Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification

Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.

Trapping of Nicotinic Acetylcholine Receptor Ligands Assayed by in vitro Cellular Studies and in vivo PET Imaging

A question relevant to nicotine addiction is how nicotine and other nicotinic receptor membrane-permeant ligands, such as the anti-smoking drug varenicline (Chantix), distribute in the brain. Previously, we found that varenicline is trapped in intracellular acidic vesicles that contain α4β2-type nicotinic receptors (α4β2Rs). Nicotine is not trapped but concentrates there. Here, combining subcellular methods with in vivo PET imaging, we present evidence that the α4β2R PET ligand, 2-FA85380 (2-FA), is trapped within α4β2R-containing acidic vesicles, while the PET ligand, Nifene, is not trapped. Additional evidence, using a fluorescent-tagged α4β2R PET ligand, Nifrolidine, identified the trapping vesicles as Golgi satellites, an organelle regulated by nicotine in neurons where α4β2Rs are expressed and traffics and processes α4β2Rs in those neurons. Using PET imaging, 2-[18F]FA kinetics in high α4β2R-expressing regions were much slower than ligand unbinding rates consistent with 2-FA trapping in Golgi satellites extending ligand residence time and 2-[18F]FA imaging of the Golgi satellites. Chloroquine, which dissipates acidic organelle pH gradients, reduced 2-[18F]FA distribution in vivo consistent with ligand trapping. In contrast, [18F]Nifene kinetics were rapid, consistent with ligand residence time reflecting ligand unbinding rates, and [18F]Nifene imaging all α4β2R pools. Specific 2-[18F]FA and [18F]Nifene signals were eliminated in β2 subunit knockout mice or by acute nicotine injections demonstrating binding to high-affinity sites on β2-containing receptors. Altogether, we find that kinetic differences in α4β2R PET ligands are consistent with their distribution among different α4β2R pools in the brain, [18F]Nifene binding and imaging all ligand-binding α4β2Rs and 2-[18F]FA imaging α4β2Rs in Golgi satellites.

Illuminate the hidden: in vivo mapping of microscale pH in the mycosphere using a novel whole-cell biosensor

The pH of an environment is both a driver and the result of diversity and functioning of microbial habitats such as the area affected by fungal hyphae (mycosphere). Here we used a novel pH-sensitive bioreporter, Synechocystis sp. PCC6803_peripHlu, and ratiometric fluorescence microscopy, to spatially and temporally resolve the mycosphere pH at the micrometre scale. Hyphae of the basidiomycete Coprionopsis cinerea were allowed to overgrow immobilised and homogeneously embedded pH bioreporters in an agarose microcosm. Signals of >700 individual cells in an area of 0.4 × 0.8 mm were observed over time and used to create highly resolved (3 × 3 µm) pH maps using geostatistical approaches. C. cinerea changed the pH of the agarose from 6.9 to ca. 5.0 after 48 h with hyphal tips modifying pH in their vicinity up to 1.8 mm. pH mapping revealed distinct microscale spatial variability and temporally stable gradients between pH 4.4 and 5.8 over distances of ≈20 µm. This is the first in vivo mapping of a mycosphere pH landscape at the microscale. It underpins the previously hypothesised establishment of pH gradients serving to create spatially distinct mycosphere reaction zones.

Submarine hydrothermal vent systems: the relevance of dynamic systems in chemical evolution and prebiotic chemistry experiments

Since their discovery, submarine hydrothermal vent systems have been pointed out as important places where chemical evolution on Earth could have occurred; and their role in the process has been highlighted. Similarly, some hypotheses have considered these systems in origin of life scenarios. In this way, many experiments have been developed, and the knowledge about these systems has increased. Due to their complexity, many experimental simulations have only included a few of the geochemical variables present in these environments, pressure and temperature. Other main variables have hardly been included, such as mineralogy, thermal and pH gradients, dissolved ions and/or redox reactions. As it has been understood, the dynamism and heterogeneity of these environments are huge, and it comprises different scales, from single vents to full hydrothermal fields. However, the vast majority of experiments focus on a specific part of these systems and do not include salinity, mineralogy and pH gradients. For this reason, in this paper, we pointed out some considerations about how this dynamism can be interpreted, and included in some models, as well their importance in prebiotic chemistry experiments and their extrapolations regarding the hypothesis about the origins of life.

Plant ecological genomics at the limits of life in the Atacama Desert

The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil–microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a “genetic goldmine” to engineer crop resilience to face climate change.

Sustained enzymatic activity and flow in crowded protein droplets

Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.

The Membrane Electrical Potential and Intracellular pH as Factors Influencing Intracellular Ascorbate Concentration and Their Role in Cancer Treatment

Ascorbate is an important element of a variety of cellular processes including the control of reactive oxygen species levels. Since reactive oxygen species are implicated as a key factor in tumorigenesis and antitumor therapy, the injection of a large amount of ascorbate is considered beneficial in cancer therapy. Recent studies have shown that ascorbate can cross the plasma membrane through passive diffusion. In contrast to absorption by active transport, which is facilitated by transport proteins (SVCT1 and SVCT2). The passive diffusion of a weak acid across membranes depends on the electrostatic potential and the pH gradients. This has been used to construct a new theoretical model capable of providing steady-state ascorbate concentration in the intracellular space and evaluating the time needed to reach it. The main conclusion of the analysis is that the steady-state intracellular ascorbate concentration weakly depends on its serum concentration but requires days of exposure to saturate. Based on these findings, it can be hypothesized that extended oral ascorbate delivery is possibly more effective than a short intravenous infusion of high ascorbate quantities.

Chemically Oscillating Reactions during the Diagenetic Formation of Ediacaran Siliceous and Carbonate Botryoids

Chemically oscillating reactions are abiotic reactions that produce characteristic, periodic patterns during the oxidation of carboxylic acids. They have been proposed to occur during the early diagenesis of sediments that contain organic matter and to partly explain the patterns of some enigmatic spheroids in malachite, phosphorite, jasper chert, and stromatolitic chert from the rock record. In this work, circularly concentric self-similar patterns are shown to form in new chemically oscillating reaction experiments with variable mixtures of carboxylic acids and colloidal silica. This is carried out to best simulate in vitro the diagenetic formation of botryoidal quartz and carbonate in two Ediacaran-age geological formations deposited after the Marinoan–Nantuo snowball Earth event in South China. Experiments performed with alkaline colloidal silica (pH of 12) show that this compound directly participates in pattern formation, whereas those with humic acid particles did not. These experiments are particularly noteworthy since they show that pattern formation is not inhibited by strong pH gradients, since the classical Belousov–Zhabotinsky reaction occurs in solution with a pH around 2. Our documentation of hundreds of classical Belousov–Zhabotinsky experiments yields a number of self-similar patterns akin to those in concretionary structures after the Marinoan–Nantuo snowball Earth event. Morphological, compositional, and size dimensional comparisons are thus established between patterns from these experiments and in botryoidal quartz and carbonate from the Doushantuo and Denying formations. Selected specimens exhibit circularly concentric layers and disseminations of organic matter in quartz and carbonate, which also occurs in association with sub-micron-size pyrite and sub-millimetre iron oxides within these patterns. X-ray absorption near edge structure (XANES) analyses of organic matter extracted from dolomite concretions in slightly younger, early Cambrian Niutitang Formation reveal the presence of carboxylic and N-bearing molecular functional groups. Such mineral assemblages, patterns, and compositions collectively suggest that diagenetic redox reactions take place during the abiotic decay of biomass, and that they involve Fe, sulphate, and organic matter, similarly to the pattern-forming experiments. It is concluded that chemically oscillating reactions are at least partly responsible for the formation of diagenetic siliceous spheroids and concretionary carbonate, which can relate to various other persistent problems in Earth and planetary sciences.

A new approach to optimize pH buffers

Buffer solutions are pervasive in chemistry, biochemistry, analytical chemistry, etc. A better understanding of buffer properties and what controls them is susceptible to be of interest in many scientific and technological fields. For instance, linear pH gradients are commonly used in electrophoresis and their optimization rests on numerical optimization of the concentrations of various weak species. It is probably generally assumed that no basic progress could be made on optimization approaches. We introduce here a new strategy to buffer optimization, based on a parametric study of the roots of the first derivative of the buffer index. In this way, it is possible to find mathematically optimal sets of parameters (pKa and concentrations). The method is applied to mixtures of 2, 3 and 4 monovalent species, which represent simple cases that do not call for overly elaborate numerical optimization techniques, but are nevertheless of practical interest in various branches of analytical chemistry.