Membrane simulations mimicking acidic pH reveal increased thickness and negative curvature in a bilayer consisting of lysophosphatidylcholines and free fatty acids

Phospholipids are key components of biological membranes and their lipolysis with phospholipase A₂ (PLA₂) enzymes occurs in different cellular pH environments. Since no studies are available on the effect of pH on PLA₂-modified phospholipid membranes, we performed 50-ns atomistic molecular dynamics simulations at three different pH conditions (pH 9.0, 7.5, and 5.5) using a fully PLA₂-hydrolyzed phosphatidylcholine (PC) bilayer which consists solely of lysophosphatidylcholine and free fatty acid molecules. We found that a decrease in pH results in lateral squeezing of the membrane, i.e. in decreased surface area per headgroup. Thus, at the decreased pH, the lipid hydrocarbon chains had larger S_CD order parameter values, and also enhanced membrane thickness, as seen in the electron density profiles across the membrane. From the lateral pressure profiles, we found that the values of spontaneous curvature of the two opposing monolayers became negative when the pH was decreased. At low pH, protonation of the free fatty acid headgroups reduces their mutual repulsion and accounts for the pH dependence of all the above-mentioned properties. The altered structural characteristics may significantly affect the overall surface properties of biomembranes in cellular vesicles, lipid droplets, and plasma lipoproteins, play an important role in membrane fission and fusion, and modify interactions between membrane lipids and the proteins embedded within them.     

Pennsylvanian palynofloras from the Itu rhythmites (Itararé Subgroup, Paraná Basin) in São Paulo State, Brazil

The rhythmites of Itu present the best exposures of glacial varvites known in the Paraná Basin, and constitute a classic geological monument related to the Late Palaeozoic Gondwanan glaciation. Palynological results in this paper are based on rhythmites from two quarries in Itu area, central-eastern State of São Paulo, Brazil, including correlate levels of the “Itu Varvite Park”, as well as based on samples from the borehole IT-IG-85 (at 171 and 228 m) drilled also in the Itu City. Well-preserved indigenous miospores and microphytoplankton elements have been recorded. The former comprise 15 spore species and 19 pollen species, of which three are recorded for the first time in the Brazilian part of the Paraná Basin (Verrucosisporites cf. V. andersonii, Convolutispora archangelskyi and Caheniasaccites verrucosus). Microalgae include prasinophyceans (Leiosphaeridia sp., Tasmanites sp., Deusilites tenuistriatus), chlorophyceans (Botryococcus braunii) and zignemataceans (Tetraporina). The palynological content confirms a late Pennsylvanian (Kasimovian/Gzhelian) age for these rhythmites, which are assigned to the Crucisaccites monoletus interval Zone, based on the record of the eponymous pollen species and Scheuringipollenites maximus. Although very scarce, prasinophycean algae suggest low salinity marine conditions.     

Constitutive mTOR activation in TSC mutants sensitizes cells to energy starvation and genomic damage via p53

Miscoordination of growth and proliferation with the cellular stress response can lead to tumorigenesis. Mammalian target of rapamycin (mTOR), a central cell growth controller, is highly activated in some malignant neoplasms, and its clinical implications are under extensive investigation. We show that constitutive mTOR activity amplifies p53 activation, in vitro and in vivo, by stimulating p53 translation. Thus, loss of TSC1 or TSC2, the negative regulators of mTOR, results in dramatic accumulation of p53 and apoptosis in response to stress conditions. In other words, the inactivation of mTOR prevents cell death by nutrient stress and genomic damage via p53. Consistently, we also show that p53 is elevated in TSC tumors, which rarely become malignant. The coordinated relationship between mTOR and p53 during cellular stress provides a possible explanation for the benign nature of hamartoma syndromes, including TSC. Clinically, this also suggests that the efficacy of mTOR inhibitors in anti-neoplastic therapy may also depend on p53 status, and mTOR inhibitors may antagonize the effects of genotoxic chemotherapeutics.     

Role of Broiler Carcasses and Processing Plant Air in Contamination of Modified-Atmosphere-Packaged Broiler Products with Psychrotrophic Lactic Acid Bacteria

Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage organisms in modified-atmosphere-packaged (MAP), cold-stored meat products. To determine if incoming broilers or the production plant environment is a source of spoilage LAB, a total of 86, 122, and 447 LAB isolates from broiler carcasses, production plant air, and MAP broiler products, respectively, were characterized using a library of HindIII restriction fragment length polymorphism (RFLP) patterns of the 16 and 23S rRNA genes as operational taxonomic units in numerical analyses. Six hundred thirteen LAB isolates from the total of 655 clustered in 29 groups considered to be species specific. Sixty-four percent of product isolates clustered either with Carnobacterium divergens or with Carnobacterium maltaromaticum type strains. The third major product-associated cluster (17% of isolates) was formed by unknown LAB. Representative strains from these three clusters were analyzed for the phylogeny of their 16S rRNA genes. This analysis verified that the two largest RFLP clusters consisted of carnobacteria and showed that the unknown LAB group consisted of Lactococcus spp. No product-associated LAB were detected in broiler carcasses sampled at the beginning of slaughter, whereas carnobacteria and lactococci, along with some other specific meat spoilage LAB, were recovered from processing plant air at many sites. This study reveals that incoming broiler chickens are not major sources of psychrotrophic spoilage LAB, whereas the detection of these organisms from the air of the processing environment highlights the role of processing facilities as sources of LAB contamination.     

Role of the V-ATPase in regulation of the vacuolar fission-fusion equilibrium

Like numerous other eukaryotic organelles, the vacuole of the yeast Saccharomyces cerevisiae undergoes coordinated cycles of membrane fission and fusion in the course of the cell cycle and in adaptation to environmental conditions. Organelle fission and fusion processes must be balanced to ensure organelle integrity. Coordination of vacuole fission and fusion depends on the interactions of vacuolar SNARE proteins and the dynamin-like GTPase Vps1p. Here, we identify a novel factor that impinges on the fusion-fission equilibrium: the vacuolar H(+)-ATPase (V-ATPase) performs two distinct roles in vacuole fission and fusion. Fusion requires the physical presence of the membrane sector of the vacuolar H(+)-ATPase sector, but not its pump activity. Vacuole fission, in contrast, depends on proton translocation by the V-ATPase. Eliminating proton pumping by the V-ATPase either pharmacologically or by conditional or constitutive V-ATPase mutations blocked salt-induced vacuole fragmentation in vivo. In living cells, fission defects are epistatic to fusion defects. Therefore, mutants lacking the V-ATPase display large single vacuoles instead of multiple smaller vacuoles, the phenotype that is generally seen in mutants having defects only in vacuolar fusion. Its dual involvement in vacuole fission and fusion suggests the V-ATPase as a potential regulator of vacuolar morphology and membrane dynamics.     

Advances in application of machine learning to life cycle assessment: a literature review

Purpose

Life Cycle Assessment (LCA) is the process of systematically assessing impacts when there is an interaction between the environment and human activity. Machine learning (ML) with LCA methods can help contribute greatly to reducing impacts. The sheer number of input parameters and their uncertainties that contribute to the full life cycle make a broader application of ML complex and difficult to achieve. Hence a systems engineering approach should be taken to apply ML in isolation to aspects of the LCA. This study addresses the challenge of leveraging ML methods to deliver LCA solutions. The overarching hypothesis is that: LCA underpinned by ML methods and informed by dynamic data paves the way to more accurate LCA while supporting life cycle decision making.

Methods

In this study, previous research on ML for LCA were considered, and a literature review was undertaken.

Results

The results showed that ML can be a useful tool in certain aspects of the LCA. ML methods were shown to be applied efficiently in optimization scenarios in LCA. Finally, ML methods were integrated as part of existing inventory databases to streamline the LCA across many use cases.

Conclusions

The conclusions of this article summarise the characteristics of existing literature and provide suggestions for future work in limitations and gaps which were found in the literature.

     

Human Adenosine A2A Receptor Binds Calmodulin with High Affinity in a Calcium-Dependent Manner

Understanding how ligands bind to G-protein-coupled receptors and how binding changes receptor structure to affect signaling is critical for developing a complete picture of the signal transduction process. The adenosine A2A receptor (A2AR) is a particularly interesting example, as it has an exceptionally long intracellular carboxyl terminus, which is predicted to be mainly disordered. Experimental data on the structure of the A2AR C-terminus is lacking, because published structures of A2AR do not include the C-terminus. Calmodulin has been reported to bind to the A2AR C-terminus, with a possible binding site on helix 8, next to the membrane. The biological meaning of the interaction as well as its calcium dependence, thermodynamic parameters, and organization of the proteins in the complex are unclear. Here, we characterized the structure of the A2AR C-terminus and the A2AR C-terminus-calmodulin complex using different biophysical methods, including native gel and analytical gel filtration, isothermal titration calorimetry, NMR spectroscopy, and small-angle X-ray scattering. We found that the C-terminus is disordered and flexible, and it binds with high affinity (K_d = 98 nM) to calmodulin without major conformational changes in the domain. Calmodulin binds to helix 8 of the A2AR in a calcium-dependent manner that can displace binding of A2AR to lipid vesicles. We also predicted and classified putative calmodulin-binding sites in a larger group of G-protein-coupled receptors.