Green Synthesis of the Triazine Derivatives and their Application for the Benign Electrocatalytic Reaction of Nitrate Reduction to Ammonia.

This work uses green sustainable reactions twice. Firstly, it is microwave synthesis: 2,4,6-tribiphenyl-4-yl-1,3,5-triazine and similar compounds were prepared in a closed microwave reactor in n-octane by the Friedel-Crafts reaction. Second, a hybrid electrocatalyst for the highly demanded electrochemical reaction of nitrate reduction to ammonia (NO3RR) was prepared based on this material. This reaction has great potential to replace the energy-intensive Haber-Bosch process, and in addition, has independent value for the elimination of nitrate contamination of water resources. As shown in the work, microwave synthesis is an eco-friendly method for the synthesis of complex organic compounds; fast, selective and with a high yield of the target product. The electrocatalyst deposited on the graphite electrode consisted of a layer of 2,4,6-tribiphenyl-4-yl-1,3,5-triazine and related compounds coated with cobalt oxide. The hybrid catalyst was firmly retained on the graphite electrode during NO3RR and the material showed impressive stability with almost no decrease in catalytic activity even after the fifth cycle. Both 2,4,6-tribiphenyl-4-yl-1,3,5-triazine and the catalyst based on this substance were characterized by SEM, XPS, XRD, UV-vis spectra, cyclic (and linear) voltammetry, and chronoamperometry. This work can serve as a starting point for the development of stable and durable electrocatalysts for NO3RR using triazine derivatives.

Enhancing Efficiency of Nitrate Reduction to Ammonia by Fe and Co Nanoparticle-Based Bimetallic Electrocatalyst.

The green and sustainable electrocatalytic conversion of nitrogen-containing compounds to ammonia is currently in high demand in order to replace the eco-unfriendly Haber-Bosch process. Model catalysts for the nitrate reduction reaction were obtained by electrodeposition of metal Co, Fe, and bimetallic Fe/Co nanoparticles from aqueous solutions onto a graphite substrate. The samples were characterized by the following methods: SEM, XRD, XPS, UV-vis spectroscopy, cyclic (and linear) voltammetry, chronoamperometry, and electrochemical impedance spectroscopy. In addition, the determination of the electrochemically active surface was also performed for all electrocatalysts. The best electrocatalyst was a sample containing Fe-nanoparticles on the layer of Co-nanoparticles, which showed a Faradaic efficiency of 58.2% (E = -0.785 V vs. RHE) at an ammonia yield rate of 14.6 µmol h-1 cm-2 (at ambient condition). An opinion was expressed to elucidate the mechanism of coordinated electrocatalytic action of a bimetallic electrocatalyst. This work can serve primarily as a starting point for future investigations on electrocatalytic conversion reactions to ammonia using model catalysts of the proposed type.

Reassessment of pore occlusion in some diatom taxa with re-evaluation of Placoneis Mereschkowsky (Bacillariophyceae: Cymbellales) and description of two new genera.

In this article, the history and taxonomy of Placoneis gastrum, the type species of the genus Placoneis, was discussed. We investigated the structure of pore occlusions in Placoneis and related genera. As a result, we propose a new classification for tectulum-like types of pore occlusions. The new classification is congruent with previously-published and newly-constructed phylogenies based on molecular data. Based on the different structures of the pore occlusions, species of Placoneis are transferred to Witkowskia gen. nov. Hence, 168 new combinations are introduced. A new diatom species, with a similar morphology to Placoneis flabellata, was discovered in Bac Kan Province, Vietnam. It is described in this article as Chudaevia densistriata sp. nov. Placoneis flabellata is transferred to Chudaevia gen. nov. We also illustrate Placoneis flabellata herein and compare it to Chudaevia densistriata sp. nov. An unknown diatom, similar to Placoneis coloradensis, was discovered in Chukotka, Russia. It is introduced as Placoneis elinae sp. nov. below. Additionally, we discuss the distribution of some species of Witkowskia gen. nov. and Chudaevia gen. nov.

Bioinformatics Analysis of Actin Interactome: Characterization of the Nuclear and Cytoplasmic Actin-Binding Proteins.

Actin is present in the cytoplasm and nucleus of every eukaryotic cell. In the cytoplasm, framework and motor functions of actin are associated with its ability to polymerize to form F-actin. In the nucleus, globular actin plays a significant functional role. For a globular protein, actin has a uniquely large number of proteins with which it interacts. Bioinformatics analysis of the actin interactome showed that only a part of actin-binding proteins are both cytoplasmic and nuclear. There are proteins that interact only with cytoplasmic, or only with nuclear actin. The first pool includes proteins associated with the formation, regulation, and functioning of the actin cytoskeleton predominate, while nuclear actin-binding proteins are involved in the majority of key nuclear processes, from regulation of transcription to DNA damage response. Bioinformatics analysis of the structure of actin-binding proteins showed that these are mainly intrinsically disordered proteins, many of which are part of membrane-less organelles. Interestingly, although the number of intrinsically disordered actin-binding proteins in the nucleus is greater than in the cytoplasm, the drivers for the formation of the membrane-less organelles in the cytoplasm are significantly (four times) greater than in the nucleus.

Clinical Evaluation of Effectiveness and Safety of Combined Use of Dietary Supplements Amberen® and Smart B® in Women with Climacteric Syndrome in Perimenopause.

INTRODUCTION: Perimenopause is a time of transition in a woman's life that links her reproductive years to the cessation of ovulation, or menopause. For many women, this time is characterized by a variety of physiological and lifestyle changes, including increasing irregularity in menstrual bleeding, frequency and severity of vasomotor symptoms, etc. Therapies evaluated specifically for the perimenopausal women are very limited. This study aimed to evaluate the effectiveness and safety of Amberen® (a succinate-based non-hormonal supplement) combined with a Smart B® (vitamin B) complex in women with typical (without complications) mild to moderate climacteric syndrome during perimenopause. METHODS: Women up to 50 years of age, in perimenopause, with vasomotor and psychosomatic symptoms of the climacteric syndrome were enrolled for the study. The trial was randomized, double-blinded, placebo-controlled, comparative, and prospective. RESULTS: A total of 106 participants were enrolled in the trial and, per protocol, 105 completed the trial. We observed statistically significant improvements in most of the Greene Climacteric Scale symptoms, State-Trait Anxiety Inventory (STAI), Hospital Anxiety and Depression Scale (HADS), and Well-being, Activity, and Mood (WAM) scores. The intervention was well tolerated with few adverse effects reported to be mild and transient. CONCLUSION: The use of this dietary supplement is safe and eliminates or improves vasomotor and psychosomatic symptoms of climacteric symptoms in perimenopausal women: it improves sleep and cognitive abilities, lowers depression and anxiety, improves mood and well-being, and positively affects quality of life. GOV IDENTIFIER: NCT03897738.

Correction: Sulatskaya et al. Structural Features of Amyloid Fibrils Formed from the Full-Length and Truncated Forms of Beta-2-Microglobulin Probed by Fluorescent Dye Thioflavin T. Int. J. Mol. Sci. 2018, 19, 2762.

In the original publication [...].

Correction: Stepanenko et al. Trypsin Induced Degradation of Amyloid Fibrils. Int. J. Mol. Sci.2021, 22, 4828.

In the original [...].

Broken but not beaten: Challenge of reducing the amyloids pathogenicity by degradation.

BACKGROUND: The accumulation of ordered protein aggregates, amyloid fibrils, accompanies various neurodegenerative diseases (such as Parkinson's, Huntington's, Alzheimer's, etc.) and causes a wide range of systemic and local amyloidoses (such as insulin, hemodialysis amyloidosis, etc.). Such pathologies are usually diagnosed when the disease is already irreversible and a large amount of amyloid plaques have accumulated. In recent years, new drugs aimed at reducing amyloid levels have been actively developed. However, although clinical trials have demonstrated a reduction in amyloid plaque size with these drugs, their effect on disease progression has been controversial and associated with significant side effects, the reasons of which are not fully understood. AIM OF REVIEW: The purpose of this review is to summarize extensive array of data on the effect of exogenous and endogenous factors (physico-mechanical effects, chemical effects of low molecular weight compounds, macromolecules and their complexes) on the structure and pathogenicity of mature amyloids for proposing future directions of the development of effective and safe anti-amyloid therapeutics. KEY SCIENTIFIC CONCEPTS OF REVIEW: Our analysis show that destruction of amyloids is in most cases incomplete and degradation products often retain the properties of amyloids (including high and sometimes higher than fibrils, cytotoxicity), accelerate amyloidogenesis and promote the propagation of amyloids between cells. Probably, the appearance of protein aggregates, polymorphic in structure and properties (such as amorphous aggregates, fibril fragments, amyloid oligomers, etc.), formed because of uncontrolled degradation of amyloids, may be one of the reasons for the ambiguous effectiveness and serious side effects of the anti-amyloid drugs. This means that all medications that are supposed to be used both for degradation and slow down the fibrillogenesis must first be tested on mature fibrils: the mechanism of drug action and cytotoxic, seeding, and infectious activity of the degradation products must be analyzed.

Von-Hippel Lindau protein amyloid formation. The role of GST-tag.

In the last decade, much attention was given to the study of physiological amyloid fibrils. These structures include A-bodies, which are the nucleolar fibrillar formations that appear in the response to acidosis and heat shock, and disassemble after the end of stress. One of the proteins involved in the biogenesis of A-bodies, regardless of the type of stress, is Von-Hippel Lindau protein (VHL). Known also as a tumor suppressor, VHL is capable to form amyloid fibrils both in vitro and in vivo in response to the environment acidification. As with most amyloidogenic proteins fusion with various tags is used to increase the solubility of VHL. Here, we first performed AFM-study of fibrils formed by VHL protein and by VHL fused with GST-tag (GST-VHL) at acidic conditions. It was shown that formed by full-length VHL fibrils are short heterogenic structures with persistent length of 2400 nm and average contour length of 409 nm. GST-tag catalyzes VHL amyloid fibril formation, superimpose chirality, increases length and level of hierarchy, but decreases rigidity of amyloid fibrils. The obtained data indicate that tagging can significantly affect the fibrillogenesis of the target protein.

Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines.

The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.

Structural determinants of odorant-binding proteins affecting their ability to form amyloid fibrils.

The formation of amyloid fibrils is associated with many severe pathologies as well as the execution of essential physiological functions by proteins. Despite the diversity, all amyloids share a similar morphology and consist of stacked ß-strands, suggesting high amyloidogenicity of native proteins enriched with ß-structure. Such proteins include those with a ß-barrel-like structure with ß-strands arranged into a cylindrical ß-sheet. However, the mechanisms responsible for destabilization of the native state and triggering fibrillogenesis have not thoroughly explored yet. Here we analyze the structural determinants of fibrillogenesis in proteins with ß-barrel structures on the example of odorant-binding protein (OBP), whose amyloidogenicity was recently demonstrated in vitro. We reveal a crucial role in the fibrillogenesis of OBPs for the "open" conformation of the molecule. This conformation is achieved by disrupting the interaction between the ß-barrel and the C-terminus of protein monomers or dimers, which exposes "sticky" amyloidogenic sites for interaction. The data suggest that the "open" conformation of OBPs can be induced by destabilizing the native ß-barrel structure through the disruption of: 1) intramolecular disulfide cross-linking and non-covalent contacts between the C-terminal fragment and ß-barrel in the protein's monomeric form, or 2) intermolecular contacts involved in domain swapping in the protein's dimeric form.

Prediction of the Feasibility of Using the ≪Gold Standard≫ Thioflavin T to Detect Amyloid Fibril in Acidic Media.

Ordered protein aggregates, amyloid fibrils, form toxic plaques in the human body in amyloidosis and neurodegenerative diseases and provide adaptive benefits to pathogens and to reduce the nutritional value of legumes. To identify the amyloidogenic properties of proteins and study the processes of amyloid fibril formation and degradation, the cationic dye thioflavin T (ThT) is the most commonly used. However, its use in acidic environments that induce amyloid formation in vitro can sometimes lead to misinterpretation of experimental results due to electrostatic repulsion. In this work, we show that calculating the net charge per residue of amyloidogenic proteins or peptides is a simple and effective approach for predicting whether their fibrils will interact with ThT at acidic pH. In particular, it was shown that at pH 2, proteins and peptides with a net charge per residue > +0.18 are virtually unstained by this fluorescent probe. The applicability of the proposed approach was demonstrated by predicting and experimentally confirming the absence of ThT interaction with amyloids formed from green fluorescent (sfGFP) and odorant-binding (bOBP) proteins, whose fibrillogenesis was first carried out in an acidic environment. Correct experimental evidence that the inability to detect these fibrils under acidic conditions is precisely because of the lack of dye binding to amyloids (and not their specific structure or the low fluorescence quantum yield of the bound dye) and that the number of ThT molecules associated with fibrils increases with decreasing acidity of the medium was obtained by using the equilibrium microdialysis approach.

Whole-genome sequence of the non-rhizobial root nodule endophyte Bosea sp. strain 685 isolated from the root nodule of Astragalus umbellatus Bunge., growing on the Kamchatka Peninsula.

This study reports the whole-genome sequence of an endosymbiotic bacteria Bosea sp. strain 685, which was isolated from the root nodule of Astragalus umbellatus Bunge. in the Kamchatka Peninsula, Russia. The genome consists of one chromosome and one plasmid with a total length of 6,795,213 bp and 65.37% of GC content.

Stress-granules, P-bodies, and cell aging: A bioinformatics study.

At the molecular level, aging is often accompanied by dysfunction of stress-induced membrane-less organelles (MLOs) and changes in their physical state (or material properties). In this work, we analyzed the proteins included in the proteome of stress granules (SGs) and P-bodies for their tendency to transform the physical state of these MLOs. Particular attention was paid to the proteins whose gene expression changes during replicative aging. It was shown that the proteome of the studied MLOs consists of intrinsically disordered proteins, 30-40% of which are potentially capable of liquid-liquid phase separation (LLPS). Proteins whose gene expression changes during the transition of human cells to a senescent state make up about 20% of the studied proteomes. There is a statistically significant increase in the number of positively charged proteins in both datasets studied compared to the complete proteomes of these organelles. An increase in the relative content of DNA-, but not RNA-binding proteins, was also found in the SG dataset with senescence-related processes. Among SGs proteins potentially involved in senescent processes, there is an increase in the abundance of potentially amyloidogenic proteins compared to the whole proteome. Proteins common to SGs and P-bodies, potentially involved in processes associated with senescence, form clusters of interacting proteins. The largest cluster is represented by RNA-binding proteins involved in RNA processing and translation regulation. These data indicate that SG proteins, but not proteins of P-bodies, are more likely to transform the physical state of MLOs. Furthermore, these MLOs can participate in processes associated with aging in a coordinated manner.

Small-angle X-ray scattering structural insights into alternative pathway of actin oligomerization associated with inactivated state.

In addition to the well-known monomeric globular (G-actin) and polymeric fibrillar (F-actin) forms, actin can exist in the so-called inactivated form (I-actin). Hsp70 chaperon, prefoldin, and CCT chaperonin are required to obtain native globular state. In contrast, I-actin is spontaneously formed in the absence of intracellular folding machinery. I-actin can be obtained from G-actin by elimination of divalent ion, incubation in presence of small concentrations of denaturants, and by heat exposure. Since G-actin is a quasi-stationary, thermodynamically unstable form, it can gradually transform into inactivated state in the absence of chelating/denaturating agents or heat exposure, but the transition is much slower. I-actin was shown to associate into oligomers up to the molecular weight of 14-16 G-actin monomers, though the structure of these oligomers remains uncharacterized. This study employs small-angle X-ray scattering to reveal novel insights into the oligomerization process of such spontaneously formed inactivated actin. These oligomers are differentiated from F-actin through comparative analysis, highlighting a unique oligomerization pathway.

PML Body Biogenesis: A Delicate Balance of Interactions.

PML bodies are subnuclear protein complexes that play a crucial role in various physiological and pathological cellular processes. One of the general structural proteins of PML bodies is a member of the tripartite motif (TRIM) family-promyelocytic leukemia protein (PML). It is known that PML interacts with over a hundred partners, and the protein itself is represented by several major isoforms, differing in their variable and disordered C-terminal end due to alternative splicing. Despite nearly 30 years of research, the mechanisms underlying PML body formation and the role of PML proteins in this process remain largely unclear. In this review, we examine the literature and highlight recent progress in this field, with a particular focus on understanding the role of individual domains of the PML protein, its post-translational modifications, and polyvalent nonspecific interactions in the formation of PML bodies. Additionally, based on the available literature, we propose a new hypothetical model of PML body formation.

Gandhia gen. nov.-A New Diatom Genus with Unusual Morphology Split Off from the Genus Navicula Bory.

A new naviculoid diatom genus, Gandhia gen. nov., was described based on a detailed morphological investigation using light and scanning electron microscopy. Gandhia obtecta (Jüttner and Cox) Kulikovskiy, Glushchenko, Iurmanov, M.Thacker, B.Karthick and Kociolek comb. nov. was previously described as a member of the genus Navicula Bory sensu lato. This species differs from other species in the genus Navicula s.l. by the presence of an internal siliceous lamina covering the alveoli and forming the image of longitudinal lines on either side of the axial area, visible in LM. The presence of this siliceous lamina is similar to laminae in genera such as Pinnularia and Gomphoneis. This unusual morphology is not typical for Navicula sensu stricto, as previously noted by other scientists. Additional investigation of Gandhia obtecta comb. nov. and Gandhia ramosissimoides (H.P. Gandhi) Kulikovskiy, Glushchenko, M.Thacker, B.Karthick and Kociolek comb. nov. from waterbodies of the Western Ghats and the Himalayan region was conducted. Comparison with other species with the same morphological features included two additional species in the genus, namely, Gandhia jakovljevicii (Hustedt) Kulikovskiy, Glushchenko, M.Thacker, B.Karthick, and Kociolek comb. nov. and Gandhia lucida (Pantocsek) Kulikovskiy, Glushchenko, M.Thacker, B.Karthick and Kociolek comb. nov. We discuss the biogeographic patterns of the species, including disjuncts between Europe and Asia.

On the Prevalence and Roles of Proteins Undergoing Liquid-Liquid Phase Separation in the Biogenesis of PML-Bodies.

The formation and function of membrane-less organelles (MLOs) is one of the main driving forces in the molecular life of the cell. These processes are based on the separation of biopolymers into phases regulated by multiple specific and nonspecific inter- and intramolecular interactions. Among the realm of MLOs, a special place is taken by the promyelocytic leukemia nuclear bodies (PML-NBs or PML bodies), which are the intranuclear compartments involved in the regulation of cellular metabolism, transcription, the maintenance of genome stability, responses to viral infection, apoptosis, and tumor suppression. According to the accepted models, specific interactions, such as SUMO/SIM, the formation of disulfide bonds, etc., play a decisive role in the biogenesis of PML bodies. In this work, a number of bioinformatics approaches were used to study proteins found in the proteome of PML bodies for their tendency for spontaneous liquid-liquid phase separation (LLPS), which is usually caused by weak nonspecific interactions. A total of 205 proteins found in PML bodies have been identified. It has been suggested that UBC9, P53, HIPK2, and SUMO1 can be considered as the scaffold proteins of PML bodies. It was shown that more than half of the proteins in the analyzed proteome are capable of spontaneous LLPS, with 85% of the analyzed proteins being intrinsically disordered proteins (IDPs) and the remaining 15% being proteins with intrinsically disordered protein regions (IDPRs). About 44% of all proteins analyzed in this study contain SUMO binding sites and can potentially be SUMOylated. These data suggest that weak nonspecific interactions play a significantly larger role in the formation and biogenesis of PML bodies than previously expected.