The Role of UPF0157 in the Folding of M. tuberculosis Dephosphocoenzyme A Kinase and the Regulation of the Latter by CTP

BACKGROUND:Targeting the biosynthetic pathway of Coenzyme A (CoA) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. Structural divergence in the organization of the penultimate and final enzymes of CoA biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme A kinase (CoaE) as a potential drug target. METHODOLOGY/PRINCIPAL FINDINGS:We report here a complete biochemical and biophysical characterization of the M. tuberculosis CoaE, an enzyme essential for the pathogen's survival, elucidating for the first time the interactions of a dephosphocoenzyme A kinase with its substrates, dephosphocoenzyme A and ATP; its product, CoA and an intrinsic yet novel inhibitor, CTP, which helps modulate the enzyme's kinetic capabilities providing interesting insights into the regulation of CoaE activity. We show that the mycobacterial enzyme is almost 21 times more catalytically proficient than its counterparts in other prokaryotes. ITC measurements illustrate that the enzyme follows an ordered mechanism of substrate addition with DCoA as the leading substrate and ATP following in tow. Kinetic and ITC experiments demonstrate that though CTP binds strongly to the enzyme, it is unable to participate in DCoA phosphorylation. We report that CTP actually inhibits the enzyme by decreasing its Vmax. Not surprisingly, a structural homology search for the modeled mycobacterial CoaE picks up cytidylmonophosphate kinases, deoxycytidine kinases, and cytidylate kinases as close homologs. Docking of DCoA and CTP to CoaE shows that both ligands bind at the same site, their interactions being stabilized by 26 and 28 hydrogen bonds respectively. We have also assigned a role for the universal Unknown Protein Family 0157 (UPF0157) domain in the mycobacterial CoaE in the proper folding of the full length enzyme. CONCLUSIONS/SIGNIFICANCE:In view of the evidence presented, it is imperative to assign a greater role to the last enzyme of Coenzyme A biosynthesis in metabolite flow regulation through this critical biosynthetic pathway

Validation of clinical acceptability of deep-learning-based automated segmentation of organs-at-risk for head-and-neck radiotherapy treatment planning

IntroductionOrgan-at-risk segmentation for head and neck cancer radiation therapy is a complex and time-consuming process (requiring up to 42 individual structure, and may delay start of treatment or even limit access to function-preserving care. Feasibility of using a deep learning (DL) based autosegmentation model to reduce contouring time without compromising contour accuracy is assessed through a blinded randomized trial of radiation oncologists (ROs) using retrospective, de-identified patient data.MethodsTwo head and neck expert ROs used dedicated time to create gold standard (GS) contours on computed tomography (CT) images. 445 CTs were used to train a custom 3D U-Net DL model covering 42 organs-at-risk, with an additional 20 CTs were held out for the randomized trial. For each held-out patient dataset, one of the eight participant ROs was randomly allocated to review and revise the contours produced by the DL model, while another reviewed contours produced by a medical dosimetry assistant (MDA), both blinded to their origin. Time required for MDAs and ROs to contour was recorded, and the unrevised DL contours, as well as the RO-revised contours by the MDAs and DL model were compared to the GS for that patient.ResultsMean time for initial MDA contouring was 2.3 hours (range 1.6-3.8 hours) and RO-revision took 1.1 hours (range, 0.4-4.4 hours), compared to 0.7 hours (range 0.1-2.0 hours) for the RO-revisions to DL contours. Total time reduced by 76% (95%-Confidence Interval: 65%-88%) and RO-revision time reduced by 35% (95%-CI,-39%-91%). All geometric and dosimetric metrics computed, agreement with GS was equivalent or significantly greater (p<0.05) for RO-revised DL contours compared to the RO-revised MDA contours, including volumetric Dice similarity coefficient (VDSC), surface DSC, added path length, and the 95%-Hausdorff distance. 32 OARs (76%) had mean VDSC greater than 0.8 for the RO-revised DL contours, compared to 20 (48%) for RO-revised MDA contours, and 34 (81%) for the unrevised DL OARs.ConclusionDL autosegmentation demonstrated significant time-savings for organ-at-risk contouring while improving agreement with the institutional GS, indicating comparable accuracy of DL model. Integration into the clinical practice with a prospective evaluation is currently underway

A dynamic leaf gas-exchange strategy is conserved in woody plants under changing ambient CO2: evidence from carbon isotope discrimination in paleo and CO2 enrichment studies

Rising atmospheric [CO2 ], ca , is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas-exchange that include maintaining a constant leaf internal [CO2 ], ci , a constant drawdown in CO2 (ca - ci ), and a constant ci /ca . These strategies can result in drastically different consequences for leaf gas-exchange. The accuracy of Earth systems models depends in part on assumptions about generalizable patterns in leaf gas-exchange responses to varying ca . The concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these strategies, provides a unifying framework for understanding leaf gas-exchange responses to ca . To assess leaf gas-exchange regulation strategies, we analyzed patterns in ci inferred from studies reporting C stable isotope ratios (δ(13) C) or photosynthetic discrimination (∆) in woody angiosperms and gymnosperms that grew across a range of ca spanning at least 100 ppm. Our results suggest that much of the ca -induced changes in ci /ca occurred across ca spanning 200 to 400 ppm. These patterns imply that ca - ci will eventually approach a constant level at high ca because assimilation rates will reach a maximum and stomatal conductance of each species should be constrained to some minimum level. These analyses are not consistent with canalization towards any single strategy, particularly maintaining a constant ci . Rather, the results are consistent with the existence of a broadly conserved pattern of stomatal optimization in woody angiosperms and gymnosperms. This results in trees being profligate water users at low ca , when additional water loss is small for each unit of C gain, and increasingly water-conservative at high ca , when photosystems are saturated and water loss is large for each unit C gain. This article is protected by copyright. All rights reserved.Rising atmospheric [CO2], c(a), is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water, and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas-exchange that include maintaining a constant leaf internal [CO2], c(i), a constant drawdown in CO2 (c(a)-c(i)), and a constant c(i)/c(a). These strategies can result in drastically different consequences for leaf gas-exchange. The accuracy of Earth systems models depends in part on assumptions about generalizable patterns in leaf gas-exchange responses to varying c(a). The concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these strategies, provides a unifying framework for understanding leaf gas-exchange responses to c(a). To assess leaf gas-exchange regulation strategies, we analyzed patterns in c(i) inferred from studies reporting C stable isotope ratios (C-13) or photosynthetic discrimination () in woody angiosperms and gymnosperms that grew across a range of c(a) spanning at least 100ppm. Our results suggest that much of the c(a)-induced changes in c(i)/c(a) occurred across c(a) spanning 200 to 400ppm. These patterns imply that c(a)-c(i) will eventually approach a constant level at high c(a) because assimilation rates will reach a maximum and stomatal conductance of each species should be constrained to some minimum level. These analyses are not consistent with canalization toward any single strategy, particularly maintaining a constant c(i). Rather, the results are consistent with the existence of a broadly conserved pattern of stomatal optimization in woody angiosperms and gymnosperms. This results in trees being profligate water users at low c(a), when additional water loss is small for each unit of C gain, and increasingly water-conservative at high c(a), when photosystems are saturated and water loss is large for each unit C gain

Comparison of the Metabolic Effects of Ritonavir-Boosted Darunavir or Atazanavir Versus Raltegravir, and the Impact of Ritonavir Plasma Exposure: ACTG 5257

Background. Metabolic effects following combination antiretroviral therapy (cART) vary by regimen type. Changes in metabolic effects were assessed following cART in the AIDS Clinical Trials Group (ACTG) A5257 study, and correlated with plasma ritonavir trough concentrations (C24)

Comparison of the Metabolic Effects of Ritonavir-Boosted Darunavir or Atazanavir Versus Raltegravir, and the Impact of Ritonavir Plasma Exposure: ACTG 5257

Background. Metabolic effects following combination antiretroviral therapy (cART) vary by regimen type. Changes in metabolic effects were assessed following cART in the AIDS Clinical Trials Group (ACTG) A5257 study, and correlated with plasma ritonavir trough concentrations (C24)

Global Patterns and Controls of Nutrient Immobilization On Decomposing Cellulose In Riverine Ecosystems

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature

Regional And Watershed-Scale Coherence In the Stable-Oxygen and Carbon Isotope Ratio Time Series In Tree Rings Of Coast Redwood (Sequoia sempervirens)

Coast redwood (Sequoia sempervirens) ecosystems are strongly influenced by the presence of summer marine fog, and variation in fog frequency is closely linked to climate variation in the NE Pacific region. Because oxygen isotope composition (¹⁸O) of organic matter records distinct water sources (e.g. summertime fog vs. winter precipitation) and carbon isotopes (¹³C) are typically sensitive to humidity and water status, it then follows that inter-annual variation in tree-ring isotope ratios, which are coherent across multiple sites, should preserve a potentially powerful proxy for climate reconstruction. Here we present an analysis of a 50-year time series for both ¹⁸O and ¹³C values from subdivided tree rings obtained from multiple redwood trees at multiple sites. Within-site and between site correlations were highly significant (p < 0.01) for the ¹⁸O time series indicating a regionally coherent common forcing of ¹⁸O fractionation. Within-site and between-site correlation coefficients were lower for the ¹³C than for the ¹⁸O time series although most were still significant (at least to p < 0.05). The hypothesized reason for the differences in the correlation is that carbon isotope discrimination is more sensitive to microenvironmental and tree-level physiological variation than is ¹⁸O fractionation. Stable-isotope variation in tree-ring cellulose was similar between slope, gully and riparian micro-habitats within a single watershed, implying that minor topographic variation when sampling should not be a major concern. These results indicate that stable-isotope time series from redwood tree rings are strongly influenced by regional climate drivers and potentially valuable proxies for Pacific coastal climate variability.This item is part of the Tree-Ring Research (formerly Tree-Ring Bulletin) archive. For more information about this peer-reviewed scholarly journal, please email the Editor of Tree-Ring Research at [email protected]

Climate in the Great Lakes Region Between 14,000 and 4000 Years Ago from Isotopic Composition of Conifer Wood

The isotopic composition of ancient wood has the potential to provide information about past environments. We analyzed the d13C, d18O, and d2H of cellulose of conifer trees from several cross-sections at each of 9 sites around the Great Lakes region ranging from ~4000 to 14,000 cal BP. Isotopic values of Picea, Pinus, and Thuja species seem interchangeable for d18O and d2H comparisons, but Thuja appears distinctly different from the other 2 in its d13C composition. Isotopic results suggest that the 2 sites of near-Younger Dryas age experienced the coldest conditions, although the Gribben Basin site near the Laurentide ice sheet was relatively dry, whereas the Liverpool site 500 km south was moister. The spatial isotopic variability of 3 of the 4 sites of Two Creeks age shows evidence of an elevation effect, perhaps related to sites farther inland from the Lake Michigan shoreline experiencing warmer daytime growing season temperatures. Thus, despite floristic similarity across sites (wood samples at 7 of the sites being Picea), the isotopes appear to reflect environmental differences that might not be readily evident from a purely floristic interpretation of macrofossil or pollen identification.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202

Climate in the Great Lakes Region Between 14,000 and 4000 Years Ago from Isotopic Composition of Conifer Wood

The isotopic composition of ancient wood has the potential to provide information about past environments. We analyzed the d13C, d18O, and d2H of cellulose of conifer trees from several cross-sections at each of 9 sites around the Great Lakes region ranging from ~4000 to 14,000 cal BP. Isotopic values of Picea, Pinus, and Thuja species seem interchangeable for d18O and d2H comparisons, but Thuja appears distinctly different from the other 2 in its d13C composition. Isotopic results suggest that the 2 sites of near-Younger Dryas age experienced the coldest conditions, although the Gribben Basin site near the Laurentide ice sheet was relatively dry, whereas the Liverpool site 500 km south was moister. The spatial isotopic variability of 3 of the 4 sites of Two Creeks age shows evidence of an elevation effect, perhaps related to sites farther inland from the Lake Michigan shoreline experiencing warmer daytime growing season temperatures. Thus, despite floristic similarity across sites (wood samples at 7 of the sites being Picea), the isotopes appear to reflect environmental differences that might not be readily evident from a purely floristic interpretation of macrofossil or pollen identification.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202