Investigation of the Presence of Fibrillin in Sea Cucumber (Apostichopus japonicus) Body Wall by Utilizing Targeted Proteomics and Visualization Strategies

Fibrillin is an important structural protein in connective tissues. The presence of fibrillin in sea cucumber Apostichopus japonicus is still poorly understood, which limits our understanding of the role of fibrillin in the A. japonicus microstructure. The aim of this study was to clarify the presence of fibrillin in the sea cucumber A. japonicus body wall. Herein, the presence of fibrillin in sea cucumber A. japonicus was investigated by utilizing targeted proteomics and visualization strategies. The contents of three different isoforms of fibrillin with high abundance in A. japonicus were determined to be 0.96, 2.54, and 0.15 μg/g (wet base), respectively. The amino acid sequence of fibrillin (GeneBank number: PIK56741.1) that started at position 631 and ended at position 921 was selected for cloning and expressing antigen. An anti-A. japonicus fibrillin antibody with a titer greater than 1:64 000 was successfully obtained. It was observed that the distribution of fibrillin in the A. japonicus body wall was scattered and dispersed in the form of fibril bundles at the microscale. It further observed that fibrillin was present near collagen fibrils and some entangled outside the collagen fibrils at the nanoscale. Moreover, the stoichiometry of the most dominant collagen and fibrillin molecules in A. japonicus was determined to be approximately 250:1. These results contribute to an understanding of the role of fibrillin in the sea cucumber microstructure.

Stoichiometry for entry and binding properties of the Env protein of R5 T cell-tropic HIV-1 and its evolutionary variant of macrophage-tropic HIV-1

Human immunodeficiency virus type 1 typically requires a high density of CD4 for efficient entry as a mechanism to target CD4+ T cells (T-tropic), with CCR5 being used most often as the coreceptor. When target T cells are limiting, the virus can evolve to infect cells with a low density of CD4 such as macrophages (M-tropic). The entry phenotype is known to be encoded in the viral Env protein on the surface of the virus particle. Using data showing a dose response for infectivity based on CD4 surface density, we built a model consistent with T-tropic viruses requiring multiple CD4 molecules to mediate infection, whereas M-tropic viruses can infect cells using a single CD4 receptor molecule interaction. We also found that T-tropic viruses bound to the surface of cells with a low density of CD4 are released more slowly than M-tropic viruses which we modeled to be due to multiple interactions of the T-tropic virus with multiple CD4 molecules to allow the initial stable binding. Finally, we found that some M-tropic Env proteins, as the gp120 subunit, possess an enhanced affinity for CD4 compared with their T-tropic pair, indicating that the evolution of macrophage tropism can be reflected both in the closed Env trimer conformation on the virion surface and, in some cases, also in the open confirmation of gp120 Env. Collectively, these studies reveal differences in the stoichiometry of interaction of T-tropic and M-tropic viruses with CD4 and start to identify the basis of binding differences at the biochemical level.

IMPORTANCE

Human immunodeficiency virus type 1 normally targets CD4+ T cells for viral replication. When T cells are limiting, the virus can evolve to infect myeloid cells. The evolutionary step involves a change from requiring a high surface density of CD4 for entry to being able to infect cells with a low density of CD4, as is found on myeloid lineage cells such as macrophage and microglia. Viruses able to infect macrophages efficiently are most often found in the CNS late in the disease course, and such viruses may contribute to neurocognitive impairment. Here, we examine the CD4 binding properties of the viral Env protein to explore these two different entry phenotypes.

Reinforcing Protein Biochemistry: A Two-Week Experiment Studying Iron(III) Binding by the Transferrin Protein through Stoichiometric Determination, Stability Analysis, and Visualization of the Binding Site

The two-week protein biochemistry experience described herein focuses on reinforcing key biochemical concepts and achieving significant learning domain accomplishments for students (Content Knowledge, Logical Mathematical Reasoning, Visualization, Information Literacy, and Knowledge Integration) and valuable teaching opportunities for instructors. The experience encompasses an exploration of the transport protein serum transferrin as an important regulator of Fe(III) biochemistry and incorporates techniques to assess protein-metal stoichiometry and protein stability and to perform molecular visualization. Students gain practical experience in utilizing spectrophotometric analysis for constructing stoichiometric curves, in performing urea-PAGE, and in applying the PyMOL program to evaluate metal coordination at a protein binding site and the associated protein structural change. The learning and teaching accomplishments provide valuable skills that can be extended into research and translated to other teaching formats.

Sex-specific scaling of leaf phosphorus vs. nitrogen under unequal reproductive requirements in Eurya japonica, a dioecious plant

PREMISE

Previous work searching for sexual dimorphism has largely relied on the comparison of trait mean vectors between sexes in dioecious plants. Whether trait scaling (i.e., the ratio of proportional changes in covarying traits) differs between sexes, along with its functional significance, remains unclear.

METHODS

We measured 10 vegetative traits pertaining to carbon, water, and nutrient economics across 337 individuals (157 males and 180 females) of the diocious species Eurya japonica during the fruiting season in eastern China. Piecewise structural equation modeling was employed to reveal the scaling relationships of multiple interacting traits, and multivariate analysis of (co)variance was conducted to test for intersexual differences.

RESULTS

There was no sexual dimorphism in terms of trait mean vectors across the 10 vegetative traits in E. japonica. Moreover, most relationships for covarying trait pairs (17 out of 19) exhibited common scaling slopes between sexes. However, the scaling slopes for leaf phosphorus (P) vs. nitrogen (N) differed between sexes, with 5.6- and 3.0-fold increases of P coinciding with a 10-fold increase of N in male and female plants, respectively.

CONCLUSIONS

The lower ratio of proportional changes in P vs. N for females likely reflects stronger P limitation for their vegetative growth, as they require greater P investments in fruiting. Therefore, P vs. N scaling can be a key avenue allowing for sex-specific strategic optimization under unequal reproductive requirements. This study uncovers a hidden aspect of secondary sex character in dioecious plants, and highlights the use of trait scaling to understand sex-defined economic strategies.

Elemental and macromolecular plasticity of Chlamydomonas reinhardtii (Chlorophyta) in response to resource limitation and growth rate

With the ongoing differential disruption of the biogeochemical cycles of major elements that are essential for all life (carbon, nitrogen, and phosphorus), organisms are increasingly faced with a heterogenous supply of these elements in nature. Given that photosynthetic primary producers form the base of aquatic food webs, impacts of changed elemental supply on these organisms are particularly important. One way that phytoplankton cope with the differential availability of nutrients is through physiological changes, resulting in plasticity in macromolecular and elemental biomass composition. Here, we assessed how the green alga Chlamydomonas reinhardtii adjusts its macromolecular (e.g., carbohydrates, lipids, and proteins) and elemental (C, N, and P) biomass pools in response to changes in growth rate and the modification of resources (nutrients and light). We observed that Chlamydomonas exhibits considerable plasticity in elemental composition (e.g., molar ratios ranging from 124 to 971 for C:P, 4.5 to 25.9 for C:N, and 15.1 to 61.2 for N:P) under all tested conditions, pointing to the adaptive potential of Chlamydomonas in a changing environment. Exposure to low light modified the elemental and macromolecular composition of cells differently than limitation by nutrients. These observed differences, with potential consequences for higher trophic levels, included smaller cells, shifts in C:N and C:P ratios (due to proportionally greater N and P contents), and differential allocation of C among macromolecular pools (proportionally more lipids than carbohydrates) with different energetic value. However, substantial pools of N and P remained unaccounted for, especially at fast growth, indicating accumulation of N and P in forms we did not measure.

Ca2+/CaM dependent protein kinase II (CaMKII)α and CaMKIIβ hub domains adopt distinct oligomeric states and stabilities

Ca2+ /calmodulin-dependent protein kinase II (CaMKII) is a multidomain serine/threonine kinase that plays important roles in the brain, heart, muscle tissue, and eggs/sperm. The N-terminal kinase and regulatory domain is connected by a flexible linker to the C-terminal hub domain. The hub domain drives the oligomeric organization of CaMKII, assembling the kinase domains into high local concentration. Previous structural studies have shown multiple stoichiometries of the holoenzyme as well as the hub domain alone. Here, we report a comprehensive study of the hub domain stoichiometry and stability in solution. We solved two crystal structures of the CaMKIIβ hub domain that show 14-mer (3.1 Å) and 16-mer (3.4 Å) assemblies. Both crystal structures were determined from crystals grown in the same drop, which suggests that CaMKII oligomers with different stoichiometries likely coexist. To further interrogate hub stability, we employed mass photometry and temperature denaturation studies of CaMKIIβ and CaMKIIα hubs, which highlight major differences between these highly similar domains. We created a dimeric CaMKIIβ hub unit using rational mutagenesis, which is significantly less stable than the oligomer. Both hub domains populate an intermediate during unfolding. We found that multiple CaMKIIβ hub stoichiometries are present in solution and that larger oligomers are more stable. CaMKIIα had a narrower distribution of molecular weight and was distinctly more stable than CaMKIIβ.

The Sensitivity of Structure to Ionic Radius and Reaction Stoichiometry: A Crystallographic Study of Metal Coordination and Hydrogen Bonding in Barbiturate Complexes of All Five Alkali Metals Li-Cs

A systematic study has been conducted on barbiturate complexes of all five alkali metals, Li-Cs, prepared from metal carbonates or hydroxides in an aqueous solution without other potential ligands present, varying the stoichiometric ratio of metal ion to barbituric acid (BAH). Eight polymeric coordination compounds (two each for Na, K, and Rb and one each for Li and Cs) have been characterised by single-crystal X-ray diffraction. All contain some combination of barbiturate anion BA- (necessarily in a 1:1 ratio with the metal cation M+), barbituric acid, and water. All organic species and water molecules are coordinated to the metal centres via oxygen atoms as either terminal or bridging ligands. Coordination numbers range from 4 (for the Li complex) to 8 (for the Cs complex). Extensive hydrogen bonding plays a significant role in all the crystal structures, almost all of which include pairs of N-H···O hydrogen bonds linking BA- and/or BAH components into ribbons extending in one dimension. Factors influencing the structure adopted by each compound include cation size and reaction stoichiometry as well as hydrogen bonding.

Stoichiometrically Optimized Electrochromic Complex [V2 O2+ξ (OH)3-ξ ] Based Electrode: Prototype Supercapacitor with Multicolor Indicator

The systematic structure modification of metal oxides is becoming more attractive, and effective strategies for structural tunning are highly desirable for improving their practical color-modulating energy storage performances. Here, the ability of a stoichiometrically tuned oxide-hydroxide complex of porous vanadium oxide, namely [V2 O2+ξ (OH)3-ξ ]ξ = 0:3 for multifunctional electrochromic supercapacitor application is demonstrated. Theoretically, the pre-optimized oxide complex is synthesized using a simple wet chemical etching technique in its optimized stoichiometry [V2 O2+ξ (OH)3-ξ ] with ξ = 0, providing more electroactive surface sites. The multifunctional electrode shows a high charge storage property of 610 Fg-1 at 1A g-1 , as well as good electrochromic properties with high color contrast of 70% and 50% at 428 and 640 nm wavelengths, faster switching, and high coloration efficiency. When assembled in a solid-state symmetric electrochromic supercapacitor device, it exhibits an ultrahigh power density of 1066 mWcm-2 , high energy density of 246 mWhcm-2 , and high specific capacitance of 290 mFcm-2 at 0.2 mAcm-2 . A prepared prototype device displays red when fully charged, green when half charged, and blue when fully discharged. A clear evidence of optimizing the multifunctional performance of electrochromic supercapacitor by stoichiometrical tuning is presented along with demonstrating a device prototype of a 25 cm2 large device for real-life applications.

Two-way NxP fertilisation experiment on barley (Hordeum vulgare) reveals shift from additive to synergistic N-P interactions at critical phosphorus fertilisation level

In a pot experiment, we investigated synergistic interaction of N and P fertilisation on barley biomass (Hordeum vulgare) on both shoot and root level with the aim to determine whether N-P interaction would be the same for all levels of N and P fertilisation. We further aimed to determine whether there was a critical level of N and/or P fertilisation rate, above which, a decrease in resource allocation to roots (as nutrient availability increased) could be demonstrated. Barley plants were grown from seed on a nutrient poor substrate and subjected to a two-way NxP fertilisation gradient using a modified Hoagland fertilisation solution. We observed N-P interactions in shoot and root biomass, and N and P use-efficiencies. A synergistic response in biomass was observed only above a critical level of P fertilisation when P was not limiting growth. Furthermore, we found that the same incremental increase in N:P ratio of applied fertiliser elicited different responses in shoot and root biomass depending on P treatment and concluded that barley plants were less able to cope with increasing stoichiometric imbalance when P was deficient. We provide, for the first time, stoichiometric evidence that critical levels for synergistic interactions between N-P may exist in crop plants.

A Systematic Review and Comprehensive Evaluation of Human Intervention Studies to Unravel the Bioavailability of Hydroxycinnamic Acids

Significance: Hydroxycinnamic acids (HCAs) are the main phenolic acids in the western diet. Harmonizing the available information on the absorption, distribution, metabolism, and excretion (ADME) of HCAs is fundamental to unraveling the compounds responsible for their health effects. This work systematically assessed pharmacokinetics, including urinary recovery, and bioavailability of HCAs and their metabolites, based on literature reports. Recent Advances: Forty-seven intervention studies with coffee, berries, herbs, cereals, tomato, orange, grape products, and pure compounds, as well as other sources yielding HCA metabolites, were included. Up to 105 HCA metabolites were collected, mainly acyl-quinic and C6-C3 cinnamic acids. C6-C3 cinnamic acids, such as caffeic and ferulic acid, reached the highest blood concentrations (maximum plasma concentration [Cmax] = 423 nM), with time to reach Cmax (Tmax) values ranging from 2.7 to 4.2 h. These compounds were excreted in urine in higher amounts than their phenylpropanoic acid derivatives (4% and 1% of intake, respectively), but both in a lower percentage than hydroxybenzene catabolites (11%). Data accounted for 16 and 18 main urinary and blood HCA metabolites, which were moderately bioavailable in humans (collectively 25%). Critical Issues: A relevant variability emerged. It was not possible to unequivocally assess the bioavailability of HCAs from each ingested source, and data from some plant based-foods were absent or inconsistent. Future Directions: A comprehensive study investigating the ADME of HCAs derived from their most important dietary sources is urgently required. Eight key metabolites were identified and reached interesting plasma Cmax concentrations and urinary recoveries, opening up new perspectives to evaluate their bioactivity at physiological concentrations. Antioxid. Redox Signal. 40, 510-541.

Plant-soil interactions alter nitrogen and phosphorus dynamics in an advancing subarctic treeline

Treelines advance due to climate warming. The impacts of this vegetation shift on plant-soil nutrient cycling are still uncertain, yet highly relevant as nutrient availability stimulates tree growth. Here, we investigated nitrogen (N) and phosphorus (P) in plant and soil pools along two tundra-forest transects on Kola Peninsula, Russia, with a documented elevation shift of birch-dominated treeline by 70 m during the last 50 years. Results show that although total N and P stocks in the soil-plant system did not change with elevation, their distribution was significantly altered. With the transition from high-elevation tundra to low-elevation forest, P stocks in stones decreased, possibly reflecting enhanced weathering. In contrast, N and P stocks in plant biomass approximately tripled and available P and N in the soil increased fivefold toward the forest. This was paralleled by decreasing carbon (C)-to-nutrient ratios in foliage and litter, smaller C:N:P ratios in microbial biomass, and lower enzymatic activities related to N and P acquisition in forest soils. An incubation experiment further demonstrated manifold higher N and P net mineralization rates in litter and soil in forest compared to tundra, likely due to smaller C:N:P ratios in decomposing organic matter. Overall, our results show that forest expansion increases the mobilization of available nutrients through enhanced weathering and positive plant-soil feedback, with nutrient-rich forest litter releasing greater amounts of N and P upon decomposition. While the low N and P availability in tundra may retard treeline advances, its improvement toward the forest likely promotes tree growth and forest development.

Untargeted Metabolomics Based on UPLC-Q-Exactive-Orbitrap-MS/MS Revealed the Differences and Correlations between Different Parts of the Root of Paeonia lactiflora Pall

BACKGROUND

Paeonia lactiflora Pall. (PLP) is a plant with excellent ornamental and therapeutic value that can be utilized in traditional Chinese medicine as Paeoniae Radix Alba (PRA) and Paeoniae Radix Rubra (PRR). PRA must undergo the "peeling" process, which involves removing the cork and a portion of the phloem. PLP's biological function is strongly linked to its secondary metabolites, and the distribution of metabolites in different regions of the PLP rhizome causes changes in efficacy when PLP is processed into various therapeutic compounds.

METHODS

The metabolites of the cork (cor), phloem (phl), and xylem (xyl) were examined in the roots of PLP using a metabolomics approach based on UPLC-Q-Exactive-Orbitrap-MS/MS (UPLC-MS/MS), and the differential metabolites were evaluated using multivariate analysis.

RESULTS

Significant changes were observed among the cor, phl, and xyl samples. In both positive and negative ion modes, a total of 15,429 peaks were detected and 7366 metabolites were identified. A total of 525 cor-phl differential metabolites, 452 cor-xyl differential metabolites, and 328 phl-xyl differential metabolites were evaluated. Flavonoids, monoterpene glycosides, fatty acids, sugar derivatives, and carbohydrates were among the top 50 dissimilar chemicals. The key divergent metabolic pathways include linoleic acid metabolism, galactose metabolism, ABC transporters, arginine biosynthesis, and flavonoid biosynthesis.

CONCLUSION

The cor, phl, and xyl of PLP roots exhibit significantly different metabolite types and metabolic pathways; therefore, "peeling" may impact the pharmaceutical effect of PLP. This study represents the first metabolomics analysis of the PLP rhizome, laying the groundwork for the isolation and identification of PLP pharmacological activity, as well as the quality evaluation and efficacy exploration of PLP.

Seasonal variations in C/N/P/K stoichiometric characteristics in different plant organs in the various forest types of Sygera Mountain

We explored the resource acquisition and growth strategies of plants adapting to different environments, focusing on the typical forest types of Sygera Mountain: Pinus armandii, Picea likiangensis var. Linzhiensis, Abies georgei var. Smithii, and Juniperus saltuaria. Then, we analyzed the nutrient content and stoichiometric ratios of C, N, P, and K in different plant organs (leaves, branches, trunks, and roots) to examine the stoichiometric characteristics and nutrient balance mechanisms in these forests. Results show that within the same forest type, different plant organs exhibit high C and low N, P, and K levels. N content in all organs followed the order leaves > branches > roots > trunks. During the growth phase, the concentrations of P and K in PLL and AGS follow the order branches > leaves > roots > trunks. In the dormant phase, the distribution in different organs had the order leaves > branches > roots > trunks. C content remained relatively stable over time. In the same organ across different forest types, increase in nitrogen content in plant leaves is an active adaptation of JS plants, indicating that JS has a conservative growth strategy and can adapt to environmental stress. Owing to the influence of seasons, the evolution process of N and P content fluctuates, allocating nutrients to supporting and transporting organs for resource optimization and allocation. The N and P content were lower in the growth phase than in the dormant phase. Seasonal variations in the C/N, C/P, and C/K ratios in different forests were inversely correlated with changes in N, P, and K content in plant organs, supporting the "growth rate hypothesis." Stoichiometric analysis suggests that different limiting elements exist in organs across various forest types. Principal component analysis indicates that the seasonal patterns of stoichiometric ratios in the organs of different forest types show species-specific characteristics, reflecting the evolutionary nutrient utilization strategies of plant genera. In summary, plant growth in different Sygera Mountain forest types is limited by N and P, with a high tendency toward nitrogen limitation. The nutrient utilization and distribution differences among various organs during different growth stages are primarily influenced by the limited availability of environmental nutrients and inherent physiological characteristics of the plants.

The scaling of elemental stoichiometry and growth rate over the course of bamboo ontogeny

Stoichiometric rules may explain the allometric scaling among biological traits and body size, a fundamental law of nature. However, testing the scaling of elemental stoichiometry and growth to size over the course of plant ontogeny is challenging. Here, we used a fast-growing bamboo species to examine how the concentrations and contents of carbon (C), nitrogen (N) and phosphorus (P), relative growth rate (G), and nutrient productivity scale with whole-plant mass (M) at the culm elongation and maturation stages. The whole-plant C content vs M and N content vs P content scaled isometrically, and the N or P content vs M scaled as a general 3/4 power function across both growth stages. The scaling exponents of G vs M and N (and P) productivity in newly grown mass vs M relationships across the whole growth stages decreased as a -1 power function. These findings reveal the previously undocumented generality of stoichiometric allometries over the course of plant ontogeny and provide new insights for understanding the origin of ubiquitous quarter-power scaling laws in the biosphere.

Single-Molecule Imaging Reveals Differential AT1R Stoichiometry Change in Biased Signaling

G protein-coupled receptors (GPCRs) represent promising therapeutic targets due to their involvement in numerous physiological processes mediated by downstream G protein- and β-arrestin-mediated signal transduction cascades. Although the precise control of GPCR signaling pathways is therapeutically valuable, the molecular details for governing biased GPCR signaling remain elusive. The Angiotensin II type 1 receptor (AT1R), a prototypical class A GPCR with profound implications for cardiovascular functions, has become a focal point for biased ligand-based clinical interventions. Herein, we used single-molecule live-cell imaging techniques to evaluate the changes in stoichiometry and dynamics of AT1R with distinct biased ligand stimulations in real time. It was revealed that AT1R existed predominantly in monomers and dimers and underwent oligomerization upon ligand stimulation. Notably, β-arrestin-biased ligands induced the formation of higher-order aggregates, resulting in a slower diffusion profile for AT1R compared to G protein-biased ligands. Furthermore, we demonstrated that the augmented aggregation of AT1R, triggered by activation from each biased ligand, was completely abrogated in β-arrestin knockout cells. These findings furnish novel insights into the intricate relationship between GPCR aggregation states and biased signaling, underscoring the pivotal role of molecular behaviors in guiding the development of selective therapeutic agents.

A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities

Brine shrimp (Artemia) are the only animals to thrive at sodium concentrations above 4 M. Salt excretion is powered by the Na+,K+-ATPase (NKA), a heterodimeric (αβ) pump that usually exports 3Na+ in exchange for 2 K+ per hydrolyzed ATP. Artemia express several NKA catalytic α-subunit subtypes. High-salinity adaptation increases abundance of α2KK, an isoform that contains two lysines (Lys308 and Lys758 in transmembrane segments TM4 and TM5, respectively) at positions where canonical NKAs have asparagines (Xenopus α1's Asn333 and Asn785). Using de novo transcriptome assembly and qPCR, we found that Artemia express two salinity-independent canonical α subunits (α1NN and α3NN), as well as two β variants, in addition to the salinity-controlled α2KK. These β subunits permitted heterologous expression of the α2KK pump and determination of its CryoEM structure in a closed, ion-free conformation, showing Lys758 residing within the ion-binding cavity. We used electrophysiology to characterize the function of α2KK pumps and compared it to that of Xenopus α1 (and its α2KK-mimicking single- and double-lysine substitutions). The double substitution N333K/N785K confers α2KK-like characteristics to Xenopus α1, and mutant cycle analysis reveals energetic coupling between these two residues, illustrating how α2KK's Lys308 helps to maintain high affinity for external K+ when Lys758 occupies an ion-binding site. By measuring uptake under voltage clamp of the K+-congener 86Rb+, we prove that double-lysine-substituted pumps transport 2Na+ and 1 K+ per catalytic cycle. Our results show how the two lysines contribute to generate a pump with reduced stoichiometry allowing Artemia to maintain steeper Na+ gradients in hypersaline environments.

Quantifying energy and nutrient fluxes in coral reef food webs

The movement of energy and nutrients through ecological communities represents the biological 'pulse' underpinning ecosystem functioning and services. However, energy and nutrient fluxes are inherently difficult to observe, particularly in high-diversity systems such as coral reefs. We review advances in the quantification of fluxes in coral reef fishes, focusing on four key frameworks: demographic modelling, bioenergetics, micronutrients, and compound-specific stable isotope analysis (CSIA). Each framework can be integrated with underwater surveys, enabling researchers to scale organismal processes to ecosystem properties. This has revealed how small fish support biomass turnover, pelagic subsidies sustain fisheries, and fisheries benefit human health. Combining frameworks, closing data gaps, and expansion to other aquatic ecosystems can advance understanding of how fishes contribute to ecosystem functions and services.

Unique Substrate Recognition and Sodium-Substrate Binding Stoichiometry in a Bacterial Serotonin Transporter, TuriSERT

All resolved high-resolution structures of the transporters in the neurotransmitter sodium symporter (NSS) family revealed that the NSS members share common structural and mechanistic features for substrate and ion binding and transport. However, a recently reported bacterial orthologue of the human serotonin transporter (hSERT), TuriSERT, possesses a structural characteristic specific for amino acid substrate binding but does transport a biogenic amine. The unique structural feature of TuriSERT requires a novel configuration for coordinating its substrate and ions. In the present study, we characterized TuriSERT expressed in Escherichia coli cells with a fluorescent substrate by biochemical, structural, and pharmacological approaches. Substrate transport by TuriSERT requires Na+ but not Cl-. Replacement of Asp262 by asparagine renders TuriSERT Cl--dependent. Substitutions of the corresponding Na1 residues did not alter Na+ dependence on substrate transport, whereas the mutation of a Na2 site residue led to a loss of transport activity, suggesting that Na+ binds only to the Na2 site in TuriSERT. In addition, substitutions of several residues essential for recognizing 5-hydroxytryptamine (5-HT) in hSERT had little effect on 5-HT displacement potency in transport assay for TuriSERT. In contrast, mutations of the residues that are proposed to coordinate with 5-HT in our docking model dramatically reduced 5-HT displacement. Furthermore, our results indicated that all tested antidepressants showed a weak inhibitory effect on TuriSERT. The present study demonstrated the existence of a unique substrate binding site and 1:1 stoichiometry of sodium-substrate binding in TuriSERT, a novel structural finding for the NSS transporters.

Seasonal variation in C:N:P stoichiometry, nonstructural carbohydrates, and carbon isotopes of two coniferous pioneer tree species in subtropical China

The characteristics of C:N:P stoichiometry, nonstructural carbohydrate (NSC) content, and C stable isotopes and their relationships affect plant responses to environmental changes and are critical to understanding the ecosystem carbon and water cycles. We investigated the water use strategies and physiological changes of two pioneer tree species (Pinus armandii and Pinus yunnanensis) in response to seasonal drought in subtropical China. The seasonal variation in needle δ13C values, C:N:P stoichiometry, and NSC contents of the two tree species were studied in 25-year-old plantation in central Yunnan Province. The needle δ13C values of both species were highest in summer. Soluble sugars, starch and NSC content of the two tree species decreased from spring to winter, while there was no significant difference in the seasonal variation of soluble sugars/starch in P. armandii needles, the maximum soluble sugars/starch in P. yunnanensis needles was in autumn. In addition, the C, N, and P contents of the needles and the C:N and C:P ratios of the two species showed different seasonal fluctuations, whereas the N:P ratio decreased with the season. The C:N:P stoichiometry and NSC content of the needles showed significant correlations, whereas the needle δ13C was weakly correlated with C:N:P stoichiometry and NSC content. Phenotypic plasticity analysis and principal component analysis revealed that the needle nutrient characteristics (NSC and P contents and N:P ratio) and needle δ13C values were critical indicators of physiological adaptation strategies of P. armandii and P. yunnanensis for coping with seasonal variation. These results increase our understanding of the water-use characteristics of the two pioneer tree species and the dynamic balance between the NSC, C, N, and P contents of the needles.

Quantitative Super-Resolution Microscopy Reveals the Relationship between CENP-A Stoichiometry and Centromere Physical Size

Centromeric chromatin is thought to play a critical role in ensuring the faithful segregation of chromosomes during mitosis. However, our understanding of this role is presently limited by our poor understanding of the structure and composition of this unique chromatin. The nucleosomal variant, CENP-A, localizes to narrow regions within the centromere, where it plays a major role in centromeric function, effectively serving as a platform on which the kinetochore is assembled. Previous work found that, within a given cell, the number of microtubules within kinetochores is essentially unchanged between CENP-A-localized regions of different physical sizes. However, it is unknown if the amount of CENP-A is also unchanged between these regions of different sizes, which would reflect a strict structural correspondence between these two key characteristics of the centromere/kinetochore assembly. Here, we used super-resolution optical microscopy to image and quantify the amount of CENP-A and DNA within human centromere chromatin. We found that the amount of CENP-A within CENP-A domains of different physical sizes is indeed the same. Further, our measurements suggest that the ratio of CENP-A- to H3-containing nucleosomes within these domains is between 8:1 and 11:1. Thus, our results not only identify an unexpectedly strict relationship between CENP-A and microtubules stoichiometries but also that the CENP-A centromeric domain is almost exclusively composed of CENP-A nucleosomes.

Foliar elementome and functional traits relationships identify tree species niche in French Guiana rainforests

Biogeochemical niche (BN) hypothesis aims to relate species/genotype elemental composition with its niche based on the fact that different elements are involved differentially in distinct plant functions. We here test the BN hypothesis through the analysis of the 10 foliar elemental concentrations and 20 functional-morphological of 60 tree species in a French Guiana tropical forest. We observed strong legacy (phylogenic + species) signals in the species-specific foliar elemental composition (elementome) and, for the first time, provide empirical evidence for a relationship between species-specific foliar elementome and functional traits. Our study thus supports the BN hypothesis and confirms the general niche segregation process through which the species-specific use of bio-elements drives the high levels of α-diversity in this tropical forest. We show that the simple analysis of foliar elementomes may be used to test for BNs of co-occurring species in highly diverse ecosystems, such as tropical rainforests. Although cause and effect mechanisms of leaf functional and morphological traits in species-specific use of bio-elements require confirmation, we posit the hypothesis that divergences in functional-morphological niches and species-specific biogeochemical use are likely to have co-evolved.

Leaf nitrogen and phosphorus stoichiometry of the halophytes across China

Halophytes play a crucial role in the ecological restoration of saline and alkaline land and hold promising benefits to food security in China. Although a variety of aspects of halophytes have been extensively addressed, there is still a lack of overall understanding of the leaf nitrogen (N) and phosphorus (P) stoichiometric characteristics, especially at a national scale. We compiled a national dataset of 311 observations from 113 sampling sites across China to explore the changing trends and influencing factors on leaf N and P concentrations, and N:P ratio of halophytes. The results showed that leaf N concentration decreased significantly with increasing latitude (LAT), which was mainly driven by the mean annual temperature (MAT) and mean annual precipitation (MAP). The leaf P concentration increased remarkably with increasing longitude (LON), which was induced by the variation in soil total P (TP) content. The leaf N:P ratio increased as LAT increased and LON decreased, which was potentially regulated by the MAT, MAP, and soil TP content. The scaling exponents of the N-P relationship differed significantly among halophyte types and were 0.40, 0.87, and 1.39 for euhalophyte, pseudohalophyte, and recretohalophyte, respectively. The leaf N concentration exhibited significant differences among ecosystem types and halophyte types, whereas the leaf P concentration and N:P ratio remained relatively stable. In summary, the leaf N concentration and N-P scaling exponent might be the classification criteria for halophyte types from the perspective of plant nutrient resource allocation. Moreover, this study characterized the spatial distribution and allocation strategy of leaf N and P stoichiometry in halophytes by data integration analysis, providing the basic information for nutrient management in the processes of the future domestication and introduction of halophytes.

Towards a mechanistic understanding of the impacts of nitrogen deposition on producer-consumer interactions

Nitrogen (N) deposition has increased substantially since the second half of the 20th century due to human activities. This increase of reactive N into the biosphere has major implications for ecosystem functioning, including primary production, soil and water chemistry and producer community structure and diversity. Increased N deposition is also linked to the decline of insects observed over recent decades. However, we currently lack a mechanistic understanding of the effects of high N deposition on individual fitness, species richness and community structure of both invertebrate and vertebrate consumers. Here, we review the effects of N deposition on producer-consumer interactions, focusing on five existing ecological frameworks: C:N:P ecological stoichiometry, trace element ecological stoichiometry, nutritional geometry, essential micronutrients and allelochemicals. We link reported N deposition-mediated changes in producer quality to life-history strategies and traits of consumers, to gain a mechanistic understanding of the direction of response in consumers. We conclude that high N deposition influences producer quality via eutrophication and acidification pathways. This makes oligotrophic poorly buffered ecosystems most vulnerable to significant changes in producer quality. Changes in producer quality between the reviewed frameworks are often interlinked, complicating predictions of the effects of high N deposition on producer quality. The degree and direction of fitness responses of consumers to changes in producer quality varies among species but can be explained by differences in life-history traits and strategies, particularly those affecting species nutrient intake regulation, mobility, relative growth rate, host-plant specialisation, ontogeny and physiology. To increase our understanding of the effects of N deposition on these complex mechanisms, the inclusion of life-history traits of consumer species in future study designs is pivotal. Based on the reviewed literature, we formulate five hypotheses on the mechanisms underlying the effects of high N deposition on consumers, by linking effects of nutritional ecological frameworks to life-history strategies. Importantly, we expect that N-deposition-mediated changes in producer quality will result in a net decrease in consumer community as well as functional diversity. Moreover, we anticipate an increased risk of outbreak events of a small subset of generalist species, with concomitant declines in a multitude of specialist species. Overall, linking ecological frameworks with consumer life-history strategies provides a mechanistic understanding of the impacts of high N deposition on producer-consumer interactions, which can inform management towards more effective mitigation strategies.

Quality matters: Stoichiometry of resources modulates spatial feedbacks in aquatic-terrestrial meta-ecosystems

Species dispersal and resource spatial flows greatly affect the dynamics of connected ecosystems. So far, research on meta-ecosystems has mainly focused on the quantitative effect of subsidy flows. Yet, resource exchanges at heterotrophic-autotrophic (e.g. aquatic-terrestrial) ecotones display a stoichiometric asymmetry that likely matters for functioning. Here, we joined ecological stoichiometry and the meta-ecosystem framework to understand how subsidy stoichiometry mediates the response of the meta-ecosystem to subsidy flows. Our model results demonstrate that resource flows between ecosystems can induce a positive spatial feedback loop, leading to higher production at the meta-ecosystem scale by relaxing local ecosystem limitations ('spatial complementarity'). Furthermore, we show that spatial flows can also have an unexpected negative impact on production when accentuating the stoichiometric mismatch between local resources and basal species needs. This study paves the way for studies on the interdependency of ecosystems at the landscape extent.

Seaweed biogeochemistry: Global assessment of C:N and C:P ratios and implications for ocean afforestation

Algal carbon-to-nitrogen (C:N) and carbon-to-phosphorus (C:P) ratios are fundamental for understanding many oceanic biogeochemical processes, such as nutrient flux and climate regulation. We synthesized literature data (444 species, >400 locations) and collected original samples from Tasmania, Australia (51 species, 10 locations) to update the global ratios of seaweed carbon-to-nitrogen (C:N) and carbon-to-phosphorus (C:P). The updated global mean molar ratio for seaweed C:N is 20 (ranging from 6 to 123) and for C:P is 801 (ranging from 76 to 4102). The C:N and C:P ratios were significantly influenced by seawater inorganic nutrient concentrations and seasonality. Additionally, C:N ratios varied by phyla. Brown seaweeds (Ochrophyta, Phaeophyceae) had the highest mean C:N of 27.5 (range: 7.6-122.5), followed by green seaweeds (Chlorophyta) of 17.8 (6.2-54.3) and red seaweeds (Rhodophyta) of 14.8 (5.6-77.6). We used the updated C:N and C:P values to compare seaweed tissue stoichiometry with the most recently reported values for plankton community stoichiometry. Our results show that seaweeds have on average 2.8 and 4.0 times higher C:N and C:P than phytoplankton, indicating seaweeds can assimilate more carbon in their biomass for a given amount of nutrient resource. The stoichiometric comparison presented herein is central to the discourse on ocean afforestation (the deliberate replacement of phytoplankton with seaweeds to enhance the ocean biological carbon sink) by contributing to the understanding of the impact of nutrient reallocation from phytoplankton to seaweeds under large-scale seaweed cultivation.

Homogeneity- and Stoichiometry-Induced Electrical and Optical Properties of Cu-Se Thin Films by RF Sputtering Power

P-type Cu-Se thin films were deposited on glass substrates at room temperature using radio frequency magnetron sputtering by a single multi-component CuSe2 target. When using a multi-component target, the impact of the sputtering power on the homogeneity and stoichiometry within the thin films should be investigated in the depth direction to demonstrate a secondary effect on the electrical and optical properties of the thin films. Systematic characterization of the Cu-Se thin films, including the morphology, microstructure, chemical composition, and depth-directional chemical bonding state and defect structure of the thin films, revealed that the sputtering power played an important role in the homogeneity and stoichiometry of the thin films. At very low and very high sputtering power levels, the Cu-Se thin films exhibited more deviations from stoichiometry, while an optimized sputtering power resulted in more homogenous thin films with improved stoichiometry across the entire thin film thickness in the X-ray photoelectron spectroscopy depth profile, despite showing Se deficiency at all depths. A rapid decrease in carrier concentration, indicating a reduction in the net effect of total defects, was obtained at the optimized sputtering power with less deviation from stoichiometry in the Cu-Se thin films and the closest stoichiometric ratio at an intermediate depth.

Nutrient conditions mediate mycorrhizal effects on biomass production and cell wall chemistry in poplar

Large-scale biofuel production from lignocellulosic feedstock is limited by the financial and environmental costs associated with growing and processing lignocellulosic material and the resilience of these plants to environmental stress. Symbiotic associations with arbuscular (AM) and ectomycorrhizal (EM) fungi represent a potential strategy for expanding feedstock production while reducing nutrient inputs. Comparing AM and EM effects on wood production and chemical composition is a necessary step in developing biofuel feedstocks. Here, we assessed the productivity, biomass allocation and secondary cell wall (SCW) composition of greenhouse-grown Populus tremuloidesMichx. inoculated with either AM or EM fungi. Given the long-term goal of reducing nutrient inputs for biofuel production, we further tested the effects of nutrient availability and nitrogen:phosphorus stoichiometry on mycorrhizal responses. Associations with both AM and EM fungi increased plant biomass by 14-74% depending on the nutrient conditions but had minimal effects on SCW composition. Mycorrhizal plants, especially those inoculated with EM fungi, also allocated a greater portion of their biomass to roots, which could be beneficial in the field where plants are likely to experience both water and nutrient stress. Leaf nutrient content was weakly but positively correlated with wood production in mycorrhizal plants. Surprisingly, phosphorus played a larger role in EM plants compared with AM plants. Relative nitrogen and phosphorus availability were correlated with shifts in SCW composition. For AM associations, the benefit of increased wood biomass may be partially offset by increased lignin content, a trait that affects downstream processing of lignocellulosic tissue for biofuels. By comparing AM and EM effects on the productivity and chemical composition of lignocellulosic tissue, this work links broad functional diversity in mycorrhizal associations to key biofuel traits and highlights the importance of considering both biotic and abiotic factors when developing strategies for sustainable biofuel production.

Characterization of Volatile Organic Compounds in Five Celery (Apium graveolens L.) Cultivars with Different Petiole Colors by HS-SPME-GC-MS

Celery (Apium graveolens L.) is an important vegetable crop cultivated worldwide for its medicinal properties and distinctive flavor. Volatile organic compound (VOC) analysis is a valuable tool for the identification and classification of species. Currently, less research has been conducted on aroma compounds in different celery varieties and colors. In this study, five different colored celery were quantitatively analyzed for VOCs using HS-SPME, GC-MS determination, and stoichiometry methods. The result revealed that γ-terpinene, d-limonene, 2-hexenal,-(E)-, and β-myrcene contributed primarily to the celery aroma. The composition of compounds in celery exhibited a correlation not only with the color of the variety, with green celery displaying a higher concentration compared with other varieties, but also with the specific organ, whereby the content and distribution of volatile compounds were primarily influenced by the leaf rather than the petiole. Seven key genes influencing terpenoid synthesis were screened to detect expression levels. Most of the genes exhibited higher expression in leaves than petioles. In addition, some genes, particularly AgDXS and AgIDI, have higher expression levels in celery than other genes, thereby influencing the regulation of terpenoid synthesis through the MEP and MVA pathways, such as hydrocarbon monoterpenes. This study identified the characteristics of flavor compounds and key aroma components in different colored celery varieties and explored key genes involved in the regulation of terpenoid synthesis, laying a theoretical foundation for understanding flavor chemistry and improving its quality.

Adaptation versus plastic responses to temperature, light, and nitrate availability in cultured snow algal strains

Snow algal blooms are widespread, dominating low temperature, high light, and oligotrophic melting snowpacks. Here, we assessed the photophysiological and cellular stoichiometric responses of snow algal genera Chloromonas spp. and Microglena spp. in their vegetative life stage isolated from the Arctic and Antarctic to gradients in temperature (5 - 15°C), nitrate availability (1 - 10 µmol L-1), and light (50 and 500 µmol photons m-2 s-1). When grown under gradients in temperature, measured snow algal strains displayed Fv/Fm values increased by ∼115% and electron transport rates decreased by ∼50% at 5°C compared to 10 and 15°C, demonstrating how low temperatures can mimic high light impacts to photophysiology. When using carrying capacity as opposed to growth rate as a metric for determining the temperature optima, these snow algal strains can be defined as psychrophilic, with carrying capacities ∼90% higher at 5°C than warmer temperatures. All strains approached Redfield C:N stoichiometry when cultured under nutrient replete conditions regardless of temperature (5.7 ± 0.4 across all strains), whereas significant increases in C:N were apparent when strains were cultured under nitrate concentrations that reflected in situ conditions (17.8 ± 5.9). Intra-specific responses in photophysiology were apparent under high light with Chloromonas spp. more capable of acclimating to higher light intensities. These findings suggest that in situ conditions are not optimal for the studied snow algal strains, but they are able to dynamically adjust both their photochemistry and stoichiometry to acclimate to these conditions.

Different solubilizing ability of cyclodextrin derivatives for cholesterol in Niemann-Pick disease type C treatment

BACKGROUND

Niemann-Pick disease type C (NPC) is a fatal neurodegenerative disorder caused by abnormal intracellular cholesterol trafficking. Cyclodextrins (CDs), the most promising therapeutic candidates for NPC, but with concerns about ototoxicity, are cyclic oligosaccharides with dual functions of unesterified cholesterol (UC) shuttle and sink that catalytically enhance the bidirectional flux and net efflux of UC, respectively, between the cell membrane and the extracellular acceptors. However, the properties of CDs that regulate these functions and how they could be used to improve treatments for NPC are unclear.

METHODS

We estimated CD-UC complexation for nine CD derivatives derived from native α-, β-, and γ-CD with different cavity sizes, using solubility and molecular docking analyses. The stoichiometry and complexation ability of the resulting complexes were investigated in relation to the therapeutic effectiveness and toxicity of each CD derivative in NPC experimental models.

FINDINGS

We found that shuttle and sink activities of CDs are dependent on cavity size-dependent stoichiometry and substituent-associated stability of CD-UC complexation. The ability of CD derivatives to form 1:1 and 2:1 complexes with UC were correlated with their ability to normalize intracellular cholesterol trafficking serving as shuttle and with their cytotoxicity associated with cellular UC efflux acting as sink, respectively, in NPC model cells. Notably, the ability of CD derivatives to form an inclusion complex with UC was responsible for not only efficacy but ototoxicity, while a representative derivative without this ability negligibly affected auditory function, underscoring its preventability.

CONCLUSIONS

Our findings highlight the importance of strategies for optimizing the molecular structure of CDs to overcome this functional dilemma in the treatment of NPC.

Provenance variation of root C, N, P, and K stoichiometric characteristics under different diameter classes of Larix gmelinii

For exploring the difference of root stoichiometric characteristics among diameter classes and provenances, we examined the contents and stoichiometric ratios of carbon (C), nitrogen (N), phosphorus (P), and potassium (K) in three diameter classes of roots (0-1, 1-2 and 2-5 mm, respectively) of 39-year-old Larix gmelinii grown in a common garden. The results showed that root element contents and their stoichiometric ratios had significant difference among three diameter classes of roots. C content, C:N, C:P, C:K were the lowest, and N, P, K contents, N:P, and N:K were the highest in 0-1 mm diameter class roots. Compared with the 1-2 and 2-5 mm diameter class roots, 0-1 mm diameter class roots had different seasonal dynamics, which might be caused by the fact that 0-1 mm diameter class roots are absorptive roots and the other diameter class roots are transport roots. There was no provenance difference in C content among all diameter class roots, while significant provenance differences were found in N, K contents, C:N, and C:K in 0-1 mm diameter class roots, and great provenance differences for in P content, C:P, N:P, and N:K in 0-1 and 1-2 mm diameter class roots. N content, K content, C:P, N:P, and N:K in 0-1 mm diameter class roots had positive correlation with the aridity index of seed-source sites, while the P content, C:N and C:K had negative correlations. The stoichiometric characteristics were related with the diameter (or function) of roots, and had significant provenance differences in 0-1 mm (absorptive root) and 1-2 mm diameter class roots, which might be attributed to their genotypic adaptation to the environment of seed-source sites.

Feeding the fever: Complex host-pathogen dynamics along continuous resource gradients

Food has long been known to perform dual functions of nutrition and medicine, but mounting evidence suggests that complex host-pathogen dynamics can emerge along continuous resource gradients. Empirical examples of nonmonotonic responses of infection with increasing host resources (e.g., low prevalence at low and high resource supply but high prevalence at intermediate resources) have been documented across the tree of life, but these dynamics, when observed, often are interpreted as nonintuitive, idiosyncratic features of pathogen and host biology. Here, by developing generalized versions of existing models of resource dependence for within- and among-host infection dynamics, we provide a synthetic view of nonmonotonic infection dynamics. We demonstrate that where resources jointly impact two (or more) processes (e.g., growth, defense, transmission, mortality, predation), nonmonotonic infection dynamics, including alternative states, can emerge across a continuous resource supply gradient. We review the few empirical examples that concurrently measured resource effects on multiple rates and pair this with a wide range of examples in which resource dependence of multiple rates could generate nonmonotonic infection outcomes under realistic conditions. This review and generalized framework highlight the likely generality of such resource effects in natural systems and point to opportunities ripe for future empirical and theoretical work.

Ecological Stoichiometry and Stock Distribution of C, N, and P in Three Forest Types in a Karst Region of China

Ecological stoichiometry plays important roles in understanding the nutrient constraints on tree growth and development, as well in maintaining ecosystem services in forests, yet the characteristics of carbon:nitrogen:phosphorous (C:N:P) stoichiometry in forests under karst environment have not been sufficiently evaluated. In this study, concentration, distribution, stocks of Nitrogen (N) and Phosphorous (P), and ecological stoichiometry were studied in three common forest types: Masson pine natural forests (MPNF), Masson pine plantation forests (MPPF), and Slash pine plantation forests (SPPF) in a karst region of southwestern China. Results showed that N concentrations were higher in overstory than in understory and litter in the studied forests. However, P concentration was relatively low in overstory component of the forested ecosystems. Meanwhile, the N and P concentrations were higher in SPPF in the stem and litter, while these contents were higher in MPPF and MPNP in the overstory and understory. The N and P stocks ranged from 5.7-6.2 t ha^-1, and 0.5-0.6 t ha^-1 in the examined forests. The ecological stoichiometry of C:N:P in the three forest types was similar in litter (46-49:2:1), and relatively steady in soil (250-320:13-16:1) and tree leaf (100-200:14-20:1). Soil P status was the primary limiting factor in affecting tree growth in MPPF and SPPF (N:P ratio > 16), while both N and P conditions were the main restrictive factors in MPNP (N:P ratio = 15) in the study area. Our study provides scientific references and useful datasets of C:N:P stoichiometry for sustainable management of forest ecosystems in karst regions.

Nutrient stoichiometric and resorption characteristics of the petals of four common urban greening Rosaceae tree species

Objective

Nutrient resorption efficiency and stoichiometric ratios are important strategies for understanding plants. The present study examined whether or not the nutrient resorption process of plant petals is similar to that of leaves and other vegetative organs, as well as the nutrient restriction status of the whole flowering process of plants in urban ecosystems.

Methods

Four Rosaceae tree species, Prunus yedoensis Matsum, Prunus serrulata var. lannesiana, Malus micromalus Makino, and Prunus cerasifera 'Atropurpurea', were selected as urban greening species to analyze the contents of C, N, P, and K elements in the petals and their stoichiometric ratios and nutrient resorption efficiencies.

Results

The results show interspecific differences in nutrient contents, stoichiometric ratios, and nutrient resorption efficiency of the fresh petals and petal litter of the four Rosaceae species. The nutrient resorption process was similar to that of the leaves before the petals fell. The nutrient contents of petals were higher than that of leaves at the global level, but the stoichiometric ratio and nutrient resorption efficiency of petals were lower. According to the "relative resorption hypothesis", N was limiting during the entire flowering period. The nutrient resorption efficiency of petals was positively correlated with nutrient variation. The correlation between the nutrient resorption efficiency of petals with nutrient content and stoichiometric ratio of petal litter was stronger.

Conclusion

The experimental results provide scientific basis and theoretical support for the selection, scientific maintenance and fertilization management of Rosaceae tree species in urban greening.

Testing the Influence of Laser Pulse Energy and Rate in the Atom Probe Tomography Analysis of Minerals

The use of atom probe tomography (APT) for mineral analysis is contributing to fundamental studies in Earth Sciences. Meanwhile, the need for standardization of this technique is becoming evident. Pending the use of mineral standards, the optimization of analysis parameters is needed to facilitate the study of different mineral groups in terms of data collection and quality. The laser pulse rate and energy are variables that highly affect the atom evaporation process occurring during APT analysis, and their testing is important to forecast mineral behavior and obtain the best possible data. In this study, five minerals representative of major groups (albite, As-pyrite, barite, olivine, and monazite) were analyzed over a range of laser pulse energies (10-50 pJ) and rates (100-250 kHz) to assess output parameter quality and evaluate compositional estimate stoichiometry. Among the studied minerals, As-pyrite, with the higher thermal conductivity and lower band gap, was the most affected by the laser pulse variation. Chemical composition estimates equal or close to the general chemical formula were achieved for monazite and As-pyrite. The analysis of multihit events has proved to be the best strategy to verify the efficacy of the evaporation process and to evaluate the best laser pulse setting for minerals.

Tree canopy cover affects basal resources and nutrient profiles of Aedes and Culex larvae in cemetery vases in New Orleans, Louisiana, United States

Cemetery vases are important habitat for vector mosquito production, yet there is limited understanding on their food web dynamics and how they vary across environmental gradients. Tree cover is one factor that varies widely across cemeteries, and influence food webs by means of detrital inputs, temperature mediation, and light availability. Such information can be important for determining mosquito adult body size, fecundity, and competition outcomes, all of which may influence mosquito population and disease risk. This study evaluates the relationship between tree canopy cover and indicators of basal resources for Aede aegypti (L.), Aedes albopictuss (Skuse), and Culex quinquefasciatus (Say) larvae, such as stable isotopes (δ13C and δ15N) and nutrient stoichiometry in cemeteries of New Orleans, Louisiana (USA). Stable isotope values suggest that larvae feed directly on the Particulate Organic Matter (POM) suspended in the vase's water, and that POM composition influence the nutrient profiles of mosquito larvae. The POM of open canopy vases had higher δ13C values, than that of closed canopy vases indicating differences in relative proportion of basal carbon sources, with open canopy POM having a lower proportion of allochthonous carbon, and a higher proportion of authoctonous carbon. Accordingly, mosquito larvae collected from open canopy vases had higher δ13C values, and higher C:N than larvae from closed canopy vases. The results of this study show a shift in food web dynamics driven by canopy cover in cemetery vases that directly influence the nutrient profiles of mosquito larvae. The implications for mosquito ecology, and vector management are discussed.

Foliar nutrient resorption stoichiometry and microbial phosphatase catalytic efficiency together alleviate the relative phosphorus limitation in forest ecosystems

Understanding how plants adapt to spatially heterogeneous phosphorus (P) supply is important to elucidate the effect of environmental changes on ecosystem productivity. Plant P supply is concurrently controlled by plant internal conservation and external acquisition. However, it is unclear how climate, soil, and microbes influence the contributions and interactions of the internal and external pathways for plant P supply. Here, we measured P and nitrogen (N) resorption efficiency, litter and soil acid phosphatase (AP) catalytic parameters (V_max(s) and K_m ), and soil physicochemical properties at four sites spanning from cold temperate to tropical forests. We found that the relative P limitation to plants was generally higher in tropical forests than temperate forests, but varied greatly among species and within sites. In P-impoverished habitats, plants resorbed more P than N during litterfall to maintain their N : P stoichiometric balance. In addition, once ecosystems shifted from N-limited to P-limited, litter- and soil-specific AP catalytic efficiency (V_max(s) /K_m ) increased rapidly, thereby enhancing organic P mineralization. Our findings suggested that ecosystems develop a coupled aboveground-belowground strategy to maintain P supply and N : P stoichiometric balance under P-limitation. We also highlighted that N cycle moderates P cycles and together shape plant P acquisition in forest ecosystems.

Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs

Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.

C, N, and P stoichiometry for leaf litter of 62 woody species in a subtropical evergreen broadleaved forest

To understand leaf litter stoichiometry in a subtropical evergreen broadleaved forest, we measured the contents of carbon (C), nitrogen (N) and phosphorus (P) in leaf litters of 62 main woody species in a natural forest of C. kawakamii Nature Reserve in Sanming, Fujian Province. Differences in leaf litter stoichiometry were analyzed across leaf forms (evergreen, deciduous), life forms (tree, semi-tree or shrub), and main families. Additionally, the phylogenetic signal was measured by Blomberg's K to explore the correlation between family level differentiation time and litter stoichiometry. Our results showed that the contents of C, N and P in the litter of 62 woody species were 405.97-512.16, 4.45-27.11, and 0.21-2.53 g·kg^-1, respectively. C/N, C/P and N/P were 18.6-106.2, 195.9-2146.8, and 3.5-68.9, respectively. Leaf litter P content of evergreen tree species was significantly lower than that of deciduous tree species, and C/P and N/P of evergreen tree species were significantly higher than those of deciduous tree species. There was no significant difference in C, N content and C/N between the two leaf forms. There was no significant difference in litter stoichiometry among trees, semi-trees and shrubs. Effects of phylogeny on C, N content and C/N in leaf litter was significant, but not on P content, C/P and N/P. Family differentiation time was negatively correlated with leaf litter N content, and positively correlated with C/N. Leaf litter of Fagaceae had high C and N contents, C/P and N/P, and low P content and C/N, with an opposite trend for Sapidaceae. Our findings indicated that litter in subtropical forest had high C, N content and N/P, but low P content, C/N, and C/P, compared with the global scale average value. Litter of tree species in older sequence of evolutionary development had lower N content but higher C/N. There was no difference of leaf litter stoichiometry among life forms. There were significant differences in P content, C/P, and N/P between different leaf forms, with a characteristic of convergence.

Stoichiometric homeostasis of N:P ratio drives species-specific symbiotic N fixation inhibition under N addition

Introduction

Symbiotic N fixation inhibition induced by N supply to legumes is potentially regulated by the relative N and P availability in soil. However, the specific responses of different legume species to changes in N:P availability remain unclear, and must be better understood to optimize symbiotic N fixation inputs under N enrichment. This study investigated mechanisms by which soil N and P supply influence the symbiotic N fixation of eight legume species, to quantify the inter-specific differences, and to demonstrate how these differences can be determined by the stoichiometric homeostasis in N:P ratios (HN:P).

Methods

Eight herbaceous legume species were grown separately in outdoor pots and treated with either no fertilizer (control), N fertilizer (14 g N m-2), P fertilizer (3.5 g P m-2) or both N and P fertilizer. Plant nutrients, stoichiometric characteristics, root biomass, non-structural carbohydrates (NSC), rhizosphere chemistry, P mobilization, root nodulation and symbiotic N fixation were measured.

Results

N addition enhanced rhizosphere P mobilization but drove a loss of root biomass and root NSC via exudation of P mobilization compound (organic acid), especially so in treatments without P addition. N addition also induced a 2-14% or 14-36% decline in symbiotic N fixation per plant biomass by legumes in treatments with or without P addition, as a result of decreasing root biomass and root NSC. The changes in symbiotic N fixation were positively correlated with stoichiometric homeostasis of N:P ratios in intact plants without root nodules, regardless of P additions.

Discussion

This study indicates that N addition can induce relative P limitations for growth, which can stimulate rhizosphere P mobilization at the expense of root biomass and carbohydrate concentrations, reducing symbiotic N fixation in legumes. Legume species that had less changes in plant N:P ratio, such as Lespedeza daurica and Medicago varia maintained symbiotic N fixation to a greater extent under N addition.

Consistent physiological, ecological and evolutionary effects of fire regime on conservative leaf economics strategies in plant communities

The functional response of plant communities to disturbance is hypothesised to be controlled by changes in environmental conditions and evolutionary history of species within the community. However, separating these influences using direct manipulations of repeated disturbances within ecosystems is rare. We evaluated how 41 years of manipulated fire affected plant leaf economics by sampling 89 plant species across a savanna-forest ecotone. Greater fire frequencies created a high-light and low-nitrogen environment, with more diverse communities that contained denser leaves and lower foliar nitrogen content. Strong trait-fire coupling resulted from the combination of significant intraspecific trait-fire correlations being in the same direction as interspecific trait differences arising through the turnover in functional composition along the fire-frequency gradient. Turnover among specific clades helped explain trait-fire trends, but traits were relatively labile. Overall, repeated burning led to reinforcing selective pressures that produced diverse plant communities dominated by conservative resource-use strategies and slow soil nitrogen cycling.

Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.

Role of Monomer/Tetramer Equilibrium of Rod Visual Arrestin in the Interaction with Phosphorylated Rhodopsin

The phototransduction cascade in vertebrate rod visual cells is initiated by the photoactivation of rhodopsin, which enables the activation of the visual G protein transducin. It is terminated by the phosphorylation of rhodopsin, followed by the binding of arrestin. Here we measured the solution X-ray scattering of nanodiscs containing rhodopsin in the presence of rod arrestin to directly observe the formation of the rhodopsin/arrestin complex. Although arrestin self-associates to form a tetramer at physiological concentrations, it was found that arrestin binds to phosphorylated and photoactivated rhodopsin at 1:1 stoichiometry. In contrast, no complex formation was observed for unphosphorylated rhodopsin upon photoactivation, even at physiological arrestin concentrations, suggesting that the constitutive activity of rod arrestin is sufficiently low. UV-visible spectroscopy demonstrated that the rate of the formation of the rhodopsin/arrestin complex well correlates with the concentration of arrestin monomer rather than the tetramer. These findings indicate that arrestin monomer, whose concentration is almost constant due to the equilibrium with the tetramer, binds to phosphorylated rhodopsin. The arrestin tetramer would act as a reservoir of monomer to compensate for the large changes in arrestin concentration in rod cells caused by intense light or adaptation.

Ecosystem-level effects of re-oligotrophication and N:P imbalances in rivers and estuaries on a global scale

Trends and ecological consequences of phosphorus (P) decline and increasing nitrogen (N) to phosphorus (N:P) ratios in rivers and estuaries are reviewed and discussed. Results suggest that re-oligotrophication is a dominant trend in rivers and estuaries of high-income countries in the last two-three decades, while in low-income countries widespread eutrophication occurs. The decline in P is well documented in hundreds of rivers of United States and the European Union, but the biotic response of rivers and estuaries besides phytoplankton decline such as trends in phytoplankton composition, changes in primary production, ecosystem shifts, cascading effects, changes in ecosystem metabolism, etc., have not been sufficiently monitored and investigated, neither the effects of N:P imbalance. N:P imbalance has significant ecological effects that need to be further investigated. There is a growing number of cases in which phytoplankton biomass have been shown to decrease due to re-oligotrophication, but the potential regime shift from phytoplankton to macrophyte dominance described in shallow lakes has been documented only in a few rivers and estuaries yet. The main reasons why regime shifts are rarely described in rivers and estuaries are, from one hand the scarcity of data on macrophyte cover trends, and from the other hand physical factors such as peak flows or high turbidity that could prevent a general spread of submerged macrophytes as observed in shallow lakes. Moreover, re-oligotrophication effects on rivers may be different compared to lakes (e.g., lower dominance of macrophytes) or estuaries (e.g., limitation of primary production by N instead of P) or may be dependent on river/estuary type. We conclude that river and estuary re-oligotrophication effects are complex, diverse and still little known, and in some cases are equivalent to those described in shallow lakes, but the regime shift is more likely to occur in mid to high-order rivers and shallow estuaries.

Stoichiometry, Orbital Configuration, and Metal-to-Insulator Transition in Nd0.8Sr0.2NiO3 Films

The discovery of superconductivity in the infinite-layer nickelate Nd_0.8Sr_0.2NiO₂ has motivated tremendous efforts for its significance toward the understanding of high-temperature superconductivity. However, the synthesis of infinite-layer nickelates is instable and has become a hindrance to experimental progress. Optimizing the growth of precursor Nd_0.8Sr_0.2NiO₃ by pulsed laser deposition is crucial for obtaining infinite-layer nickelates. By systematically investigating the growth of Nd_0.8Sr_0.2NiO₃ with wide range of conditions, we found that the laser fluence plays a critical role in determining the stoichiometry, lattice structure, and electronic properties. A higher Ni deficiency and larger c-axis lattice constant appeared with the lower laser fluence. At 0.6 J/cm², the Ni deficiency is as large as 25%. According to X-ray absorption spectra and X-ray linear dichroism, we further find that (i) there are no obvious changes of the Ni valence and (ii) the energy level of the d_x²-y² orbital gradually increases relative to the d_3z²-r² orbital with increasing Ni deficiency. What is more, the onset temperature and magnitude of the resistivity change at the metal-to-insulator transitions (MITs) also are found to decrease with increasing laser fluence during the growth.

Direct Observation of Off-Stoichiometry-Induced Phase Transformation of 2D CdSe Quantum Nanosheets

Crystal structures determine material properties, suggesting that crystal phase transformations have the potential for application in a variety of systems and devices. Phase transitions are more likely to occur in smaller crystals; however, in quantum-sized semiconductor nanocrystals, the microscopic mechanisms by which phase transitions occur are not well understood. Herein, the phase transformation of 2D CdSe quantum nanosheets caused by off-stoichiometry is revealed, and the progress of the transformation is directly observed by in situ transmission electron microscopy. The initial hexagonal wurtzite-CdSe nanosheets with atomically uniform thickness are transformed into cubic zinc blende-CdSe nanosheets. A combined experimental and theoretical study reveals that electron-beam irradiation can change the stoichiometry of the nanosheets, thereby triggering phase transformation. The loss of Se atoms induces the reconstruction of surface atoms, driving the transformation from wurtzite-CdSe(11 2 ¯ $\bar{2}$ 0) to zinc blende-CdSe(001) 2D nanocrystals. Furthermore, during the phase transformation, unconventional dynamic phenomena occur, including domain separation. This study contributes to the fundamental understanding of the phase transformations in 2D quantum-sized semiconductor nanocrystals.

Conformational antigenic heterogeneity as a cause of the persistent fraction in HIV-1 neutralization

Background Neutralizing antibodies (NAbs) protect against HIV-1 acquisition in animal models and show promise in treatment of infection. They act by binding to the viral envelope glycoprotein (Env), thereby blocking its receptor interactions and fusogenic function. The potency of neutralization is largely determined by affinity. Less well explained is the persistent fraction, the plateau of remaining infectivity at the highest antibody concentrations. Results We observed different persistent fractions for NAb neutralization of pseudovirus derived from two Tier-2 isolates of HIV-1, BG505 (Clade A) and B41 (Clade B): it was pronounced for B41 but not BG505 neutralization by NAb PGT151, directed to the interface between the outer and transmembrane subunits of Env, but negligible for either virus by NAb PGT145 to an apical epitope. Autologous neutralization by poly- and monoclonal NAbs from rabbits immunized with soluble native-like B41 trimer also left substantial persistent fractions. These NAbs largely target a cluster of epitopes in a hole in the dense glycan shield of Env around residue 289. We partially depleted B41-virion populations by incubating them with PGT145- or PGT151-conjugated beads. Each depletion reduced the sensitivity to the depleting NAb and enhanced it to the other. Autologous neutralization by the rabbit NAbs was reduced for PGT145-depleted and enhanced for PGT151-depleted B41 pseudovirus. Those changes in sensitivity encompassed both potency and the persistent fraction. We then compared soluble native-like BG505 and B41 Env trimers affinity-purified by one of three NAbs: 2G12, PGT145, or PGT151. Surface plasmon resonance showed differences among the fractions in antigenicity, including kinetics and stoichiometry, congruently with the differential neutralization. The large persistent fraction after PGT151 neutralization of B41 was attributable to low stoichiometry, which we explained structurally by the conformational plasticity of B41 Env. Conclusion Distinct antigenic forms even of clonal HIV-1 Env, detectable among soluble native-like trimer molecules, are distributed over virions and may profoundly mold neutralization of certain isolates by certain NAbs. Affinity purifications with some antibodies may yield immunogens that preferentially expose epitopes for broadly active NAbs, while shielding less cross-reactive ones. NAbs reactive with multiple conformers will together reduce the persistent fraction after passive and active immunization.

Comparative study of characteristic compounds of three species of truffle

The Panxi area in Sichuan Province is the main area for the production of truffles in China, and several species of truffle are known to exist in this region. Nevertheless, it is unclear what the differences in chemical composition between the truffles are. Using an ultra-high-performance liquid chromatography quadrupole/orbitrap high-resolution mass spectrometry coupled with Compound Discoverer 3.0, we identified chemical components in three mainly known truffles from the Panxi region. Further analysis of chemical composition differences was conducted using principal component analysis, and orthogonal partial least squares discriminant analysis. Note that, 78.9% of the variance was uncovered by the principal component analysis model. As a result of the orthogonal partial least squares discriminant analysis model, the three species of truffles (Tuber pesudohimalayense, Tuber indicum, and Tuber sinense) from Panxi were better discriminated, with R² X, R² Y, and Q² being 0.821, 0.993, and 0.947, respectively. In this study, 87 components were identified. T. pesudohimalayense contained significantly higher levels of nine different compounds than the other two species. Hence, it was possible to identify similarities and differences between three species of truffles from Panxi in terms of chemical composition. This can be used as a basis for quality control.

m6A-SAC-seq for quantitative whole transcriptome m6A profiling

N⁶-methyladenosine (m⁶A) is the most abundant mRNA modification in mammalian cells, regulating many physiological processes. Here we describe a method for base-resolution, quantitative m⁶A sequencing in the whole transcriptome. The enzyme and small-molecule cofactor used in this protocol are prepared by recombinant protein expression and organic synthesis, respectively. Then the library can be prepared from various types of RNA samples using a ligation-based strategy, with m⁶A modifications being labeled by the enzyme and cofactor. Detailed instructions on ensuing data analysis are also included in this protocol. The method generates highly reproducible results, uncovering 31,233-129,263 sites using as little as 2 ng of poly A⁺ RNA. These identified sites correspond well with previous m⁶A profiling results, covering over 65% of peaks detected by the antibody-based approaches. Compared with other currently available methods, this method can be applied to various types of biological samples, including fresh and frozen tissues as well as formalin-fixed paraffin-embedded samples, providing a quantitative method to uncover new insights into m⁶A biology. The protocol requires basic expertise in molecular biology, recombinant protein expression and organic synthesis. The whole protocol can be done in 15 days, with the library preparation taking 5 days.

Phosphorus limitation of early growth differs between nitrogen-fixing and nonfixing dry tropical forest tree species

Tropical forests are often characterized by low soil phosphorus (P) availability, suggesting that P limits plant performance. However, how seedlings from different functional types respond to soil P availability is poorly known but important for understanding and modeling forest dynamics under changing environmental conditions. We grew four nitrogen (N)-fixing Fabaceae and seven diverse non-N-fixing tropical dry forest tree species in a shade house under three P fertilization treatments and evaluated carbon (C) allocation responses, P demand, P-use, investment in P acquisition traits, and correlations among P acquisition traits. Nitrogen fixers grew larger with increasing P addition in contrast to non-N fixers, which showed fewer responses in C allocation and P use. Foliar P increased with P addition for both functional types, while P acquisition strategies did not vary among treatments but differed between functional types, with N fixers showing higher root phosphatase activity (RPA) than nonfixers. Growth responses suggest that N fixers are limited by P, but nonfixers may be limited by other resources. However, regardless of limitation, P acquisition traits such as mycorrhizal colonization and RPA were nonplastic across a steep P gradient. Differential limitation among plant functional types has implications for forest succession and earth system models.