A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes.

Coarse-grained resource allocation models (C-GRAMs) are simple mathematical models of cell physiology, where large components of the macromolecular composition are abstracted into single entities. The dynamics and steady-state behaviour of such models provides insights on optimal allocation of cellular resources and have explained experimentally observed cellular growth laws, but current models do not account for the uptake of compound sources of carbon and nitrogen. Here, we formulate a C-GRAM with nitrogen and carbon pathways converging on biomass production, with parametrizations accounting for respirofermentative and purely respiratory growth. The model describes the effects of the uptake of sugars, ammonium and/or compound nutrients such as amino acids on the translational resource allocation towards proteome sectors that maximized the growth rate. It robustly recovers cellular growth laws including the Monod law and the ribosomal growth law. Furthermore, we show how the growth-maximizing balance between carbon uptake, recycling, and excretion depends on the nutrient environment. Lastly, we find a robust linear correlation between the ribosome fraction and the abundance of amino acid equivalents in the optimal cell, which supports the view that simple regulation of translational gene expression can enable cells to achieve an approximately optimal growth state.

Fission yeast obeys a linear size law under nutrient titration.

Steady-state cell size and geometry depend on growth conditions. Here, we use an experimental setup based on continuous culture and single-cell imaging to study how cell volume, length, width and surface-to-volume ratio vary across a range of growth conditions including nitrogen and carbon titration, the choice of nitrogen source, and translation inhibition. Overall, we find cell geometry is not fully determined by growth rate and depends on the specific mode of growth rate modulation. However, under nitrogen and carbon titrations, we observe that the cell volume and the growth rate follow the same linear scaling.

Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast.

Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Here, we determined the importance of the growth rate in explaining relative changes in protein and mRNA levels in the simple eukaryote Schizosaccharomyces pombe grown on non-limiting nitrogen sources. Although expression of half of fission yeast genes was significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production apart from RNA polymerase II-dependent transcription. Negatively correlated genes belonged mainly to the environmental stress response programme. Critically, metabolic enzymes, which represent ∼55-70% of the proteome by mass, showed mostly condition-specific regulation. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate-dependent and nutrient-specific gene expression.

A computational method for prioritizing targeted therapies in precision oncology: performance analysis in the SHIVA01 trial.

Precision oncology is currently based on pairing molecularly targeted agents (MTA) to predefined single driver genes or biomarkers. Each tumor harbors a combination of a large number of potential genetic alterations of multiple driver genes in a complex system that limits the potential of this approach. We have developed an artificial intelligence (AI)-assisted computational method, the digital drug-assignment (DDA) system, to prioritize potential MTAs for each cancer patient based on the complex individual molecular profile of their tumor. We analyzed the clinical benefit of the DDA system on the molecular and clinical outcome data of patients treated in the SHIVA01 precision oncology clinical trial with MTAs matched to individual genetic alterations or biomarkers of their tumor. We found that the DDA score assigned to MTAs was significantly higher in patients experiencing disease control than in patients with progressive disease (1523 versus 580, P = 0.037). The median PFS was also significantly longer in patients receiving MTAs with high (1000+ <) than with low (<0) DDA scores (3.95 versus 1.95 months, P = 0.044). Our results indicate that AI-based systems, like DDA, are promising new tools for oncologists to improve the clinical benefit of precision oncology.

Chitotriosidase gene polymorphisms and mutations limit the determination of chitotriosidase expression in sarcoidosis.

Serum chitotriosidase (CTO) activity was proposed as a biomarker in sarcoidosis being potentially useful in diagnostics. Nevertheless, a common duplication polymorphism (c.1049_1072dup24, Dup24) of the CTO gene influences CTO activity and thereby compromises its use in sarcoidosis. Here we aimed to substitute CTO activity with CTO concentration to prevent the confounding effect of Dup24. CTO activity, concentration and genetic backgrounds were determined in 80 histopathology proven sarcoidosis patients and 133 healthy individuals. CTO activities were lower in healthy individuals and sarcoidosis patients heterozygous for Dup24 mutation (472 ± 367 mU/L, n = 49; 2300 ± 2105 mU/L, n = 29) than in homozygous wild types (838 ± 856 mU/L, n = 81; 5125 ± 4802 mU/L, n = 48; p < 0.001, respectively). Sera of Dup24 homozygous individuals had no CTO activity. CTO concentrations were also lower in healthy individuals and sarcoidosis patients heterozygous for Dup24 mutation (7.2 ± 1.9 µg/L, n = 11; 63.16 ± 56.5 µg/L, n = 29) than in homozygous wild types (18.9 ± 13.0 µg/L, n = 36; 157.1 ± 132.4 µg/L, n = 47, p < 0.001, respectively) suggestive for an interaction between Dup24 mutation and CTO concentration determinations. We also identified a healthy Hungarian male subject without CTO activity carrying a rare mutation (c.(965_993)del), which mutation has been considered unique for Cypriot population to date. Taken together, CTO concentration determination does not add to the CTO activity measurement when CTO is used as a biomarker in sarcoidosis. Therefore, genotyping of CTO gene should be involved in the interpretation of laboratory findings.

Prediction of lung function and lung density of young adults who had bronchopulmonary dysplasia.

COPD risk is jointly determined by fetal lung development, lung growth rate and lung growth duration leading to the maximally attained level of lung function in early adulthood. Bronchopulmonary dysplasia (BPD) is considered a developmental arrest of alveolarisation. Long-term outcome studies of adult survivors born before the introduction of surfactant therapy ("old BPD") showed impaired lung function. We aimed to predict adult lung function and lung density in a cohort of premature infants born in the surfactant era, representing "new BPD". We studied a cohort of young adults born between 1987 and 1998, with (n=36) and without (n=28) BPD, treated in a single centre. Their perinatal characteristics and pulmonary function in infancy were studied by regression analysis for correlation with adult lung function and tissue lung density, all expressed by z-scores, at a mean age of 19.7±1.1 and 21±2.2 years, respectively. Although BPD adults had on average lower forced expiratory volume in 1 s (zFEV1)/forced vital capacity (FVC) and zFEV1 than those without, 55% of the BPD group had zFEV1/FVC values above the lower limit of normal (LLN). Moreover, above LLN values of diffusing capacity of the lung for carbon monoxide (zD LCO) was present in 89% of BPD adults and lung density in 71%. Only higher oxygen supply (F IO2) at 36 weeks post-conception of BPD subjects had a trend with lower zFEV1 (B=-6.4; p=0.053) and lower zD LCO (B=-4.1; p=0.023) at adulthood. No statistically significant predictors of new BPD were identified.

Combined application of angiotensin converting enzyme and chitotriosidase analysis improves the laboratory diagnosis of sarcoidosis.

Establishing the diagnosis of sarcoidosis most often requires biopsy and histopathologic evaluation, since there is no single marker with sufficient specificity and sensitivity for the disease. Our aims were to determine and compare the diagnostic accuracies of several potential biomarkers and to develop a combined biomarker analysis tool for the diagnosis of sarcoidosis. 133 healthy individuals and 104 patients with suspected sarcoidosis and diagnostic thoracic surgery were enrolled into this study. Histopathologic results were contrasted to biomarker levels of chitotriosidase (CTO), serum amyloid-A (SAA), soluble interleukin-2 receptor (sIL-2R), lysozyme (LZM) or angiotensin converting enzyme (ACE). Sarcoidosis was confirmed by histopathology in 69 patients. CTO activity, sIL-2R concentration and ACE activity could discriminate between sarcoidosis and control patients, while SAA and LZM concentrations could not. A new combined parameter, which was derived from the multiplication of ACE by CTO activities (double product) showed the best diagnostic accuracy in this clinical study: (AUC = 0.898, sensitivity: 90.5%, specificity: 79.3%, positive and negative predictive values: 90.5% and 79.3%, respectively). Sarcoidosis can be diagnosed with the combined analysis of ACE and CTO activities more accurately than with single serum biomarkers in the absence of invasive biopsy in the majority of cases with pulmonary manifestation of sarcoidosis.

Noise propagation in an integrated model of bacterial gene expression and growth.

In bacterial cells, gene expression, metabolism, and growth are highly interdependent and tightly coordinated. As a result, stochastic fluctuations in expression levels and instantaneous growth rate show intricate cross-correlations. These correlations are shaped by feedback loops, trade-offs and constraints acting at the cellular level; therefore a quantitative understanding requires an integrated approach. To that end, we here present a mathematical model describing a cell that contains multiple proteins that are each expressed stochastically and jointly limit the growth rate. Conversely, metabolism and growth affect protein synthesis and dilution. Thus, expression noise originating in one gene propagates to metabolism, growth, and the expression of all other genes. Nevertheless, under a small-noise approximation many statistical quantities can be calculated analytically. We identify several routes of noise propagation, illustrate their origins and scaling, and establish important connections between noise propagation and the field of metabolic control analysis. We then present a many-protein model containing >1000 proteins parameterized by previously measured abundance data and demonstrate that the predicted cross-correlations between gene expression and growth rate are in broad agreement with published measurements.

Valorization of biomass: deriving more value from waste.

Most of the carbon-based compounds currently manufactured by the chemical industry are derived from petroleum. The rising cost and dwindling supply of oil have been focusing attention on possible routes to making chemicals, fuels, and solvents from biomass instead. In this context, many recent studies have assessed the relative merits of applying different dedicated crops to chemical production. Here, we highlight the opportunities for diverting existing residual biomass--the by-products of present agricultural and food-processing streams--to this end.

Molecular mapping of the acid catalysed dehydration of fructose.

Several intermediates and different reaction paths were identified for the acid catalysed conversion of fructose to 5-(hydroxymethyl)-2-furaldehyde (HMF) in different solvents. The structural information combined with results of isotopic-labelling experiments allowed the determination of the irreversibility of the three steps from the fructofuranosyl oxocarbenium ion to HMF as well as the analogous pyranose route.

Generation of (nonafluoro-tert-butoxy)methyl ponytails for enhanced fluorous partition of aromatics and heterocycles.

The reaction of sodium perfluoro-tert-butoxide with benzylic carbon-bromide bond(s) leads to the formation of (nonafluoro-tert-butoxy)methyl ponytail(s), which can enhance the fluorous solubility and partition of aromatics and heterocycles.

Fluorous hydroformylation.

The application of fluorous phosphine-modified catalysts for the hydroformylation of olefins is reviewed.

Fluorous hydrogenation.

The application of fluorous phosphine-modified catalysts for the hydrogenation of olefins is reviewed.

Imidazolium ionic liquids as solvents for cerium(IV)-mediated oxidation reactions.

Use of imidazolium ionic liquids as solvents for organic transformations with tetravalent cerium salts as oxidizing agents was evaluated. Good solubility was found for ammonium hexanitratocerate(IV) (ceric ammonium nitrate, CAN) and cerium(IV) triflate in 1-alkyl-3-methylimidazolium triflate ionic liquids. Oxidation of benzyl alcohol to benzaldehyde in 1-ethyl-3-methylimidazolium triflate was studied by in-situ FTIR spectroscopy and 13C NMR spectroscopy on carbon-13-labeled benzyl alcohol. Careful control of the reaction conditions is necessary because ammonium hexanitratocerate(IV) dissolved in an ionic liquid can transform benzyl alcohol not only into benzaldehyde but also into benzyl nitrate or benzoic acid. The selectivity of the reaction of cerium(IV) triflate with benzyl alcohol in dry ionic liquids depends on the degree of hydration of cerium(IV) triflate: anhydrous cerium(IV) triflate transforms benzyl alcohol into dibenzyl ether, whereas hydrated cerium(IV) triflate affords benzaldehyde as the main reaction product. Reactions of ammonium hexanitratocerate(IV) with organic substrates other than benzyl alcohol have been explored. 1,4-Hydroquinone is quantitatively transformed into 1,4-quinone. Anisole and naphthalene are nitrated. For the cerium-mediated oxidation reactions in ionic liquids, high reaction temperatures are an advantage because under these conditions smaller amounts of byproducts are formed.

Modular synthesis of fluorous trialkylphosphines.

A modular synthetic protocol was developed for the preparation of fluorous trialkylphosphines with a different number of methylene spacers and various lengths of the fluorous ponytails P[(CH(2))(A)R(FX)][(CH(2))(B)R(FY)][(CH(2))(C)R(FZ)] (A, B, C = 3 and 4; X, Y, Z = 4, 6, and 8). [reaction: see text]