that reflect the interindividual variability during resistance exercise. OBJECTIVE: In this work, we examined whether the manipulation of velocity or intensity would disrupt an algorithmic extraction of single repetitions, contraction-phase specific and total TUT. METHODS: Twenty-seven participants performed four sets of three repetitions of their 30% and 80% 1-RM with velocities of 1 s, 2 s, 6 s and 8 s per repetition, respectively. An algorithm extracted the number of repetitions, single repetition, contraction-phase specific and total TUT. All exercises were video-recorded. The video recordings served as the gold standard to which algorithmically-derived TUT was compared. The agreement between the methods was examined using Limits of Agreement (LoA). The Pearson correlation coefficients were used to calculate the association, and the intraclass correlation coefficient (ICC 2.1) examined the interrater reliability. RESULTS: The calculated error rate for the algorithmic detection of the number of single repetitions derived from two smartphones accelerometers was 1.9%. The comparison between algorithmically-derived, contraction-phase specific TUT against video, revealed a high degree of correlation (r > 0.94) for both exercise machines. The agreement between the two methods was high on both exercise machines, intensities and velocities and was as follows: LoA ranged from -0.21 to 0.22 seconds for single repetition TUT (2.57% of mean TUT), from -0.24 to 0.22 seconds for concentric contraction TUT (6.25% of mean TUT), from -0.22 to 0.24 seconds for eccentric contraction TUT (5.52% of mean TUT) and from -1.97 to 1.00 seconds for total TUT (5.13% of mean TUT). Interrater reliability for single repetition, contraction-phase specific TUT was high (ICC > 0.99). CONCLUSION: Neither intensity nor velocity disrupts the proposed algorithmic data extraction approach. Therefore, smartphone accelerometers can be used to extract scientific mechano-biological descriptors of dynamic resistance exercise with intensities ranging from 30% to 80% of the 1-RM with velocities ranging from 1 s to 8 s per repetition, respectively, thus making this simple method a reliable tool for resistance exercise mechano-biological descriptors extraction.

Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins.

In this chapter, we provide a practical guide on how to plan, execute, and interpret atomistic and coarse-grained molecular dynamics (MD) simulations of lipid-modified proteins in model membranes. After outlining some key practical considerations when planning such simulations, we survey resources and techniques to obtain force field parameters for nonconventional amino acids, such as posttranslationally lipid-modified amino acids that are unique to this class of proteins. We then describe the protocols to build, setup, and run the simulations, followed by a brief comment on the analysis and interpretation of the simulations. Finally, examples of insights that could be gained from atomistic and coarse-grained MD simulations of lipidated proteins will be provided, using RAS proteins as illustrative examples. Throughout the chapter, we highlight the main advantages and limitations of simulating RAS and related lipid-modified G-proteins in biomimetic membranes.

IGFBP-2 partly mediates the early metabolic improvements caused by bariatric surgery.

Insulin-like growth factor-binding protein (IGFBP)-2 is a circulating biomarker of cardiometabolic health. Here, we report that circulating IGFBP-2 concentrations robustly increase after different bariatric procedures in humans, reaching higher levels after biliopancreatic diversion with duodenal switch (BPD-DS) than after Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG). This increase is closely associated with insulin sensitization. In mice and rats, BPD-DS and RYGB operations also increase circulating IGFBP-2 levels, which are not affected by SG or caloric restriction. In mice, Igfbp2 deficiency significantly impairs surgery-induced loss in adiposity and early improvement in insulin sensitivity but does not affect long-term enhancement in glucose homeostasis. This study demonstrates that the modulation of circulating IGFBP-2 may play a role in the early improvement of insulin sensitivity and loss of adiposity brought about by bariatric surgery.

Biochemistry tests in hospitalized COVID-19 patients: Experience from a Canadian tertiary care centre.

BACKGROUND: Coronavirus Disease 2019 (COVID-19) has variable clinical presentation, from asymptomatic to severe disease leading to death. Biochemical markers may help with management and prognostication of COVID-19 patients; however, their utility is still under investigation. METHODS: A retrospective study was conducted to evaluate alanine aminotransferase, C-reactive protein (CRP), ferritin, lactate, and high sensitivity troponin T (TnT) levels in 67 patients who were admitted to a Canadian tertiary care centre for management of COVID-19. Logistic, cause-specific Cox proportional-hazards, and accelerated failure time regression modelling were performed to assess the associations of initial analyte concentrations with in-hospital death and length of stay in hospital; joint modelling was performed to assess the associations of the concentrations over the course of the hospital stay with in-hospital death. RESULTS: Initial TnT and CRP concentrations were associated with length of stay in hospital. Eighteen patients died (27%), and the median initial TnT concentration was higher in patients who died (55 ng/L) than those who lived (16 ng/L; P < 0.0001). There were no survivors with an initial TnT concentration > 64 ng/L. While the initial TnT concentration was predictive of death, later measurements were not. Only CRP had prognostic value with both the initial and subsequent measurements: a 20% increase in the initial CRP concentration was associated with a 14% (95% confidence interval (CI): 1-29%) increase in the odds of death, and the hazard of death increased 14% (95% CI: 5-25%) for each 20% increase in the current CRP value. While the initial lactate concentration was not predictive of death, subsequent measurements were. CONCLUSION: CRP, lactate and TnT were associated with poorer outcomes and appear to be useful biochemical markers for monitoring COVID-19 patients.

Hormonal impact on photosynthesis and photoprotection in plants.

Photosynthesis is not only essential for plants, but it also sustains life on Earth. Phytohormones play crucial roles in developmental processes, from organ initiation to senescence, due to their role as growth and developmental regulators, as well as their central role in the regulation of photosynthesis. Furthermore, phytohormones play a major role in photoprotection of the photosynthetic apparatus under stress conditions. Here, in addition to discussing our current knowledge on the role of the phytohormones auxin, cytokinins, gibberellins, and strigolactones in promoting photosynthesis, we will also highlight the role of abscisic acid beyond stomatal closure in modulating photosynthesis and photoprotection under various stress conditions through crosstalk with ethylene, salicylates, jasmonates, and brassinosteroids. Furthermore, the role of phytohormones in controlling the production and scavenging of photosynthesis-derived reactive oxygen species, the duration and extent of photo-oxidative stress and redox signaling under stress conditions will be discussed in detail. Hormones have a significant impact on the regulation of photosynthetic processes in plants under both optimal and stress conditions, with hormonal interactions, complementation, and crosstalk being important in the spatiotemporal and integrative regulation of photosynthetic processes during organ development at the whole-plant level.

Assessment of the biochemical pathways for acetaminophen toxicity: Implications for its carcinogenic hazard potential.

In 2019 California's Office of Environmental Health Hazard Assessment (OEHHA) initiated a review of the carcinogenic hazard potential of acetaminophen. In parallel with this review, herein we evaluated the mechanistic data related to the steps and timing of cellular events following therapeutic recommended (≤4 g/day) and higher doses of acetaminophen that may cause hepatotoxicity to evaluate whether these changes indicate that acetaminophen is a carcinogenic hazard. At therapeutic recommended doses, acetaminophen forms limited amounts of N-acetyl-p-benzoquinone-imine (NAPQI) without adverse cellular effects. Following overdoses of acetaminophen, there is potential for more extensive formation of NAPQI and depletion of glutathione, which may result in mitochondrial dysfunction and DNA damage, but only at doses that result in cell death - thus making it implausible for acetaminophen to induce the kind of stable, genetic damage in the nucleus indicative of a genotoxic or carcinogenic hazard in humans. The collective data demonstrate a lack of a plausible mechanism related to carcinogenicity and are consistent with rodent cancer bioassays, epidemiological results reviewed in companion manuscripts in this issue, as well as conclusions of multiple international health authorities.

Investigating antimicrobial compounds in South African Combretaceae species using a biochemometric approach.

ETHNOPHARMACOLOGICAL RELEVANCE: Many species within the family Combretaceae are popular medicinal plants that are used traditionally to treat various conditions, of which many are related to bacterial infections. Global concerns regarding the increasing resistance of pathogens towards currently available antibiotics have encouraged researchers to find new drugs with antibacterial activity, particularly from plant sources. AIM OF THE STUDY: This study was aimed at exploring the broad-spectrum antibacterial potential of methanol extracts of species representing four genera of Combretaceae (Combretum, Pteleopsis, Quisqualis, Terminalia), indigenous to South Africa, using a biochemometric approach. MATERIALS AND METHODS: The microdilution assay was used to determine the antibacterial activities, measured as minimum inhibitory concentrations (MICs), of the 51 methanol extracts representing 35 Combretaceae species, against nine species of pathogenic bacteria. Integrative biochemometric analysis was performed, thereby correlating the MIC values with the metabolomic data obtained from ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis. Orthogonal projections to latent structures-discriminant analysis (OPLS-DA) models were constructed for six pathogens displaying variation in their susceptibility towards the extracts. RESULTS: Evaluation of the overall MIC values obtained indicated that extracts of species from the four genera displayed the highest activity towards Bacillus cereus ATCC 11778 (average MIC 0.52 mg/mL) and Salmonella typhimurium ATCC 14028 (average MIC 0.63 mg/mL). These bacteria were the most sensitive Gram-positive and Gram-negative bacteria, respectively. Extracts from Combretum acutifolium, Combretum imberbe and Combretum elaeagnoides were the most active, with average MIC values of 0.70 mg/mL, 0.52 mg/mL and 0.45 mg/mL, respectively. Five triterpenoid compounds were tentatively identified as biomarkers from the biochemometric analysis. CONCLUSION: Correlation of the phytochemistry of species from four genera in the Combretaceae family with antibacterial activity revealed that triterpenoids are responsible for the broad-spectrum antibacterial activity observed.

Sensitivity analysis of the reaction occurrence and recurrence times in steady-state biochemical networks.

Continuous-time stationary Markov jump processes among discrete sites are encountered in disparate biochemical ambits. Sites and connecting dynamical events form a 'network' in which the sites are the available system's states, and the events are site-to-site transitions, or even neutral processes in which the system does not change site but the event is however detectable. Examples include conformational transitions in single biomolecules, stochastic chemical kinetics in the space of the molecules copy numbers, and even macroscopic steady-state reactive mixtures if one adopts the viewpoint of a tagged molecule (or even of a molecular moiety) whose state may change when it is involved in a chemical reaction. Among the variety of dynamical descriptors, here we focus on the first occurrence times (starting from a given site) and on the recurrence times of an event of interest. We develop the sensitivity analysis for the lowest moments of the statistical distribution of such times with respect to the rate constants of the network. In particular, simple expressions and inequalities allow us to establish a direct relationship between selective variation of rate constants and effect on average times and variances. As illustrative cases we treat the substrate inhibition in enzymatic catalysis in which a tagged enzyme molecule jumps between three states, and the basic two-site model of stochastic gene expression in which the single gene switches between active and inactive forms.

Green Synthesis of Copper Oxide Nanoparticles using Cucumis Sativus (Cucumber) Extracts and their Bio-Physical and Biochemical Characterization for Cosmetic and Dermatologic Applications.

BACKGROUND & OBJECTIVE: Nanoparticles are used in cosmetic and dermatologic products, due to better skin penetration properties. Incorporation of natural products exhibiting medicinal properties in nano-preparations could significantly improve the efficacy of these products and improve the quality of life without the side effects of synthetic formulations. METHODS: We here report the green synthesis of Copper Oxide nanoparticles, using Cucumber extract, and their detailed bio-physical and bio-chemical characterization. RESULTS: These Copper Oxide-Cucumber nanoparticles exhibit significant anti-bacterial and anti-fungal properties, Ultra Violet-radiation protection ability and reactive-oxygen species inhibition properties. Importantly, these nanoparticles do not exhibit significant cellular toxicity and, when incorporated in skin cream, exhibit skin rejuvenating properties. CONCLUSION: Our findings have implications for nanoparticle-based cosmetics and dermatologic applications.

Neuroevolutive Algorithms Applied for Modeling Some Biochemical Separation Processes.

Combining artificial neural networks with evolutive/bioinspired approaches is a technique that can solve a variety of issues regarding the topology determination and training for neural networks or for process optimization. In this chapter, the main mechanisms used in neuroevolution are discussed and some biochemical separation examples are given to underline the efficiency of these tools. For the current case studies (reactive extraction of folic acid and pertraction of vitamin C), the bioinspired metaheuristic included in the neuroevolutive procedures is represented by Differential Evolution, an algorithm that has shown a great potential to solve a variety of problems from multiple domains.

Targeted Growth Medium Dropouts Promote Aromatic Compound Synthesis in Crude E. coli Cell-Free Systems.

Progress in cell-free protein synthesis (CFPS) has spurred resurgent interest in engineering complex biological metabolism outside of the cell. Unlike purified enzyme systems, crude cell-free systems can be prepared for a fraction of the cost and contain endogenous cellular pathways that can be activated for biosynthesis. Endogenous activity performs essential functions in cell-free systems including substrate biosynthesis and energy regeneration; however, use of crude cell-free systems for bioproduction has been hampered by the under-described complexity of the metabolic networks inherent to a crude lysate. Physical and chemical cultivation parameters influence the endogenous activity of the resulting lysate, but targeted efforts to engineer this activity by manipulation of these nongenetic factors has been limited. Here growth medium composition was manipulated to improve the one-pot in vitro biosynthesis of phenol from glucose via the expression of Pasteurella multocida phenol-tyrosine lyase in crude E. coli lysates. Crude cell lysate metabolic activity was focused toward the limiting precursor tyrosine by targeted growth medium dropouts guided by proteomics. The result is the activation of a 25-step enzymatic reaction cascade involving at least three endogenous E. coli metabolic pathways. Additional modification of this system, through CFPS of feedback intolerant AroG improves yield. This effort demonstrates the ability to activate a long, complex pathway in vitro and provides a framework for harnessing the metabolic potential of diverse organisms for cell-free metabolic engineering. The more than 6-fold increase in phenol yield with limited genetic manipulation demonstrates the benefits of optimizing growth medium for crude cell-free extract production and illustrates the advantages of a systems approach to cell-free metabolic engineering.

A kinetic rationale for functional redundancy in fatty acid biosynthesis.

Cells build fatty acids with biocatalytic assembly lines in which a subset of enzymes often exhibit overlapping activities (e.g., two enzymes catalyze one or more identical reactions). Although the discrete enzymes that make up fatty acid pathways are well characterized, the importance of catalytic overlap between them is poorly understood. We developed a detailed kinetic model of the fatty acid synthase (FAS) of Escherichia coli and paired that model with a fully reconstituted in vitro system to examine the capabilities afforded by functional redundancy in fatty acid synthesis. The model captures-and helps explain-the effects of experimental perturbations to FAS systems and provides a powerful tool for guiding experimental investigations of fatty acid assembly. Compositional analyses carried out in silico and in vitro indicate that FASs with multiple partially redundant enzymes enable tighter (i.e., more independent and/or broader range) control of distinct biochemical objectives-the total production, unsaturated fraction, and average length of fatty acids-than FASs with only a single multifunctional version of each enzyme (i.e., one enzyme with the catalytic capabilities of two partially redundant enzymes). Maximal production of unsaturated fatty acids, for example, requires a second dehydratase that is not essential for their synthesis. This work provides a kinetic, control-theoretic rationale for the inclusion of partially redundant enzymes in fatty acid pathways and supplies a valuable framework for carrying out detailed studies of FAS kinetics.

The biochemistry of low-carbohydrate and ketogenic diets.

PURPOSE OF REVIEW: To summarize the underlying biochemical basis for low-carbohydrate and ketogenic diets (LC/KD) and provide mechanisms to account for demonstrated effectiveness. RECENT FINDINGS: LC/KD continue to have success, to outperform other diets as well as most drugs for weight loss and diabetes treatment. In many cases, LC/KD can effect remission (absence of drugs) or reversal (only metformin or nondiabetes drugs) of type 2 diabetes and can provide a significant adjunct to pharmacology in type 1. Medication is reduced or eliminated in most cases. The results are consistent with the biochemical rationale which stresses the global effects of the glucose-insulin axis. SUMMARY: Evidence for the superior effectiveness of LC/KD for metabolic disease is now overwhelming. At the same time, the approach has received only limited support, and in many cases, persistence of the traditional opposition. Clinical practice or research must confront this crisis in order to bring practice in line with current science and to avoid continued harm to medicine and ultimately, the patient.

Deciphering anomalous heterogeneous intracellular transport with neural networks.

Intracellular transport is predominantly heterogeneous in both time and space, exhibiting varying non-Brownian behavior. Characterization of this movement through averaging methods over an ensemble of trajectories or over the course of a single trajectory often fails to capture this heterogeneity. Here, we developed a deep learning feedforward neural network trained on fractional Brownian motion, providing a novel, accurate and efficient method for resolving heterogeneous behavior of intracellular transport in space and time. The neural network requires significantly fewer data points compared to established methods. This enables robust estimation of Hurst exponents for very short time series data, making possible direct, dynamic segmentation and analysis of experimental tracks of rapidly moving cellular structures such as endosomes and lysosomes. By using this analysis, fractional Brownian motion with a stochastic Hurst exponent was used to interpret, for the first time, anomalous intracellular dynamics, revealing unexpected differences in behavior between closely related endocytic organelles.

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture.

Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system.IMPORTANCE The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.

Anomalous thermal fluctuation distribution sustains proto-metabolic cycles and biomolecule synthesis.

An environment far from equilibrium is thought to be a necessary condition for the origin and persistence of life. In this context we report open-flow simulations of a non-enzymic proto-metabolic system, in which hydrogen peroxide acts both as oxidant and driver of thermochemical cycling. We find that a Gaussian perturbed input produces a non-Boltzmann output fluctuation distribution around the mean oscillation maximum. Our main result is that net biosynthesis can occur under fluctuating cyclical but not steady drive. Consequently we may revise the necessary condition to "dynamically far from equilibrium".