The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Small multi-purpose reservoir ensemble planning

People living in arid areas with highly variable rainfall, experience droughts and floods and often have insecure livelihoods. Small multi-purpose reservoirs are a widely used form of infrastructure for the provision of water. They supply water for domestic use, livestock watering, small scale irrigation, and other beneficial uses. The reservoirs are hydrologically linked by the streams that have been dammed. Although reservoirs store a large quantity of water and have a significant effect on downstream flows, they have rarely been considered as systems, with synergies and tradeoffs resulting from the number and density of their structures. Often reservoirs were constructed in a series of projects funded by different agencies, at different times, with little or no coordination among the implementing partners. A significant number are functioning sub-optimally and/or are falling into disrepair. This indicates that there is room for improvement in the planning, operation, and maintenance of small reservoirs. The water management institutions in Volta, Limpopo, and Sao Francisco Basins are being revamped to better serve their constituencies. We have an opportunity to collaborate with government officials, stakeholders, and farmers who are actively looking for ways to improve the planning process. The Small Reservoir Project team developed a tool kit to support the planning, development, and management of small reservoir ensembles on the basin level and the use of small multi-purpose reservoirs that are properly located, well designed, operated and maintained in sustainable fashion, and economically viable on the local/community level. There are tools to improve intervention planning, storage estimation and the analysis of the hydrology, ecology and health of small reservoirs. There ara also tools for the analysis of institutional and economic aspects of the reservoirs. The toolkit not only includes the necessary analytical instruments, but also a set of process oriented tools for improved participatory decision making. The Tool Kit is meant to be a living “document” with additional tools and experiences to be added as they are developed

Preferential Paths of Air-water Two-phase Flow in Porous Structures with Special Consideration of Channel Thickness Effects.

Accurate understanding and predicting the flow paths of immiscible two-phase flow in rocky porous structures are of critical importance for the evaluation of oil or gas recovery and prediction of rock slides caused by gas-liquid flow. A 2D phase field model was established for compressible air-water two-phase flow in heterogenous porous structures. The dynamic characteristics of air-water two-phase interface and preferential paths in porous structures were simulated. The factors affecting the path selection of two-phase flow in porous structures were analyzed. Transparent physical models of complex porous structures were prepared using 3D printing technology. Tracer dye was used to visually observe the flow characteristics and path selection in air-water two-phase displacement experiments. The experimental observations agree with the numerical results used to validate the accuracy of phase field model. The effects of channel thickness on the air-water two-phase flow behavior and paths in porous structures were also analyzed. The results indicate that thick channels can induce secondary air flow paths due to the increase in flow resistance; consequently, the flow distribution is different from that in narrow channels. This study provides a new reference for quantitatively analyzing multi-phase flow and predicting the preferential paths of immiscible fluids in porous structures

Machine Learning Framework to Identify Individuals at Risk of Rapid Progression of Coronary Atherosclerosis: From the PARADIGM Registry.

Background Rapid coronary plaque progression (RPP) is associated with incident cardiovascular events. To date, no method exists for the identification of individuals at risk of RPP at a single point in time. This study integrated coronary computed tomography angiography-determined qualitative and quantitative plaque features within a machine learning (ML) framework to determine its performance for predicting RPP. Methods and Results Qualitative and quantitative coronary computed tomography angiography plaque characterization was performed in 1083 patients who underwent serial coronary computed tomography angiography from the PARADIGM (Progression of Atherosclerotic Plaque Determined by Computed Tomographic Angiography Imaging) registry. RPP was defined as an annual progression of percentage atheroma volume ≥1.0%. We employed the following ML models: model 1, clinical variables; model 2, model 1 plus qualitative plaque features; model 3, model 2 plus quantitative plaque features. ML models were compared with the atherosclerotic cardiovascular disease risk score, Duke coronary artery disease score, and a logistic regression statistical model. 224 patients (21%) were identified as RPP. Feature selection in ML identifies that quantitative computed tomography variables were higher-ranking features, followed by qualitative computed tomography variables and clinical/laboratory variables. ML model 3 exhibited the highest discriminatory performance to identify individuals who would experience RPP when compared with atherosclerotic cardiovascular disease risk score, the other ML models, and the statistical model (area under the receiver operating characteristic curve in ML model 3, 0.83 [95% CI 0.78-0.89], versus atherosclerotic cardiovascular disease risk score, 0.60 [0.52-0.67]; Duke coronary artery disease score, 0.74 [0.68-0.79]; ML model 1, 0.62 [0.55-0.69]; ML model 2, 0.73 [0.67-0.80]; all P<0.001; statistical model, 0.81 [0.75-0.87], P=0.128). Conclusions Based on a ML framework, quantitative atherosclerosis characterization has been shown to be the most important feature when compared with clinical, laboratory, and qualitative measures in identifying patients at risk of RPP

Mass spectrometry of B. subtilis CopZ: Cu(I)-binding and interactions with bacillithiol

CopZ from Bacillus subtilis is a well-studied member of the highly conserved family of Atx1-like copper chaperones. It was previously shown via solution and crystallographic studies to undergo Cu(I)-mediated dimerisation, where the CopZ dimer can bind between one and four Cu(I) ions. However, these studies could not provide information about the changing distribution of species at increasing Cu(I) levels. To address this, electrospray ionisation mass spectrometry using soft ionisation was applied to CopZ under native conditions. Data revealed folded, monomeric CopZ in apo- and Cu(I)-bound forms, along with Cu(I)-bound dimeric forms of CopZ at higher Cu(I) loading. Cu4(CopZ)2 was the major dimeric species at loadings >1 Cu(I)/CopZ, indicating the cooperative formation of the tetranuclear Cu(I)-bound species. As the principal low molecular weight thiol in B. subtilis, bacillithiol (BSH) may play a role in copper homeostasis. Mass spectrometry showed that increasing BSH led to a reduction in Cu(I)-bound dimeric forms, and the formation of S-bacillithiolated apo-CopZ and BSH adducts of Cu(I)-bound forms of CopZ, where BSH likely acts as a Cu(I) ligand. These data, along with the high affinity of BSH for Cu(I), determined here to be β2(BSH) = ∼4 × 1017 M−2, are consistent with a role for BSH alongside CopZ in buffering cellular Cu(I) levels. Here, mass spectrometry provides a high resolution overview of CopZ–Cu(I) speciation that cannot be obtained from less discriminating solution-phase methods, thus illustrating the potential for the wider application of this technique to studies of metal–protein interactions

Clinical risk factors and atherosclerotic plaque extent to define risk for major events in patients without obstructive coronary artery disease: the long-term coronary computed tomography angiography CONFIRM registry.

AimsIn patients without obstructive coronary artery disease (CAD), we examined the prognostic value of risk factors and atherosclerotic extent.Methods and resultsPatients from the long-term CONFIRM registry without prior CAD and without obstructive (≥50%) stenosis were included. Within the groups of normal coronary computed tomography angiography (CCTA) (N = 1849) and non-obstructive CAD (N = 1698), the prognostic value of traditional clinical risk factors and atherosclerotic extent (segment involvement score, SIS) was assessed with Cox models. Major adverse cardiac events (MACE) were defined as all-cause mortality, non-fatal myocardial infarction, or late revascularization. In total, 3547 patients were included (age 57.9 ± 12.1 years, 57.8% male), experiencing 460 MACE during 5.4 years of follow-up. Age, body mass index, hypertension, and diabetes were the clinical variables associated with increased MACE risk, but the magnitude of risk was higher for CCTA defined atherosclerotic extent; adjusted hazard ratio (HR) for SIS >5 was 3.4 (95% confidence interval [CI] 2.3-4.9) while HR for diabetes and hypertension were 1.7 (95% CI 1.3-2.2) and 1.4 (95% CI 1.1-1.7), respectively. Exclusion of revascularization as endpoint did not modify the results. In normal CCTA, presence of ≥1 traditional risk factors did not worsen prognosis (log-rank P = 0.248), while it did in non-obstructive CAD (log-rank P = 0.025). Adjusted for SIS, hypertension and diabetes predicted MACE risk in non-obstructive CAD, while diabetes did not increase risk in absence of CAD (P-interaction = 0.004).ConclusionAmong patients without obstructive CAD, the extent of CAD provides more prognostic information for MACE than traditional cardiovascular risk factors. An interaction was observed between risk factors and CAD burden, suggesting synergistic effects of both

Influence of canopy fruit location on morphological, histochemical and biochemical changes in two oil olive cultivars

The influence of different irradiance conditions was evaluated under natural solar radiation by comparing well-exposed (in) and shaded fruit (out) in canopies of olive trees (Olea europaea L). Over a 2-year period, from 50 days after full bloom up to harvest time, “in” and “out” olive samples of two genotypes (“Frantoio Millennio” and “Coratina 5/19”) were periodically collected. Morphological, histochemical, and biochemical analysis were performed to study the changes on fruit morphometric traits, oil body accumulation, and b-glucosidase enzyme activity. Some parameters were modified by shading inside the canopy in which the proportion of incident photosynthetically active radiation intercepted by the crop was 47%. Shaded fruits developed at slow rate and were characterized by late darkgoing time, reduced size, with a tendency toward oblong shape. The rapid histochemical procedure proposed to estimate the oil body accumulation during fruit ripening showed that a reduced irradiance caused a decrease in oil body density. The canopy position influenced, in a different way, the b-glucosidase activity in relation to the fruit-ripening stage in both genotypes. These findings indicate that providing an adequate and uniform lighting of the olive canopy by careful choices of orchard management practices can be a key factor for several yield components

NUMERICAL MODELING OF LEAN SPRAY LIFTED FLAMES IN INCLINED MULTI-BURNER ARRANGEMENTS

Modern combustors operate with lean mixtures to prevent Nitrogen oxides (NOx) formation by limiting the peaks of the temperature inside the combustion chamber. One of the main drawbacks of these technologies is the higher risk of Lean Blow-Off (LBO) compared to the state-of-art Rich Quench Lean combustors. To limit this possibility, combustor designers introduced pioneering concepts for this component. In this fashion, the CHAiRLIFT (Compact Helical Arranged combustoRs with lean LIFTed flames) concept founds its advantages in the structure of the combustion chamber. It combines two concepts: the tilting of the burner’s axis relative to the engine axis with a low-swirl lifted spray flame. Here, the combustion can be stabilized at very low equivalence ratios thanks to the interaction between consecutive burners. A numerical analysis was carried out to support the experimental campaign aiming to investigate the performance of the burner under different tilting angles for the burners. Twophase simulations of the CHAiRLIFT full rig burner were performed in the commercial CFD suite ANSYS Fluent and the results were compared with the available experimental data. Furthermore, a deeper sensitivity to the tilting angle was conducted through the introduction of specific performance parameters to assess the performance and to seek the best promising setup. The outcomes have shown that tilt angles between 20° and 30° could lead to an improvement of the exhaust recirculation, regarding the considered operating conditions

Study on the morphological evolution of bud break in Vitis vinifera L.

The aims are to evaluate morpho-anatomical bud development during dormancy and to compare the heat requirement needed to start bud break in several grapevine cultivars characterised by different geographic origins. A detailed description is presented of the bud growth stages of Vitis vinifera cultivars to contribute to the standardisation of national and international testing systems of fruit growing. Based on the general BBCH-scale, the codes describe the first stages of budbreak in several cultivars with different geographical origins. Dormancy release was evaluated both under natural and forcing conditions, appropriate method to establish the budbreak of deciduous species. The cultivars were characterised in relation to the achievement of complete bud scale opening stage (03 of BBCH scale) which is suggested to consider as an early and indicator of budbreak.