Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses

Impact of environmental salinity on the MAPK-NFAT5 pathway in Trachemys scripta elegans and its role in osmoregulaton

Globally, sea level rise (SLR) leads to salinization of coastal freshwater, in where organisms might be affected and in turn promote osmoregulation and adaptation in response to freshwater salinization. Trachemys scripta elegans a freshwater turtle species, exhibits remarkable tolerance to varying salinity environments, yet the underlying regulatory mechanisms remain poorly understood. This study aimed to elucidate the molecular mechanisms of osmoregulation in this species based on previous RNA-seq data. Our findings revealed that when exposed to 5 PSU (5 ‰) and 15 PSU (15 ‰) salinities, the turtles exhibited increased concentrations of ions (Na+, K+) and urea in urine, along with elevated osmotic pressures in both plasma and urine. Additionally, the protein levels of aquaporins (AQPs) and transporters of ions and organic osmolytes in the kidney were upregulated in saline water. Notably, the transcriptional level of the hypertonic regulator NFAT5 was significantly elevated, accompanied by an increase in phosphorylated NFAT5 levels in the nucleus of renal tubular epithelial cells. Furthermore, we observed upregulated phosphorylated levels of MAPKs in saline water. The use of MAPK inhibitors effectively blocked the transcription of NFAT5 and osmoregulatory target genes. Collectively, these results suggest that T. scripta elegans activates the MAPK-NFAT5 signaling pathway to modulate osmotic pressure in adaptation to saline water environments. Our study provides valuable insights into the osmoregulatory responses of aquatic organisms to saline environments and aids in understanding the adaptability of organisms inhabiting coastal areas facing rising sea levels.

Transcriptome Analysis of Stinging Catfish (Heteropneustes fossilis) Kidney Reveals its Role During Adaptation to Hypertonic Environment

The facultative air-breather stinging catfish Heteropneustes fossilis can easily adapt to anisotonic environment up to a level of 6 ppt. The teleost kidney is an essential osmoregulatory organ and plays a vital role in immune system maintenance. We took kidney samples from control and 100 mM NaCl-treated stinging catfish to study the molecular responses to salinity stress by looking at the DEGs. We used high-throughput sequencing followed by de novo transcriptome assembly to analyze the transcriptome of the fish. A total of 89,813 unigene transcripts with 47.28% GC content and 901 bp average length were produced during the final contig assembly. A BLAST search revealed that 45,855 unigenes had a considerable amount of similarity to sequences found in the Swiss-Prot and Ref-Seq databases. Comparative transcriptome analysis revealed that 1660 genes were differentially expressed (693 were upregulated and 967 downregulated) in the kidneys of fish treated with NaCl compared to control kidneys. Several GO pathway terms, including "inflammatory response" and "neutrophil chemotaxis" in the biological process category, "cytoplasm" and "integral component of membrane" in the cellular component category, and "metal ion binding" and "DNA binding," in the molecular function category, were found to be significantly over-represented by enrichment and functional analysis of the DEGs. In addition, there was an overrepresentation of KEGG pathways like "chemokine signaling pathway," "cytokine-cytokine receptor interaction," and "metabolic pathways." The current work demonstrates that tolerance to hypertonic environmental stress necessitates the activation of many molecular pathways involved in sustaining the physiological systems in air-breathing stinging catfish. Adaptation is achieved through the enrichment of genes related to metabolic pathways, immune system response, stress response such as apoptosis and protein folding, and transporter of molecules involved in ionic and osmoregulation.

Distantly related bacteria share a rigid proteome allocation strategy with flexible enzyme kinetics

Bacteria are known to allocate their proteomes according to how fast they grow, and the allocation strategies employed strongly affect bacterial adaptation to different environments. Much of what is currently known about proteome allocation is based on extensive studies of the model organism Escherichia coli. It is not clear how much of E. coli's proteome allocation strategy is applicable to other species, particularly since different species can grow at vastly different rates even in the same growth condition. In this study, we investigate differences in nutrient-dependent proteome allocation programs adopted by several distantly related bacterial species, including Vibrio natriegens, one of the fastest-growing bacteria known. Extensive quantitative proteome characterization across conditions reveals an invariant allocation program in response to changing nutrients despite systemic, species-specific differences in enzyme kinetics. This invariant program is not organized according to the growth rate but is based on a common internal metric of nutrient quality after scaling away species-specific differences in enzyme kinetics, with the faster species behaving as if it is growing under a higher temperature. The flexibility of enzyme kinetics and the rigidity of proteome allocation programs across species defy common notions of evolvability and resource optimization. Our results suggest the existence of a blueprint of proteome allocation shared by diverse bacterial species, with implications on common underlying regulatory strategies. Further knowledge on the existence and organization of such phylogeny-transcending relations also promises to simplify the bottom-up description and understanding of bacterial behaviors in ecological communities.

Small organic osmolytes accelerate actin filament assembly and stiffen filaments

Actin filament assembly and mechanics are crucial for maintenance of cell structure, motility, and division. Actin filament assembly occurs in a crowded intracellular environment consisting of various types of molecules, including small organic molecules known as osmolytes. Ample evidence highlights the protective functions of osmolytes such as trimethylamine-N-oxide (TMAO), including their effects on protein stability and their ability to counteract cellular osmotic stress. Yet, how TMAO affects individual actin filament assembly dynamics and mechanics is not well understood. We hypothesize that, owing to its protective nature, TMAO will enhance filament dynamics and stiffen actin filaments due to increased stability. In this study, we investigate osmolyte-dependent actin filament assembly and bending mechanics by measuring filament elongation rates, steady-state filament lengths, and bending persistence lengths in the presence of TMAO using total internal reflection fluorescence microscopy and pyrene assays. Our results demonstrate that TMAO increases filament elongation rates as well as steady-state average filament lengths, and enhances filament bending stiffness. Together, these results will help us understand how small organic osmolytes modulate cytoskeletal protein assembly and mechanics in living cells.

Specific ion effects enhance local structure in zwitterionic osmolyte solutions

Zwitterionic osmolytes are widely known to have a protein-protective effect against high salt concentration, but a mechanistic picture of osmolyte function remains elusive. Here total scattering is used to determine the room temperature liquid structure of two model cytosol solutions containing trimethylglycine (TMG) with either sodium or potassium chloride. H/D isotopic substitution is used to obtain differential neutron scattering cross sections at multiple contrasts in addition to an X-ray structure factor, and an Empirical Potential Structure Refinement (EPSR) simulation is fitted to the experimental data. We reveal the nature of the interaction between TMG molecules and ions in solution, observing binding between cations and the TMG carboxylate group. We observe three key specific ion effects: first, that sodium ions are more tightly localised at the carboxylate group; second, that sodium localisation in turn promotes head-to-head bridging between carboxylate groups when compared to potassium or no added ions, resulting in strong oxygen-oxygen correlations; and third, that sodium ions promote TMG clusters with greater orientational order, more fully shielding the ion but also in turn limiting access to the carboxylate groups for other molecules. These observations have implications for the bioavailability and protein-stabilising effect of osmolytes under changing extracellular salt conditions.

Lipid Properties and Metabolism in Response to Cold

Temperature directly shapes insect physiology and has a preponderant effect on life history traits. Winter conditions in temperate and polar regions are especially challenging for insects. Extremely low temperatures can indeed compromise insect survival by promoting freezing of body fluids, but mild cold temperatures above 0 °C (i.e., chilling) can also lead to complex and severe physiological dysregulations. Among physiological damages due to freezing and chilling, insect lipids are one of the primary targets. As low temperatures tend to rigidify phospholipid bilayers, membrane functions are compromised in the cold. Lipid rigidification due to cold also decreases the accessibility of fat stores for metabolic enzymes, and therefore their availability for basal metabolism. These deleterious effects, combined with low food availability in winter, result in substantial nutritional challenges for overwintering insects. Consequently, lipid modifications such as homeoviscous adaptation of cell membranes, fluidity maintenance of fat reserves, cuticular lipid accumulation, and production of antifreeze glycolipids are essential components of the physiological response to cold stress. The aim of the present chapter is to present the physiological challenges caused by low temperatures, the lipid modifications linked with cold tolerance in insects, and the molecular regulation of lipid metabolism during cold exposure.

Effect of osmolytes on the conformational stability of Aβ(25-35): A circular dichroism analysis

Alzheimer's (AD) is a neurodegenerative disease characterized by the onset and progression of mental decline. AD aetiopathogenesis is still questioned; however, according to one of the most accredited hypotheses, the accumulation of amyloid plaques formed by aggregated Aβ peptides is the primary cause of neuronal function loss. Accordingly, hundreds of molecules have been screened for their possible action to prevent or destroy amyloid aggregates. Following this track, osmolytes, naturally occurring small molecules produced by several organisms in response to external stressors, were recently evaluated as modulators of Aβ aggregation. In this study, we examined the conformational stability of Aβ(25-35) when exposed to the osmolytes acetylcholine (ACh), succinylcholine (SCh), and betaine (Bet). Aβ(25-35) is the shortest fragment known for replicating the aggregation process seen in Aβ peptides. By collecting circular dichroism (CD) spectra in water and different membrane-mimicking systems, we investigated the potential of the mentioned osmolytes to stabilize the soluble conformations of Aβ(25-35) and preserve them from denaturing conditions. Our data suggest that Bet is a promising small molecule that can safeguard the soluble form of Aβ peptide and is effective in counteracting environmental conditions by favoring the amyloid aggregation associated with pathology progression.

Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov

Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41GT as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813TS (=BAABNI000000000.1TS) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891T outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.

Transcriptomic and Metabolomic Analyses Reveal Response Mechanisms of Sinonovacula Constricta to Saline-Alkalinity Stresses

The razor clam (Sinonovacula constricta) is a key species in marine aquaculture, known for its wide salinity adaptation, and potential for cultivation in saline-alkaline water. Understanding its response mechanisms is crucial for expanding its farming into these regions. This study reveals the response mechanisms of S. constricta in response to low-salinity alkaline stress through a combined analysis of transcriptomics and metabolomics. After 24 h of salt-alkali stress (SA group), 1378 differentially expressed genes (DEGs) were identified, with enriched pathways including glycerophospholipid metabolism, serine, taurine, and hypotaurine metabolism. Additionally, 341 significantly different metabolites (SDMs) were found, primarily involved in taurine and hypotaurine metabolism, purine metabolism, and the FoxO signaling pathway, etc. Both DEGs and SDMs were notably enriched in hypotaurine metabolism, glycerophospholipid metabolism, and the mTOR signaling pathway, showing significant upregulation in the SA group. Correlation analysis found that the integrated regulatory network was involved in the synthesis of taurine, glycerophospholipids, and L-glutamic acid, and the metabolism of 3-mercaptopropionic acid. These results suggest that low salinity and alkalinity induce stress responses in S. constricta by regulating osmotic balance, phospholipid synthesis, and lipid metabolism. This study offers insights into the molecular mechanisms of salt-alkali response in S. constricta.

Chemical control of colloidal self-assembly driven by the electrosolvation force

Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions are central to a variety of molecular processes, e.g., crystallisation, biomolecular folding and condensation, pathological protein aggregation and biofouling. The electrosolvation force introduces a distinct conceptual paradigm to the existing palette of interactions that govern the spontaneous accretion and organisation of matter. However, an understanding of the underlying physical chemistry, and therefore the ability to exert control over and tune the interaction, remains incomplete. Here we provide further evidence that this force arises from the structure of the interfacial electrolyte. Neutral molecules such as a different solvent, osmolytes or surfactants, may - even at very low concentrations in the medium - disrupt or reinforce pre-existing interfacial solvent structure, thereby delivering unanticipated chemical tuning of the ability of matter to self-assemble. The observations present unexpected mechanistic elements that may explain the impact of co-solvents and osmolytes on protein structure, stability and biomolecular condensation. Our findings thus furnish insight into the microscopic mechanisms that drive the emergence of order and structure from molecular to macroscopic scales in the solution phase.

Metabolic responses provide insight into interspecific variation in heat tolerance of three co-existing pest aphid species

Global warming leads to an increase in extreme heat events, posing significant challenges for insects. Sitobion avenae, Metopolophium dirhodum and Rhopalosiphum padi are important co-existing aphid species known to cause damage to cereal crops worldwide. The three species differ in thermal tolerance, with R. padi being much more heat tolerant than the other two species. However, it remains unclear whether interspecific variation in heat tolerance is due to differences in metabolic responses to heat stress. Here, we compared their metabolic signatures during and after recovery from the same injury level of heat stress (at 34°C for half and full durations to cause 50% mortality in each species), as well as the identical duration of heat stress. Using quantitative GC-MS, we found that after the same injury level of heat exposure, the three species showed similar changes in most metabolites. However, the heat-tolerant species, R. padi, had higher levels of polyols and amino acids, and uniquely accumulated glycerol. In addition, after the same duration of heat exposure, R. padi maintained a relatively stable metabolic profile, while the less tolerant species showed marked alterations with a shift from aerobic to anaerobic metabolism. We suggest that polyols and amino acids play a pivotal role in protecting R. padi from heat damage, contributing to its superior thermal tolerance. Overall, this comparative metabolomics study provides insight into the relationship between metabolic responses and heat tolerance of co-existing species, which helps understanding of the underlying mechanism of heat tolerance.

Role of Gut Microbial Metabolites in Ischemic and Non-Ischemic Heart Failure

The effect of the gut microbiota extends beyond their habitant place from the gastrointestinal tract to distant organs, including the cardiovascular system. Research interest in the relationship between the heart and the gut microbiota has recently been emerging. The gut microbiota secretes metabolites, including Trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), bile acids (BAs), indole propionic acid (IPA), hydrogen sulfide (H2S), and phenylacetylglutamine (PAGln). In this review, we explore the accumulating evidence on the role of these secreted microbiota metabolites in the pathophysiology of ischemic and non-ischemic heart failure (HF) by summarizing current knowledge from clinical studies and experimental models. Elevated TMAO contributes to non-ischemic HF through TGF-ß/Smad signaling-mediated myocardial hypertrophy and fibrosis, impairments of mitochondrial energy production, DNA methylation pattern change, and intracellular calcium transport. Also, high-level TMAO can promote ischemic HF via inflammation, histone methylation-mediated vascular fibrosis, platelet hyperactivity, and thrombosis, as well as cholesterol accumulation and the activation of MAPK signaling. Reduced SCFAs upregulate Egr-1 protein, T-cell myocardial infiltration, and HDAC 5 and 6 activities, leading to non-ischemic HF, while reactive oxygen species production and the hyperactivation of caveolin-ACE axis result in ischemic HF. An altered BAs level worsens contractility, opens mitochondrial permeability transition pores inducing apoptosis, and enhances cholesterol accumulation, eventually exacerbating ischemic and non-ischemic HF. IPA, through the inhibition of nicotinamide N-methyl transferase expression and increased nicotinamide, NAD+/NADH, and SIRT3 levels, can ameliorate non-ischemic HF; meanwhile, H2S by suppressing Nox4 expression and mitochondrial ROS production by stimulating the PI3K/AKT pathway can also protect against non-ischemic HF. Furthermore, PAGln can affect sarcomere shortening ability and myocyte contraction. This emerging field of research opens new avenues for HF therapies by restoring gut microbiota through dietary interventions, prebiotics, probiotics, or fecal microbiota transplantation and as such normalizing circulating levels of TMAO, SCFA, BAs, IPA, H2S, and PAGln.

Gut Microbiota and Metabolic Biomarkers Associated With Longevity

The dynamic balance between pro- and anti-inflammatory networks decreases as individuals age, and intestinal dysbiosis can initiate and maintain low-grade systemic inflammation. Interactions between the microbiota and humans occur from the beginning of life and, in general, the diversity of microbiota decreases with aging. The microbiome produces different metabolites with systemic effects, including immune system regulation. This understanding will be useful in controlling inflammation and preventing metabolic changes. Therefore, this review aims to identify the main metabolites synthesized by the intestinal microbiota to be used as biomarkers associated with longevity. This is a narrative review using scientific articles published in the last 10 years in the following databases: PubMed, Scielo, and Lilacs, using the Boolean operators "and" or "or." For this review, we identified 5 articles. The main metabolites described in the literature to date are organic acids, bile acids (BAs), short-chain fatty acids, branched-chain amino acids, trimethylamine N-oxide (TMAO), and derivatives of tryptophan and indole. Among these, the only ones not yet well characterized in studies on longevity were BAs and TMAO. Glutamate and p-cresol were also highlighted in the literature, with a negative association with longevity. The others showed an association, mostly positive, and can be used as potential biomarkers correlated with healthy aging and, if better studied, as targets for intervention to promote health and well-being.

Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N

Truncated hemoglobins (TrHbs) have an ancient origin and are widely distributed in microorganisms where they often serve roles other than dioxygen transport and storage. In extremophiles, these small heme proteins must have features that secure function under challenging conditions: at minimum, they must be folded, retain the heme group, allow substrates to access the heme cavity, and maintain their quaternary structure if present and essential. The genome of the obligate psychropiezophile Shewanella benthica strain KT99 harbors a gene for a TrHb belonging to a little-studied clade of globins (subgroup 2 of group N). In the present work, we characterized the structure of this protein (SbHbN) with electronic absorption spectroscopy and X-ray crystallography and inspected its structural integrity under hydrostatic pressure with NMR spectroscopy and small-angle X-ray scattering. We found that SbHbN self-associates weakly in solution and contains an extensive network of hydrophobic tunnels connecting the active site to the surface. Amino acid replacements at the dimeric interface formed by helices G and H in the crystal confirmed this region to be the site of intermolecular interactions. High hydrostatic pressure dissociated the assemblies while the porous subunits resisted unfolding and heme loss. Preservation of structural integrity under pressure is also observed in nonpiezophilic TrHbs, which suggests that this ancient property is derived from functional requirements. Added to the inability of SbHbN to combine reversibly with dioxygen and a propensity to form heme d, the study broadens our perception of the TrHb lineage and the resistance of globins to extreme environmental conditions.

Metabolomic signatures associated with cold adaptation and seasonal acclimation of Drosophila: profiling of 43 species

Cold tolerance is a key determinant of poleward colonization in insects. However, the physiological basis underlying interspecific differences in cold tolerance is not fully understood. Here, we analyzed cold tolerance and metabolomic profiles in warm- and cold-acclimated phenotypes of 43 Drosophila species representing a latitudinal gradient from the tropics to the boreal zone. We found a strong positive correlation between cold tolerance and climatic variables associated with habitat seasonality and temperature. Including the effects of cold acclimation, we found most species have similar 'safety margins', measured as the difference between the average environmental temperature and the lower lethal temperature. Searching for metabolomic signatures of cold tolerance, we found that the warm-acclimated flies of cold-hardy species had moderately but significantly higher constitutive signals of putative cryoprotectants such as trehalose, glucose, glycerol and mannitol/sorbitol. Cold acclimation (and the transition to a winter dormant phenotype) resulted in a strong accumulation of myo-inositol, which occurred only in species of the virilis group. Other temperate and boreal species either showed only moderate, idiosyncratic accumulations of sugars/polyols and free amino acids, or did not accumulate any 'classical' cryoprotectant at all. Thus, our results suggest that the colonization of boreal regions by Drosophila does not necessarily depend on the seasonal accumulation of classical cryoprotectants. In contrast, virtually all cold-acclimated species showed a significant increase in products of phospholipid catabolism, suggesting that remodeling of biological membranes is a clear and ubiquitous signature of cold acclimation in Drosophila.

Harnessing Oxidized Amines as Robust Sorbents for Carbon Capture

Carbon capture and sequestration (CCS) is imperative to mitigating global climate change, but current implementation falls far short of that needed to reach net-zero global emissions by 2050. Aqueous amine solutions, conceived over a century ago, are the current leading technology for CO2 separations. However, amines suffer from chemical instability under scrubbing conditions, corrosiveness, and toxicity, hindering their long-term implementation at multiton scales. Herein, we demonstrate for the first time that tertiary amine N-oxides, an oxidative degradation product of amines, can remove CO2 from dilute streams, including flue gas from a natural gas-fired power plant. Our extensive spectroscopic and computational studies support that the nontoxic, noncorrosive, and inexpensive 4-methylmorpholine N-oxide (MMNO) captures CO2 under humid conditions via the formation of a hydrogen-bond-stabilized bicarbonate (HCO3-) species, despite being significantly less basic than an amine. Accelerated aging studies show that MMNO exhibits superior oxidative and thermal stability compared to structurally similar amines, highlighting the potential of eco-friendly N-oxides in industrial carbon capture applications.

Preventing epileptogenesis by interaction between inositol isomers and proteins

OBJECTIVE

Inositols play significant roles in biological systems. Myo-inositol (MI), the most prevalent isomer, functions as an osmolyte and mediates cell signal transduction. Other notable isomers include Scyllo-inositol (SCI) and D-Chiro-inositol (DCHI). Our previous investigations have highlighted MI's potential antiepileptogenic effects, although its exact mechanisms of action during epileptogenesis remain unclear. A critical, unexplored area is how inositols interact with proteins. Additionally, the antiepileptogenic capabilities of SCI and DCHI have yet to be determined. This study seeks to address these gaps.

METHODS

Inositol interacting proteins were identified by cellular thermal shift assay. Status epilepticus (SE) in rats was induced using kainic acid (KA), followed by a 28-day treatment with either MI, SCI, DCHI, or saline. The duration and frequencies of behavioral spontaneous recurrent seizures (SRS) were scored for 8 weeks by 24 h video monitoring system. The effects of inositol treatment on spatial learning and memory deficits associated with epileptogenesis were evaluated by Morris water maze test. The changes in protein amounts were studied by Western immunoblotting.

RESULTS

We identified several proteins that interact with inositols, noting both commonalities and isomer-specific associations. For the first time, we demonstrated that the treatment with SCI and DCHI, alongside MI, significantly reduces the frequency and duration of behavioral SRS in a KA-induced post-status epilepsy model in rats. This reduction persisted for 4 weeks post-treatment. Moreover, all three inositol isomers mitigated spatial learning and memory deficits associated with epileptogenesis. Alterations in the inositol interacting proteins: alpha synuclein and 14-3-3 theta were further examined 8 weeks post-SE in the hippocampus and neocortex of rats.

SIGNIFICANCE

Myo-inositol, SCI and DCHI interact with a number of proteins involved in different biological pathways. All studied inositol isomers express long-term beneficial effects on KA-induced SRS and the associated comorbidities. Inositols can be successfully used in the future for translational research.

PLAIN LANGUAGE SUMMARY

Epilepsy is a common neurological disorder characterized by spontaneous recurrent seizures and a range of associated comorbidities. The process that leads to the development of epilepsy is called epileptogenesis, and currently, no medication can effectively prevent it. Our study investigated the effects of a group of compounds-myo-inositol, scyllo-inositol, and D-chiro-inositol-that have potential antiepileptogenic properties on epilepsy induced by kainic acid. We found that: (i) the three inositol isomers share some common target proteins and also have unique ones and (ii) all of them counteract epileptogenesis and the related cognitive impairments.

Interaction studies unveil potential binding sites on bovine serum albumin for gut metabolite trimethylamine n-oxide (TMAO)

Trimethylamine-N-oxide (TMAO) is gut microbiota-derived metabolite, plays a critical role in human health and diseases such as metabolic, cardiovascular, colorectal cancer and, neurological disorders. Binding interactions between TMAO and serum albumins are crucial to understand the impact of TMAO on disease mechanisms. However, detailed insights into the interaction mechanisms, preferred binding locations, and conformational changes in BSA upon binding TMAO are still unclear. TMAO interacts with serum albumin in human body and thus, a model study of interaction for TMAO-BSA conjugate is presented in support of it. Decrease in absorbance intensity of protein upon interaction with metabolites reveals conjugate formation, while fluorescence spectroscopy indicate static quenching. Contact angle measurements further reveal the hydrophilic nature of the TMAO-BSA complex, while CD and FTIR support conformational changes in BSA upon binding but structure remain intact. Computational studies, such as molecular docking, molecular dynamics simulation and, MM/GBSA, confirm a stable complex with a binding energy of - 3.6 kcal/mol. These findings provide a foundation for understanding the pharmacodynamics and pharmacokinetics of TMAO and may aid in developing strategies for treating diseases, such as chronic kidney disease and neurological disorder where TMAO-serum albumins interaction are implicated.

Gene metabolite relationships revealed metabolic adaptations of rice salt tolerance

Environmental stresses, particularly salinity, pose significant challenges to global crop production, notably impacting the growth and yield of rice. Integrating gene expression and metabolomics data offers valuable insights into the molecular mechanisms driving salt tolerance in plants. This study examined the effects of high salinity on the roots and shoots of rice genotypes with contrasting tolerances: CSR28 (tolerant) and IR28 (sensitive) at the seedling stage. Our phenotypic and physiological assessments indicated significant differences in response to prolonged salinity exposure between the two genotypes. Notably, osmoprotectants, including amino acids and sugars, exhibited increased accumulation, whereas most organic acids showed a decline. Linear regression analyses established significant correlations between the levels of proline, myoinositol, catalase (CAT), and superoxide dismutase (SOD) and their respective encoding genes: OsP5CS2, OsIMP, OsNCA1a, and OsSOD-Fe. Furthermore, a relationship was identified between H2O2 content and the expression of glycolate oxidase (GLO), highlighting its role in initiating defense mechanisms under salinity stress. Our findings indicated specific metabolites and genes associated with distinct organs, genotypes, and timepoints that can serve as biomarkers for the development of new salt-tolerant rice varieties.

Central and nephrogenic diabetes insipidus: updates on diagnosis and management

Diabetes insipidus (DI) is a rare endocrine disease involving antidiuretic hormone (ADH), encompassing both central and nephrogenic causes. Inability to respond to or produce ADH leads to inability of the kidneys to reabsorb water, resulting in hypotonic polyuria and, if lack of hydration, hypernatremia. DI cannot be cured and is an unfamiliar disease process to many clinicians. This diagnosis must be distinguished from primary polydipsia and other causes of hypotonic polyuria. The main branchpoints in pathophysiology depend on the level of ADH pathology: the brain or the kidneys. Prompt diagnosis and treatment are critical as DI can cause substantial morbidity and mortality. The gold standard for diagnosis is a water deprivation test followed by desmopressin administration. There is promising research regarding a new surrogate marker of ADH called copeptin, which may simplify and improve the accuracy in diagnosing DI in the future. Patients with DI require adequate access to water, and there are nuances on treatment approaches depending on whether a patient is diagnosed with central or nephrogenic DI. This article describes a stepwise approach to recognition, diagnosis, and treatment of DI.

Brief Warm and Aldo-Keto Reductase Family AspiAKR1B1 Contribute to Cold Adaptation of Aleurocanthus spiniferus

Aleurocanthus spiniferus not only damages plant leaves directly but also causes a sooty blotch due to the honeydew secreted by the nymphs and adults. This pest is widespread and seems to be spreading from low latitude to higher latitude areas where winters are typically colder, indicating an increase in its cold tolerance. Changes in temperature help insects to anticipate the arrival of winter, allowing them to take defensive measures in advance. This study examines the impacts of brief warm pulses on the low-temperature tolerance of A. spiniferus, and analyzes the physiological and biochemical mechanisms underlying its cold adaptation, utilizing seasonal differences in cold tolerance. Intermittent training at 25 °C significantly improved the survival rate of overwintering nymphs (third and fourth instar) at -7 °C. Analysis of seasonal differences in the supercooling point (SCP) and freezing point (FP) revealed that overwintering nymph had the highest cold tolerance in November. Seasonal variation in levels of cold-resistant substances were also observed, with moisture decreasing during overwintering, while fat and glycerol levels increased. Conversely, glucose, sorbitol, and trehalose levels rose significantly at the end of the overwintering period. The expression profile of cold-resistant genes indicated that the aldo-keto reductase family 1 member B1 in Aleurocanthus spiniferus (AspiAKR1B1) shows a significant decrease at the end of the overwintering period. Knocking down AspiAKR1B1 led to a marked reduction in the cold tolerance of A. spiniferus. Therefore, brief warm pulses and AspiAKR1B1 are key factors contributing to the enhanced cold tolerance of A. spiniferus. This research provides theoretical support for preventing the further spread of A. spiniferus to higher latitudes, and offers technical guidance for developing effective pest control measures.

A metabolomic analysis on the toxicological effects of the universal solvent, dimethyl sulfoxide

Dimethyl sulfoxide (DMSO) is a solvent used to dissolve a variety of organic compounds. It is presumed to be non-toxic at concentrations below 1 % v/v, although several studies have demonstrated that low dose DMSO exposure can alter cellular biochemistry. This study evaluated the toxicity of DMSO at 0.0002 % v/v to the Sydney Rock oyster, Saccostrea glomerata, following 7d of exposure. Metabolites were chosen as the toxicity endpoints because they can be used as energy sources and counteract contaminant-induced stress. Relative to seawater controls, exposure to DMSO caused a 74 % significant change in metabolites in the female digestive gland, including decreases in most amino acids, carbohydrates, nicotinamides, and lipids. The female gonad showed a 43 % significant change in metabolites, with decreases in amino acids and carbohydrates, but increases in lipids. The male digestive gland showed a 29 % significant change in metabolites, with increases in lipids. The decline in metabolites in the female digestive gland, but not in the male digestive gland, may be due to their differential metabolic demands. Furthermore, pathway impact analysis revealed that DMSO exposure altered energy metabolism, disturbed osmotic balance, and induced oxidative stress in oysters. Because the effects of DMSO are not uniform across gender and tissue, use of DMSO as a solvent will confound metabolomic experimental results when comparisons among sexes and/or tissues are integral to the experimental design. There is a risk of incomplete dissolution of contaminants unless carrier solvents are used. Therefore, in practice, a solvent control along with a water control is recommended for experimentation.

Dimethyl-Sulfoxide-Free Cell Cryoprotectant Derived from Amino Acids

With the large-scale applications of cryopreservation technology in the cell therapy fields, traditional permeable cryoprotectants (CPAs) have led to serious issues, such as cell cycle arrest, inhibition of cell proliferation and differentiation, apoptosis, altered gene expression, etc. Development of green, non-toxic cryoprotectants is critically needed. Amino acids could serve as substrates for protein and cellular metabolism and as cryoprotectants with non-toxicity, balancing the intracellular water osmotic pressure. Current research on amino acids as cryoprotectants is hindered by several limitations, including unclear protection mechanisms, cryopreservation methods, and poor efficacy of individual formulations. Therefore, three specific amino acids and derivatives, including l-proline, l-carnitine, and betaine, as cryoprotectants were used for two types of cell cryopreservation. Single-factor experiments were conducted to obtain the optimal concentration range for each of the three amino acid cryoprotectants. On the basis of the key thermophysical parameters, the ability to inhibit ice crystals, and the effect after cryopreservation, multivariate orthogonal experiments were carried out to evaluate the actual effect of the three-component mixed cryoprotectant on cell cryopreservation. In comparison to the gold standard of 10% dimethyl sulfoxide (DMSO) for cell cryopreservation, the mixed cryoprotectant derived from amino acids achieves comparable preservation efficacy at lower concentrations with a convenient application method, which offers guidance for DMSO-free cryoprotectants.

Circulating Metabolite Abundances Associated With Risks of Bipolar Disorder, Schizophrenia, and Depression: A Mendelian Randomization Study

BACKGROUND

Preventive measures and treatments for psychiatric disorders are limited. Circulating metabolites are potential candidates for biomarker and therapeutic target identification, given their measurability and essential roles in biological processes.

METHODS

Leveraging large-scale genome-wide association studies, we conducted Mendelian randomization analyses to assess the associations between circulating metabolite abundances and the risks of bipolar disorder, schizophrenia, and depression. Genetic instruments were selected for 94 metabolites measured in the Canadian Longitudinal Study on Aging cohort (N = 8299). We repeated Mendelian randomization analyses based on the UK Biobank, INTERVAL, and EPIC (European Prospective Investigation into Cancer)-Norfolk studies.

RESULTS

After validating Mendelian randomization assumptions and colocalization evidence, we found that a 1 SD increase in genetically predicted circulating abundances of eicosapentaenoate and docosapentaenoate was associated with odds ratios of 0.72 (95% CI, 0.65-0.79) and 0.63 (95% CI, 0.55-0.72), respectively, for bipolar disorder. Genetically increased Ω-3 unsaturated fatty acids abundance and Ω-3-to-total fatty acids ratio, as well as genetically decreased Ω-6-to-Ω-3 ratio, were negatively associated with the risk of bipolar disorder in the UK Biobank. Genetically increased circulating abundances of 3 N-acetyl-amino acids were associated with an increased risk of schizophrenia with a maximum odds ratio of 1.31 (95% CI, 1.18-1.44) per 1 SD increase. Furthermore, a 1 SD increase in genetically predicted circulating abundance of hypotaurine was associated with an odds ratio of 0.85 (95% CI, 0.78-0.93) for depression.

CONCLUSIONS

The biological mechanisms that underlie Ω-3 unsaturated fatty acids, NAT8-catalyzed N-acetyl-amino acids, and hypotaurine warrant exploration to identify new biomarkers and potential therapeutic targets.

Metabolic-driven analytics of traumatic brain injury and neuroprotection by ethyl pyruvate

BACKGROUND

Research on traumatic brain injury (TBI) highlights the significance of counteracting its metabolic impact via exogenous fuels to support metabolism and diminish cellular damage. While ethyl pyruvate (EP) treatment shows promise in normalizing cellular metabolism and providing neuroprotection, there is a gap in understanding the precise metabolic pathways involved. Metabolomic analysis of the acute post-injury metabolic effects, with and without EP treatment, aims to deepen our knowledge by identifying and comparing the metabolite profiles, thereby illuminating the injury's effects and EP's therapeutic potential.

METHODS

In the current study, an untargeted metabolomics approach was used to reveal brain metabolism changes in rats 24 h after a controlled cortical impact (CCI) injury, with or without EP treatment. Using principal component analysis (PCA), volcano plots, Random Forest and pathway analysis we differentiated the brain metabolomes of CCI and sham injured animals treated with saline (Veh) or EP, identifying key metabolites and pathways affected by injury. Additionally, the effect of EP on the non-injured brain was also explored.

RESULTS

PCA showed a clear separation of the four study groups (sham-Veh, CCI-Veh, sham-EP, CCI-EP) based on injury. Following CCI injury (CCI-Veh), 109 metabolites belonging to the amino acid, carbohydrate, lipid, nucleotide, and xenobiotic families exhibited a twofold change at 24 h compared to the sham-Veh group, with 93 of these significantly increasing and 16 significantly decreasing (p < 0.05). CCI animals were treated with EP (CCI-EP) showed only 5 metabolites in the carbohydrate, amino acids, peptides, nucleotides, lipids, and xenobiotics super families that exhibited a twofold change, compared to the CCI-Veh group (p < 0.05). In the non-injured brain, EP treatment (sham-EP) resulted in a twofold change in 6 metabolites within the amino acid, peptide, nucleotide, and lipid super families compared to saline treated sham animals (sham-Veh, p < 0.05).

CONCLUSIONS

This study delineates the unique metabolic signatures resulting from a CCI injury and those related to EP treatment in both the injured and non-injured brain, underscoring the metabolic adaptations to brain injury and the effects of EP. Our analysis uncovers significant shifts in metabolites associated with inflammation, energy metabolism, and neuroprotection after injury, and demonstrates how EP intervention after injury alters metabolites associated with mitigating inflammation and oxidative damage.

Origin of Pressure Resistance in Deep-Sea Lactate Dehydrogenase

High hydrostatic pressure has a dramatic effect on biochemical systems, as exposure to high pressure can result in structural perturbations ranging from dissociation of protein complexes to complete denaturation. The deep ocean presents an interesting paradox since it is teeming with life despite the high-pressure environment. This is due to evolutionary adaptations in deep-sea organisms, such as amino acid substitutions in their proteins, which aid in resisting the denaturing effects of pressure. However, the physicochemical mechanism by which these substitutions can induce pressure resistance remains unknown. Here, we use molecular dynamics simulations to study pressure-adapted lactate dehydrogenase from the deep-sea abyssal grenadier (Coryphaenoides armatus), in comparison with that of the shallow-water Atlantic cod (Gadus morhua). We examined structural, thermodynamic and volumetric contributions to pressure resistance, and report that the amino acid substitutions result in a decrease in volume of the deep-sea protein accompanied by a decrease in thermodynamic stability of the native protein. Our simulations at high pressure also suggest that differences in compressibility may be important for understanding pressure resistance in deep-sea proteins.

Effect of osmolytes and posttranslational modifications on modulating the chaperone function of α-crystallin

Proteins are responsible for a vast majority of various cellular effector processes. α-crystallin is one of the most important proteins in the lens of the eye, which acts as a molecular chaperone that keeps the lens transparent and refractive. α-crystallin is categorized as an intrinsically disordered protein (IDP), devoid of a stable three-dimensional structure, in contrast to conventional globular proteins. Because of its structural flexibility, it can stop denatured proteins from aggregating and building up within the lens over time. α-crystallin's dynamic quaternary structure, which allows it to exist in a variety of oligomeric forms, from dimers to massive assemblies, improves its chaperone function and flexibility. Its intrinsically disordered nature enables it to interact with a variety of client proteins due to its large non-polar and polar residue content and lack of a hydrophobic core. Furthermore, under physiological stress, osmolytes like sorbitol, TMAO, and urea are essential in regulating the stability and function of α-crystallin. Post-translational modifications (PTMs) such as glycation, in which reducing sugars combine with amino groups on the protein to generate advanced glycation end-products, impair α-crystallin's ability to function. These AGEs can cross-link α-crystallin molecules to prevent protein aggregation, changing their structure and decreasing their chaperone action. Because of their raised blood glucose levels, diabetics have an increased chance of developing cataracts as a result of this process. Comprehending how glycation and other PTMs affect α-crystallin is crucial for formulating treatment plans to maintain lens transparency and fight cataracts linked to aging and metabolic disorders.

Role of protein aggregates in bacteria

Protein misfolding and aggregation in bacteria, induced by a variety of intrinsic and environmental stresses, have often been associated with proteostasis disruption and toxic effects. However, a growing body of evidence suggests that these aggregates may also serve as functional membrane-less organelles (MLOs), playing a protective role in bacterial cells. The main mechanism responsible for the formation of MLOs is liquid-liquid phase separation (LLPS), a process that transforms a homogenous solution of macromolecules into dense condensates (liquid droplets) and a diluted phase. Over time, these liquid droplets can be transformed into solid aggregates. Bacterial MLOs, containing one dominant component or hundreds of cytoplasmic proteins, have been shown to be involved in various processes, including replication, transcription, cell division, and stress tolerance. The protective function of bacterial MLOs involves sequestration and protection of proteins and RNA from irreversible inactivation or degradation, upregulation of molecular chaperones, and induction of a dormant state. This protective role is particularly significant in the case of pathogenic bacteria exposed to antibiotic therapy. In a dormant state triggered by protein aggregation, pathogens can survive antibiotic therapy as persisters and, after resuming growth, can cause recurrent infections. Recent research has explored the potential use of bacterial MLOs as nanoreactors that catalyze biochemical reactions or serve as protein reservoirs and biosensors, highlighting their potential in biotechnology.

Hypersalinity tolerance of mummichogs (Fundulus heteroclitus): A branchial transcriptomic analysis

Along the east coast of North America, mummichogs (Fundulus heteroclitus) are subjected to a broad range of salinities in their nearshore habitats. However, there is a paucity of information regarding the molecular and cellular processes that mummichogs (and other highly osmotolerant fishes) engage to survive environmental salinities greater than seawater (SW). To reveal branchial processes underlying their extraordinarily broad salinity tolerance, we performed an RNA-Seq analysis to identify differentially expressed genes (DEGs) in mummichogs residing in 3, 35, and 105 ppt conditions. We identified a series of DEGs previously associated with both freshwater (FW)- and SW-type ionocytes; however, the heightened expression of anoctamin 1a, a Ca2+-activated Cl- channel, in 35 and 105 ppt indicates that an undescribed Cl--secretion pathway may operate within the SW-type ionocytes of mummichogs. Concerning FW-adaptive branchial processes, we identified claudin 5a as a gene whose product may limit the diffusive loss of ions between cellular tight junctions. Further, in response to hypersaline conditions, we identified DEGs linked with myo-inositol synthesis and kinase signaling. This study provides new molecular targets for future physiological investigations that promise to reveal the mechanistic bases for how mummichogs and other euryhaline species tolerate hypersaline conditions.

Dynamic composition of stress granules in Trypanosoma brucei

Stress granules (SGs) are stress-induced RNA condensates consisting of stalled initiation complexes resulting from translational inhibition. The biochemical composition and function of SGs are highly diverse, and this diversity has been attributed to different stress conditions, signalling pathways involved and specific cell types. Interestingly, mRNA decay components, which are found in ubiquitous cytoplasmic foci known as processing bodies (PB), have also been identified in SG proteomes. A major challenge in current SG studies is to understand the cause of SG diversity, as well as the function of SG under different stress conditions. Trypanosoma brucei is a single-cellular parasite that causes Human African Trypanosomiasis (sleeping sickness). In this study, we showed that by varying the supply of extracellular carbon sources during starvation, cellular ATP levels changed rapidly, resulting in SGs of different compositions and dynamics. We identified a subset of SG components, which dissociated from the SGs in response to cellular ATP depletion. Using expansion microscopy, we observed sub-granular compartmentalization of PB- and SG-components within the stress granules. Our results highlight the importance of cellular ATP in SG composition and dynamics, providing functional insight to SGs formed under different stress conditions.

Generating interstitial water within the persisting tetrahedral H-bond network explains density increase upon compressing liquid water

Despite its ubiquitous nature, the atomic structure of water in its liquid state is still controversially debated. We use a combination of X-ray Raman scattering spectroscopy in conjunction with ab initio and path integral molecular dynamics simulations to study the local atomic and electronic structure of water under high pressure conditions. Systematically increasing fingerprints of non-hydrogen-bonded H[Formula: see text]O molecules in the first hydration shell are identified in the experimental and computational oxygen K-edge excitation spectra. This provides evidence for a compaction mechanism in terms of a continuous collapse of the second hydration shell with increasing pressure via generation of interstitial water within locally tetrahedral hydrogen-bonding environments.

Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments

The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.

Regulation of the structural dynamics, aggregation, and pathogenicity of polyQ-expanded Huntingtin by osmolytes

Huntington Disease is an autosomal dominant neurodegenerative disease caused by expansion of the polymorphic trinucleotide CAG repeat of the HTT gene to code for an expanded glutamine track of the mutant Huntingtin protein (mHTT). Like other neurodegenerative diseases, symptomatic presentation of Huntington Disease is age-dependent or age-related. This age-dependent manifestation of an autosomal dominant disease trait underscores important and possibly priming role of age-related changes in cellular physiology that are conducive to disease presentation. Herein, we present studies on the effects of osmolytes on mHTT structuring and aggregation, vis-a-vis pathogenicity. We show that stabilizing polyol osmolytes, by their generic activity in promoting protein structuring and compaction, drive aggregation of the disordered mHTT protein and simultaneously inhibit their binding to and sequestration of key transcription factors for improved homeostasis and cell survival under stress. These and related observations in the literature give strong support to the notion that lower molecular weight and structurally dynamic forms of mHTT contribute importantly to disease pathogenesis. Aging is associated with important changes in the cell environment-disease protein accumulation, reduced hydration, and macromolecular crowding as examples. These changes have significant consequences on the structuring and pathogenicity of the disordered mHTT protein. A crowded and less hydrated aging cell environment is conducive to mHTT binding to and inhibition of cell regulatory protein function on the one hand, and in promoting mHTT aggregation on the other hand, to culminate in Huntington disease presentation.

Network analysis of metabolomics, transcriptome and hormones reveals propionic acid-mediated novel survival strategy against drought in wheat

Propionic acid (PA), a low-molecular-weight organic acid, is crucial to plant life metabolism. However, the regulatory mechanism of PA-mediated drought resistance in wheat remains largely unknown. Herein, we reported on a regulatory network of PA-mediated drought resistance in wheat using integrated transcriptome and metabolomics analysis and verified genes associated with drought resistance. Compared to the water-treated group, the application of PA alleviated the damage of drought by increasing plant water content, antioxidant enzyme activities and decreasing the malondialdehyde level (MDA). Transcriptome and metabolomics analysis revealed that PA triggered upregulation of key genes and metabolites, including TaBCAT, TaALDH6A1, TaALDH7A1, TaCHI, TaFLS, chrysin, and galangin, which were involved in valine, leucine and isoleucine degradation or flavonoid biosynthesis, respectively. In addition, the expression of genes encoding auxin-related transcription factors (TFs) strikingly increased, such as auxin/indoleacetic acid (AUX/IAA) and auxin response factor (ARF). Moreover, PA activated abscisic acid (ABA) and indole-3-acetic acid (IAA) signalling pathways. Taken together, our findings suggest that PA promotes energy metabolism and antioxidant activities to confer wheat drought resistance by introducing comprehensive and systemic effects of valine, leucine and isoleucine degradation flavonoid biosynthesis. Furthermore, activated AUX/IAA and ARF TFs might serve vital roles in drought resistance via modulating IAA signalling. This study provides novel insights into PA-mediated crop resistance and the improvement of the agroecological environment.

Maize Grain Metabolite Profiling by NMR: Effects of Growing Year, Variety, and Cropping System

Considering that maize (Zea mays L.) is a staple food for a large segment of the population worldwide, many attempts have been made to improve the nutritional value of its grain and at the same time to achieve sustainable cropping systems. The present study aimed to characterize the composition and nutritional value of maize grain as influenced by cropping system, genetic background (variety), and growing year using untargeted NMR metabolomics. The composition of both water- (sugars and polyols, organic acids, and amino acids) and liposoluble metabolites (free and esterified fatty acids, sterols, and lipids) extracted from the maize grain was determined. Multivariate statistical analyses (PCA and ANOVA) pointed to the growing year and the variety as the most important random and fixed factors, respectively, influencing the metabolite profile. The samples were separated along PC1 and PC3 according to the growing year and the variety, respectively. A higher content of citric acid and diunsaturated fatty acids and a lower content of tyrosine, trigonelline, and monounsaturated fatty acids was observed in the organic with respect to the conventional variety. The effect of the cropping system was overwhelmed by the random effect of the growing year. The results provide novel knowledge on the influence of agronomic practices on maize micronutrient contents.

Structure and mechanism of the osmoregulated choline transporter BetT

The choline-glycine betaine pathway plays an important role in bacterial survival in hyperosmotic environments. Osmotic activation of the choline transporter BetT promotes the uptake of external choline for synthesizing the osmoprotective glycine betaine. Here, we report the cryo-electron microscopy structures of Pseudomonas syringae BetT in the apo and choline-bound states. Our structure shows that BetT forms a domain-swapped trimer with the C-terminal domain (CTD) of one protomer interacting with the transmembrane domain (TMD) of a neighboring protomer. The substrate choline is bound within a tryptophan prism at the central part of TMD. Together with functional characterization, our results suggest that in Pseudomonas species, including the plant pathogen P. syringae and the human pathogen Pseudomonas aeruginosa, BetT is locked at a low-activity state through CTD-mediated autoinhibition in the absence of osmotic stress, and its hyperosmotic activation involves the release of this autoinhibition.

Nanomedicines for Dry Eye Syndrome: Targeting Oxidative Stress with Modern Nanomaterial Strategies

Dry eye syndrome (DES) is a dynamic, chronic disease of the ocular surface and ocular appendages caused by inflammation. The most common symptoms include redness, itching, and blurred vision, resulting from dysfunction of the meibomian glands and impaired tear-film production. Factors contributing to the development of DES include environmental elements, such as UV radiation, and internal elements, such as hormonal imbalances. These factors increase oxidative stress, which exacerbates inflammation on the surface of the eye and accelerates the development of DES. In recent years, the incidence of DES has risen, leading to a greater need to develop effective treatments. Current treatments for dry eye are limited and primarily focus on alleviating individual symptoms, such as reducing inflammation of the ocular surface. However, it is crucial to understand the pathomechanism of the disease and tailor treatment to address the underlying causes to achieve the best possible therapeutic outcomes. Therefore, in this review, we analyzed the impact of oxidative stress on the development of DES to gain a better understanding of its pathomechanism and examined recently developed nanosystems that allow drugs to be delivered directly to the disease site.

Enhancing protein stability under stress: osmolyte-based deep eutectic solvents as a biocompatible and robust stabilizing medium for lysozyme under heat and cold shock

In biomedical and biotechnological domains, liquid protein formulations are vital tools, offering versatility across various fields. However, maintaining protein stability in a liquid form presents challenges due to environmental factors, driving research to refine formulations for broader applications. In our recent study, we investigated the relationship between deep eutectic solvents (DESs) and the natural presence of osmolytes in specific combinations, showcasing the effectiveness of a bioinspired osmolyte-based DES in stabilizing a model protein. Recognizing the need for a more nuanced understanding of osmolyte-based DES stabilization capabilities under different storage conditions, here we broadened the scope of our osmolyte-based DES experimental screening, and delved deeper into structural changes in the enzyme under these conditions. We subjected lysozyme solutions in DESs based on various kosmotropic osmolytes (TMAO, betaine, sarcosine, DMSP, ectoine, GPC, proline, sorbitol and taurine) paired either with another kosmotropic (glycerol) or with chaotropic osmolyte urea to rigorous conditions: heat shock (at 80 °C) and repetitive freeze-thaw cycles (at -20 and -80 °C). Changes in enzyme activity, colloidal stability, and conformational alterations were then monitored using bioassays, aggregation tests, and spectroscopic techniques (FT-IR and CD). Our results demonstrate the remarkable effectiveness of osmolyte-based DES in stabilizing lysozyme under stress conditions, with sarcosine- and betaine-based DESs containing glycerol as a hydrogen bond donor showing the highest efficacy, even at high enzyme loadings up to 200 mg ml-1. Investigation of the individual and combined effects of the DES components on enzyme stability confirmed the synergistic behavior of the kosmotrope-urea mixtures and the cumulative effects in kosmotrope-glycerol mixtures. Additionally, we have shown that the interplay between the enzyme's active and stable (but inactive) states is highly influenced by the water content in DESs. Finally, toxicity assessments of osmolyte-based DESs using cell lines (Caco-2, HaCaT, and HeLa) revealed no risks to human health.

Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability

In solvent-modulated protein folding, under certain physiological conditions, an equilibrium exists between the unfolded and folded states of the protein without any need to break or make a covalent bond. In this process, interactions between various protein groups (peptides) and solvent molecules are known to play a major role in determining the directionality of the chemical reaction. However, an understanding of the mechanism of action of the co(solvent) by a generic theoretical underpinning is lacking. In this study, a generic solvation model is developed based on statistical mechanics and the thermodynamic transfer free energy model by considering the microenvironment polarity of the interacting co(solvent)-protein system. According to this model, polarity and the fractional solvent-accessible surface areas contribute to the interaction energies. The present model includes various orientations of participating interactant solvent surfaces of suitable areas. As model systems, besides the backbone we consider naturally occurring amino acid residues solvated in ten different osmolytes, small organic compounds known to modulate protein stability. The present model is able to predict the correct trend of the osmolyte-peptide interactions ranging from stabilizing to destabilizing not only for the backbone but also for side chains. Our model predicts Asn, Gln, Asp, Glu, Arg and Pro to be highly stable in most of the protecting osmolytes while Ala, Val, Ile, Leu, Thr, Met, Lys, Phe, Trp and Tyr are predicted to be moderately stable, and Ser, Cys and Histidine are predicted to be least stable. However, in denaturing solvents, both backbone and side chain models show similar stabilities in urea and guanidine. One of the important aspects of this model is that it is essentially parameter-free and consistent with the electrostatics of the interaction partners that make this model suitable for estimating any solute-solvent interaction energies.

Evidence for partial functional overlap of KEA and MSL transport proteins in the chloroplast inner envelope of Arabidopsis thaliana

Arabidopsis thaliana possesses two different ion-export mechanisms in the plastid inner envelope membrane. Due to a genome duplication, the transport proteins are encoded by partly redundant loci: K+-efflux antiporter1 (KEA1) and KEA2 and mechanosensitive channel of small conductance-like2 (MSL2) and MSL3. Thus far, a functional link between these two mechanisms has not been established. Here, we show that kea1msl2 loss-of-function mutants exhibit phenotypes such as slow growth, reduced photosynthesis and changes in chloroplast morphology, several of which are distinct from either single mutants and do not resemble kea1kea2 or msl2msl3 double mutants. Our data suggest that KEA1 and MSL2 function in concert to maintain plastid ion homeostasis and osmoregulation. Their interplay is critical for proper chloroplast development, organelle function, and plant performance.

Ice in the intertidal: patterns and processes of freeze tolerance in intertidal invertebrates

Many intertidal invertebrates are freeze tolerant, meaning that they can survive ice formation within their body cavity. Freeze tolerance is a fascinating trait, and understanding its mechanisms is important for predicting the survival of intertidal animals during extreme cold weather events. In this Review, we bring together current research on the ecology, biochemistry and physiology of this group of freeze-tolerant organisms. We first introduce the ecology of the intertidal zone, then highlight the strong geographic and taxonomic biases within the current body of literature on this topic. Next, we detail current knowledge on the mechanisms of freeze tolerance used by intertidal invertebrates. Although the mechanisms of freeze tolerance in terrestrial arthropods have been well-explored, marine invertebrate freeze tolerance is less well understood and does not appear to work similarly because of the osmotic differences that come with living in seawater. Freeze tolerance mechanisms thought to be utilized by intertidal invertebrates include: (1) low molecular weight cryoprotectants, such as compatible osmolytes and anaerobic by-products; (2) high molecular weight cryoprotectants, such as ice-binding proteins; as well as (3) other molecular mechanisms involving heat shock proteins and aquaporins. Lastly, we describe untested hypotheses, methods and approaches that researchers can use to fill current knowledge gaps. Understanding the mechanisms and consequences of freeze tolerance in the intertidal zone has many important ecological implications, but also provides an opportunity to broaden our understanding of the mechanisms of freeze tolerance more generally.

Insights into the dynamic interactions of RNase a and osmolytes through computational approaches

Osmolytes are small organic molecules that are known to stabilize proteins and other biological macromolecules under various stressful conditions. They belong to various categories such as amino acids, methylamines, and polyols. These substances are commonly known as 'compatible solutes' because they do not disrupt cellular processes and help regulate the osmotic balance within cells. In the case of ribonuclease A (RNase A), which is prone to aggregation, the presence of osmolytes can help to maintain its structural stability and prevent unwanted interactions leading to protein aggregation. In this study, we investigated the interaction between RNase A and several osmolytes using molecular docking and molecular dynamics (MD) simulations. We performed molecular docking to predict the binding mode and binding affinity of each osmolyte with RNase A. MD simulations were then carried out to investigate the dynamics and stability of the RNase A-osmolyte complexes. Our results show that two osmolytes, glucosylglycerol and sucrose have favorable binding affinities with RNase A. The possible role of these osmolytes in stabilizing the RNase A and prevention of aggregation is also explored. By providing computational insights into the interaction between RNase A and osmolytes, the study offers valuable information that could aid in comprehending the mechanisms by which osmolytes protect proteins and help in designing therapeutics for protein-related disorders based on osmolytes. These findings may have significant implications for the development of novel strategies aimed at preventing protein misfolding and aggregation in diverse disease conditions.Communicated by Ramaswamy H. Sarma.

Effects of hypo-osmotic stress on osmoregulation, antioxidant response, and energy metabolism in sea cucumber Holothuria moebii under desalination environment

With global climate changing, hypo-salinity events are increasing in frequency and duration because of continuous rainfall and freshwater inflow, which causes reduced cytosolic osmolarity and cellular stress responses in aquatic animals. Sea cucumbers are considered stenohaline because they lack osmoregulatory organs and are vulnerable to salinity fluctuations. In this study, we performed multiple biochemical assays, de novo transcriptomics, and widely targeted metabolomics to comprehensively explore the osmoregulatory mechanisms and physiological responses of sea cucumber Holothuria moebii to hypo-osmotic stress, which is a representative specie that is frequently exposed to hypo-saline intertidal zones. Our results found that H. moebii contracted their ambulacral feet and oral tentacles, and the coelomic fluid ion concentrations were reduced to be consistent with the environment. The microvilli of intestines and respiratory trees underwent degeneration, and the cytoplasm exhibited swelling and vacuolation. Moreover, the Na+, K+, and Cl- concentrations and Na+/K+-ATPase activity were significantly reduced under hypo-osmotic stress. The decrease in protein kinase A activity and increase in 5'-AMP level indicated a significant inhibition of the cAMP signaling pathway to regulate ion concentrations. And small intracellular organic molecules (amino acids, nucleotides and their derivatives) also play crucial roles in osmoregulation through oxidative deamination of glutamate, nucleotide catabolism, and nucleic acid synthesis. Moreover, lysosomes and peroxisomes removed oxidative damage, whereas antioxidant metabolites, such as N-acetyl amino acids and glutathione, were increased to resist oxidative stress. With prolonged hypo-osmotic stress, glycerophospholipid metabolism was enhanced to maintain membrane stability. Furthermore, acyl-CoA-binding protein activity was significantly inhibited, and only a small amount of acylcarnitine was significantly accumulated, which indicated a disruption in energy metabolism. PPAR signaling pathway and choline content were up-regulated to promote fatty acid metabolism under hypo-osmotic stress. Overall, our results provide new insights into the osmoregulatory mechanisms and physiological responses of sea cucumbers to hypo-osmotic stress.

Low salinity influences the dose-dependent transcriptomic responses of oysters to cadmium

Species in estuaries tend to undergo both cadmium (Cd) and low salinity stress. However, how low salinity affects the Cd toxicity has not been fully understood. Investigating the impacts of low salinity on the dose-response relationships between Cd and biological endpoints has potential to enhance our understanding of the combined effects of low salinity and Cd. In this work, changes in the transcriptomes of Pacific oysters were analyzed following exposure to Cd (5, 20, 80 μg/L Cd2+) under normal (31.4 psu) and low (15.7 psu) salinity conditions, and then the dose-response relationship between Cd and transcriptome was characterized in a high-throughput manner. The benchmark dose (BMD) of gene expression, as a point of departure (POD), was also calculated based on the fitted dose-response model. We found that low salinity treatment significantly influenced the dose-response relationships between Cd and transcripts in oysters indicated by altered dose-response curves. In details, a total of 219 DEGs were commonly fitted to best models under both normal and low salinity conditions. Nearly three quarters of dose-response curves varied with salinity condition. Some monotonic dose-response curves in normal salinity condition even were replaced by nonmonotonic curves in low salinity condition. Low salinity treatment decreased the PODs of differentially expressed genes induced by Cd, suggesting that gene differential expression was more prone to being triggered by Cd in low salinity condition. The changed sensitivity to Cd in low salinity condition should be taken into consideration when using oyster as an indicator to assess the ecological risk of Cd pollution in estuaries.

Siloxane Containing Polyether Groups-Synthesis and Use as an Anti-Biocorrosion Coating

In the presented study, the effectiveness of a siloxane polyether (HOL7) coating on glass against microbiological colonization was assessed using microalgae as a key component of widespread aerial biofilms. The siloxane polyether was successfully synthesized by a hydrosilylation reaction in the presence of Karstedt's catalyst. The product structure was confirmed by NMR spectroscopy and GPC analysis. In addition, the thermal stability of HOL7 was studied by thermogravimetric measurement. Subsequently, the surfaces of glass plates were modified with the obtained organosilicon derivative. In the next step, a microalgal experiment was conducted. A mixture of four strains of algal taxa isolated from building materials was used for the experiment-Chlorodium saccharophilum PNK010, Klebsormidium flaccidum PNK013, Pseudostichococcus monallantoides PNK037, and Trebouxia aggregata PNK080. The choice of these algae followed from their wide occurrence in terrestrial environments. Application of an organofunctional siloxane compound on the glass reduced, more or less effectively, the photosynthetic activity of algal cells, depending on the concentration of the compound. Since the structure of the compound was not based on biocide-active agents, its effectiveness was associated with a reduction in water content in the cells.

Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins

Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.

Thiol dioxygenases: from structures to functions

Thiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of action and the different substrate specificity of these enzymes. Concomitantly, the physiological role of thiol dioxygenation in prokaryotes and eukaryotes has been studied through genetic and physiological approaches. Further structural characterization is necessary to enable precise and safe manipulation of thiol dioxygenases (TDOs) for therapeutic, industrial, and agricultural applications.

Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations

N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H2O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

Two populations of protein molecules detected by small-angle neutron and X-ray scattering (SANS and SAXS) in lyophilized protein:lyoprotector (disaccharide) systems

Two protein interaction peaks are observed in pharmaceutically-relevant protein (serum albumin) : disaccharide 1 : 1 and 1 : 3 (w/w) freeze-dried systems for the first time. In samples with a higher disaccharide content, the protein-protein distances are longer for both populations, while the fraction of the protein population with a shorter protein-protein distance is lower. Both factors would favor better stability against aggregation for disaccharide-rich protein formulations. This study provides direct experimental support for a "dilution" hypothesis as a potential stabilization mechanism for freeze-dried protein formulations.