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Metal–organic frameworks (MOFs) possess unique flexibility of structure and properties, which drives them toward applications as water adsorbents in many emerging technologies, such as adsorptive heat transformation, water harvesting from the air, dehumidification, and desalination. A deep understanding of the surface phenomena is a prerequisite for the target-oriented design of MOFs with the required adsorption properties. In this work, we comprehensively study the effect of functional groups on water adsorption on a series CAU-10-X substituted with both hydrophilic (X = NH2) and hydrophobic (X = NO2) groups in the linker. The adsorption equilibrium is measured at P = 7.6–42 mbar and T = 5–100 °C. The study of water adsorption by a set of mutually complementary physicochemical methods (TG, XRD in situ, FTIR, and 1H NMR relaxometry) elucidates the nature of primary adsorption sites and water adsorption mechanisms.

Using a complex of physical and electrochemical methods, the effect of R-substituent on the adsorption of 5-R-3-amino-1,2,4-triazoles on copper surface in neutral buffer solution was studied. Minim...

The effect of the natural saponin glycyrrhizic acid (GA) and polysaccharide arabinogalactan (AG) on the transmembrane potential of rat thymocytes was investigated using the potential-sensitive fluorescent probe 4-(p-dimethylaminostyryl)-1-methylpyridinium (DSM). Incubation of cells with GA in micellar form resulted in a decrease of the amplitude of observed fluorescence kinetics that points out to a decrease of the transmembrane potential. The proposed mechanism is an increase of membrane ion permeability (passive ion transport) of the plasma cell membrane due to GA incorporation. The incorporation of GA molecules into the cell membrane is extremely sensitive to the degree of GA dissociation. The neutral form of glycyrrhizic acid enters the lipid bilayer in contrast to the deprotonated anionic form. The incubation of rat thymocytes with anionic form of GA, namely with its disodium salt, has no effect on the fluorescence kinetics. The possible reasons of this phenomenon are discussed in the light of the nuclear magnetic resonance (NMR) and molecular dynamics (MD) data. The treatment of thymocytes with AG affects only the initial rate of the probe incorporation. The proposed mechanism is that AG covers the surface of the cell membrane and forms a barrier for the probe. Additionally, our experiments demonstrated that both polysaccharide AG and GA in the neutral form (but not Na2GA) effectively capture the cationic probe in an aqueous solution and then deliver it to the cell membrane.

The accessibility of glucuronoxylan from a refined, bleached Eucalyptus globulus industrial kraft pulp in 0–18% aqueous NaOH solution at room temperature (25°C) was studied. The extraction profile revealed a maximum extraction of xylan in the pulp at about 10–12% NaOH concentration and was explained by the maximum swelling of the pulp according to the Gibbs-Donnan equilibrium. The kinetics of xylan removal and the monitoring of its structural features were performed at 5 and 10% NaOH concentrations. The maximum yields of xylans with 10% and 5% NaOH were as high as 90% and 60% for 2 h extraction, respectively. The structural features of xylan were assessed by acid methanolysis and one-dimensional (1D)/two-dimensional (2D) nuclear magnetic resonance (NMR), and the molecular weight by size exclusion chromatography (SEC). The xylan extracted with 10% NaOH had a slightly higher molecular weight and a lower branching with uronic moieties than the xylan extracted with 5% NaOH. The former was less pure (contained more β-cellulose) than the latter. Structural studies by NMR resulted in the conclusion that there are at least two types of xylans removed from the pulp: one xylan with relatively high 4-O-methyl-α-D-glucuronosyl [MeGlcA-(1→] and [→2)-MeGlcA-(1→] substituents and another xylan with a much lower substitution with uronic residues.

Hypothesis Magnetic liposomes are shown to release the entrapped dye once modulated by low frequency AC MF. The mechanism and effectiveness of MF application should depend on lipid composition, magnetic nanoparticles (MNPs) properties, temperature and field parameters. Experiments The study was performed using liposomes of various lipid composition and embedded hydrophobic MNPs. The liposomes structural changes were studied by the transmission electron microscopy (TEM) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and the leakage was monitored by the fluorescent dye release. Findings Magnetic liposomes exposure to the AC MF resulted in the clustering of the MNPs in the membranes and disruption of the lipid packaging. Addition of cholesterol diminished the dye release from the saturated lipid-based liposomes. Replacement of the saturated lipid for unsaturated one also decreased the dye release. The dye release depended on the strength, but not the frequency of the field. Thus, the oscillating motion of MNPs in AC MF ruptures the gel phase membranes of saturated lipids. As the temperature increases the disruption also increases. In the liquid crystalline membranes formed by unsaturated lipids the deformations and defects created by mechanical motion of the MNPs are more likely to heal and results in decreased release.

The present paper reports about the experimental characterization of a recently developed composite sorbent of water, LiCl/vermiculite, for thermal energy storage applications. The sorption ability as well as the thermal storage capacity (TSC) of the material itself were tested in a dedicated TG/DSC apparatus, under two relevant boundary conditions, namely, seasonal (SS) and daily (DS) storage applications. The dynamic behavior of the composite sorbent was tested by means of a G-LTJ apparatus in flat-plate adsorber configuration, under both SS and DS working conditions. Finally, preliminary tests on a lab-scale TES configuration were performed and reported. The main outcomes confirm that the composite is promising for TES applications, reaching the TSC up to 2.15 kJ/g under SS conditions. The stability of the composite was proven for 14 consecutive sorption/desorption cycles under conditions similar to those at real SS and DS cycles. The kinetic adsorption tests confirmed a slowdown of the sorption dynamics when passing from 1.7–2.0 mm to 2.36–2.80 mm of the grain size. Furthermore, the adsorption kinetic under SS mode is faster than of DS one. The preliminary testing in the lab-scale TES at SS cycle allowed getting TSC up to 1.25 kJ/g with a specific power up to 2.1 kW/kg.

The difficulty of the discharge of nickel ions due to the adsorption of the addition of diaminomeleodinitrile on the electrode surface contributes to the formation of a fine crystalline precipitate with high reflectivity. Therefore, in this work, we studied the adsorption capacity of diaminomeleodinitrile on the surface of nickel from borate buffer solution in the cathodic and anodic regions. The values of its free adsorption energy were determined, which were at a potential of -0.65 V - 39.7 kJ / mol, and at 0.2 V - 66.2 kJ / mol. It was determined that diaminomeleodinitrile has adsorbed on the surface of nickel from borate buffer solution at pH = 7.4 mainly due to the forces of chemical interaction. It has been established that on the oxidized nickel surface, the adsorption of diaminomeleodinitrile begins in the region of lower concentrations compared to the “clean” surface. On average, a monolayer has formed within 60-75 min, while changes in the phase angle of the reflected light are small, due to the small size of the adsorbed molecule. It was determined that on the oxidized surface these changes are more than on the “clean” one. By method of reflective ellipsometry, which allows to measure and analyze the differences in the polarization parameters of a plane polarized light flux incident at an angle on two homogeneous media with different optical properties, the thickness of the resulting monolayer was determined. On an oxidized surface, it was ~ 0.5 nm, and on a “clean” surface, ~ 0.2 nm. When comparing these thicknesses with the size of the diaminomeleodinitrile molecule, it can be assumed that at a potential of 0.2 V, the diaminomeleodinitrile molecules are drawn out at an angle to the nickel surface, and at a potential of -0.65 V they are adsorbed flat on the nickel surface.

Interest towards adsorption heat storage, especially for long-term (seasonal) applications, is growing. The previous studies have always treated the heat storage cycle as a fully temperature-initiated process, similarly to common adsorption cooling and heating cycles. However, in long term storage applications, the discharge stage of the cycle is initiated by a jump of pressure rather than by a traditional drop of temperature. This requires specific investigations on the useful heat recoverable as well as on the adsorption dynamics.In the present paper, an appropriate experimental methodology was applied for studying the heat discharge stage. Three well known adsorbents (Mitsubishi AQSOA FAM-Z02, silica Siogel and composite LiCl/silica) were experimentally tested in a lab-scale heat storage unit, evaluating the effect of cycle operating parameters. The results, elaborated in terms of useful heat recoverable from the charged adsorbent, highlighted that the evaporation temperature and the flow rate of heat transfer fluid have a great influence on the adsorption dynamics and the useful heat. For the silica gel and FAM Z02, the maximum heat storage capacity 450 kJ/kg is reached at the evaporation temperature of 25 degrees C. The composite performs better at low evaporation temperatures, allowing heat upgrade even at 5 degrees C. The flow rate of the heat transfer fluid has a more significant effect on FAM Z02 than on the other adsorbents, for which an optimal flow rate of 1.2 kg/min was found.

Adsorption behavior of 5-carboxy-3-amino-1,2,4-triazole (COOH-ATA) on copper in neutral (pH 7.4) borate buffer solutions with and without 0.01 M NaCl was studied. Electrochemical polarization methods show significant suppression of the anodic and cathodic currents on the polarization curves in the presence of COOH-ATA. Chronopotential diagrams show increase of open circuit potential during adsorption. Ellipsometric studies has allowed to estimate the free energy of adsorption. X-ray photoelectron spectroscopy was applied to examine the surface composition after COOH-ATA adsorption from the inhibitor solution. Spectra analysis shows oxidation of copper to Cu+ and Cu2+ with surface complex formation. Protective properties in humid air and salt fog chamber of such layer are discussed.

Thermochemical energy storage (TCES) is an emerging technology promising for reuse of industrial waste heat and harvesting solar energy. Recently, a novel material, namely, a magnesium hydroxide doped with lithium nitrate LiNO3/Mg(OH)2, was suggested for TCES at temperature lower than 300 °C [ 1 ]. The LiNO3 additive to Mg(OH)2 was found to decrease the Mg(OH)2 dehydration temperature by 76 °C which, to the best of our knowledge, is the largest depression reported in the literature so far. The large heat storage capacity (1250 J/g) and fast dehydration made this material promising for TCES. In this work, the LiNO3/Mg(OH)2 is studied with a focus on the reverse reaction of its hydration by water vapour which allows the stored heat to be released. The rehydration kinetics is studied at various temperatures (90–150 °C), water vapour pressures (16.7–33.5 kPa), and LiNO3 contents (0.5–20 wt.%) to outline the boundary conditions of closed TCES cycle for which this material may be used. The material is found to be stable in ten successive de-/rehydration cycles. Finally, the applicability of the material for storage of heat from some particular heat sources is discussed.

Having observed how botanicals and other natural compounds are used by nature to control pests in the environment, we began investigating natural polymers, DNA and RNA, as promising tools for insect pest management. Over the last decade, unmodified short antisense DNA oligonucleotides have shown a clear potential for use as insecticides. Our research has concentrated mainly on Lymantria dispar larvae using an antisense oligoRING sequence from its inhibitor-of-apoptosis gene. In this article, we propose a novel biotechnology to protect plants from insect pests using DNA insecticide with improved insecticidal activity based on a new antisense oligoRIBO-11 sequence from the 5.8S ribosomal RNA gene. This investigational oligoRIBO-11 insecticide causes higher mortality among both L. dispar larvae grown in the lab and those collected from the forest; in addition, it is more affordable and faster acting, which makes it a prospective candidate for use in the development of a ready-to-use preparation.

In this paper, the sorption of the heavy metal ions (Sr2+, Ba2+, and Cs+) on the hybrid CNF/TiO2 and CNF/Fe2O3 materials is considered. The colloid–chemical properties of the TiO2 and Fe2O3 nanoparticles and carbon nanofibers in the dispersions were studied, and interaction between nanoparticles and nanofibers in accordance with the hetero-coagulation principle was estimated. The carbon nanofibers used were prepared by catalytic chemical vapor deposition of a propane–butane mixture over the nickel–copper catalyst and then functionalized by boiling in a mixture of concentrated hydrochloric and nitric acids. The TiO2 and Fe2O3 nanoparticles were synthesized via a sol–gel technique. The sol was mixed with carbon nanofibers. After drying, the hybrid materials with a uniform distribution of the oxide NPs along the nanofiber’s surface were obtained. The CNF-to-metal oxide ratios were 10:1 and 1:1. The samples were characterized by a set of physicochemical methods. The hybrid CNF/TiO2 system was found to have a synergetic effect toward the sorption of the metal ions from their aqueous solutions.

This article proposes a method for obtaining stable hydrophobic inhibitor dispersions, where the micelle core contains a hydrophobic solvent, a corrosion inhibitor and an organosilane. Such compositions can be used as polymer-type corrosion inhibitors for low-carbon steel. Using electrochemical methods, corrosion tests and X-ray photoelectron spectroscopy, features of the formation of polymeric layers of hydrophobic organosilicon dispersions were studied.

The review discusses the theoretical, experimental and toxicological aspects of the prospective biomedical application of functionalized magnetic nanoparticles (MNPs) activated by a low frequency non-heating alternating magnetic field (AMF). In this approach, known as nano-magnetomechanical activation (NMMA), the MNPs are used as mediators that localize and apply force to such target biomolecular structures as enzyme molecules, transport vesicles, cell organelles, etc., without significant heating. It is shown that NMMA can become a biophysical platform for a family of therapy methods including the addressed delivery and controlled release of therapeutic agents from transport nanomodules, as well as selective molecular nanoscale localized drugless nanomechanical impacts. It is characterized by low system biochemical and electromagnetic toxicity. A technique of 3D scanning of the NMMA region with the size of several mm to several cm over object internals has been described.

The catalytic subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) Nsp12 has a unique nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain that transfers nucleoside monophosphates to the Nsp9 protein and the nascent RNA. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites, and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation in bacterial cells) Nsp12 exists in an inactive state in which NiRAN-RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or nucleoside triphosphates (NTPs) partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote the synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN-RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and the design of its inhibitors. IMPORTANCE In vitro interrogations of the central replicative complex of SARS-CoV-2, RNA-dependent RNA polymerase (RdRp), by structural, biochemical, and biophysical methods yielded an unprecedented windfall of information that, in turn, instructs drug development and administration, genomic surveillance, and other aspects of the evolving pandemic response. They also illuminated the vast disparity in the methods used to produce RdRp for experimental work and the hidden impact that this has on enzyme activity and research outcomes. In this report, we elucidate the positive and negative effects of codon optimization on the activity and folding of the recombinant RdRp and detail the design of a highly sensitive in vitro assay of RdRp-dependent RNA synthesis. Using this assay, we demonstrate that RdRp is allosterically activated by nontemplating phosphorylated nucleotides, including naturally occurring alarmone ppGpp and synthetic remdesivir triphosphate.

The introduction of nanomaterials in medical technologies requires a more thorough study of their toxicity, as data are accumulating on the presence of toxic properties in carbon nanotubes and carbon nanofibers. Attention should also be paid to the possibility of linking the toxicity of carbon nanomaterials with an admixture of metals used in the synthesis of carbon nanofibers (CNF) as catalysts and included in the structure of nanomaterials. The CNF was prepared from methane, ethylene, and C 3 -C 4 hydrocarbon gases by chemical deposition from the gas phase on Ni-Cu/Al 2 O 3 , and 90Ni-10Cu catalysts. The gamma-aluminum oxide-polydimethylsiloxanecarbon nanofiber (Al 2 O 3 /PDMS/CNF) samples was prepared in aqueous phase. Using low-temperature sorption on nitrogen (BET method) studied porous structure and specific surface of the CNF. The MTT test, nitrogen oxide production, and apoptosis rate were used to estimate compatibility of Al 2 O 3 /PDMS/CNF with mesenchymal stem cells. It was shown that type of catalyst, raw material, and condition of temperature mode, and time exposure influenced on the characteristics of obtained CNF. Samples of Al 2 O 3 /PDMS/CNF have not affected human bone marrow mesenchymal stem cells (hBM-MSCs) proliferation and nitrogen oxide production. Whereas some Al 2 O 3 /PDMS/CNF samples significantly increased hBM-MSCs apoptosis. Thus, we have no obtained significant toxicity of the Al 2 O 3 /PDMS/CNF samples on hBM-MSCs.

SUMMARYThe catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), Nsp12, has a unique NiRAN domain that transfers nucleoside monophosphates to the Nsp9 protein. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation) Nsp12 exists in inactive state in which NiRAN/RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or NTPs partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN/RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically-linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and design of its inhibitors.HighlightsCodon-optimization of Nsp12 triggers misfolding and activity lossSlow translation, accessory Nsp7 and Nsp8 subunits, and NTPs rescue Nsp12Non-substrate nucleotides activate RNA chain synthesis, likely via NiRAN domainCrosstalk between two Nsp12 active sites that bind the same ligands

Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

Vol. 11, no. 4, e01206-20, 2020, [https://doi.org/10.1128/mBio.01206-20][1]. In the originally published version, Fig. S5 in the supplemental material was a duplicate of Table S5. Figure S5 has since been corrected online. [1]: /lookup/doi/10.1128/mBio.01206-20

BackgroundDNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood.ResultsWe present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. We employ the “guilt by association” approach to make functional inferences from comparative analysis of bacterial and archaeal genomes, based on the distribution and associations of EVE domains in (predicted) operons and functional networks of genes. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving ones. Slow-evolving EVE domains in α-proteobacteria are embedded in conserved operons, potentially involved in coupling between translation and respiration, cytochrome c biogenesis in particular, via binding 5-methylcytosine in tRNAs. In β- and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. In eukaryotes, the EVE domain-containing THYN1-like proteins have been reported to inhibit PCD and regulate the cell cycle, potentially, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. We hypothesize that the link between PCD and cytochrome c was inherited from the α-proteobacterial and proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. Fast-evolving EVE domains are typically embedded in defense contexts, including toxin-antitoxin modules and type IV restriction systems, suggesting roles in the recognition of modified bases in invading DNA molecules and targeting them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes, but in animals, the DCD proteins apparently were displaced by the extended Tudor family proteins, whose partnership with Piwi-related Argonautes became the centerpiece of the Piwi-interacting RNA (piRNA) system.ConclusionsRecognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response, and germline development in animals.

Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla., Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.

BackgroundDNA and RNA of most cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood.ResultsWe present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving. The slow-evolving EVE domains in α-proteobacteria are embedded in a conserved operonic context that implies involvement in coupling between translation and respiration, in particular, cytochrome c biogenesis, potentially, via binding 5-methylcytosine in tRNAs. In β and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. Down-regulation of the EVE-encoding operons might cause dormancy or programmed cell death (PCD). In eukaryotes, the EVE-domain-containing THYN1-like proteins appear to inhibit PCD and regulate the cell cycle, likely, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. Thus, the link between PCD and cytochrome c that appears to be universal in eukaryotes might have been inherited from the α-proteobacterial, proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. In numerous prokaryotic genomes, fast-evolving EVE domains are embedded in defense contexts, including toxin-antitoxin modules and Type IV restriction systems, all of which can also induce PCD. These EVE domains likely recognize modified bases in invading DNA molecules and target them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes but, in animals, the DCD proteins apparently were displaced by the extended Tudor family, whose partnership with Piwi-related Argonautes became the centerpiece of the piRNA system.ConclusionsRecognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response and germline development in animals.

Activated carbons are widely used for sustainable technology of adsorptive transformation and storage of heat. Here, we analyze the applicability of twelve commercial carbons and an innovative carbonaceous composite &ldquo, LiCl confined to multi-wall carbon nanotubes&rdquo, (LiCl/MWCNT) for a new cycle &ldquo, Heat from Cold&rdquo, (HeCol). It has recently been proposed for amplification of low- temperature ambient heat in cold countries. The analysis is made in terms of the methanol mass exchanged and the useful heat generated per cycle, the latter is the main performance indicator of HeCol cycles. The maximum specific useful heat, reaching 990 and 1750 J/g, can be obtained by using carbon Maxsorb III and the composite, respectively. For these materials, methanol adsorption dynamics under typical HeCol conditions are experimentally studied by the large pressure jump method. Before making this analysis, the fine carbon powder is consolidated by either using a binder or just pressing to obtain larger particles (ca. 2 mm). The methanol desorption from the consolidated samples of Maxsorb III at T = 2 &deg, C is faster than for LiCl/MWCNT, and the maximum (initial) useful power reaches (2.5&ndash, 4.0) kW/kg sorbent. It is very promising for designing compact HeCol units utilizing the carbon Maxsorb III.

Adsorptive Heat Transformation systems are at the interface between thermal and chemical engineering. Their study and development need a thorough thermodynamic analysis aimed at the smart choice of adsorbent-adsorptive pair and its fitting with a particular heat transformation cycle. This paper addresses such an analysis for a new &ldquo, Heat from Cold&rdquo, cycle proposed for amplification of the ambient heat in cold countries. A comparison of four working fluids is made in terms of the useful heat per cycle and the temperature lift. The useful heat increases in the row water &gt, ammonia &ge, methanol &gt, hydrofluorocarbon R32. A threshold mass of exchanged adsorbate, below which the useful heat equals zero, raises in the same sequence. The most promising adsorbents for this cycle are activated carbons Maxsorb III and SRD 1352/2. For all the adsorptives studied, a linear relationship F = A&middot, &Delta, T is found between the Dubinin adsorption potential and the driving temperature difference &Delta, T between the two natural thermal baths. It allows the maximum temperature lift during the heat generation stage to be assessed. Thus, a larger &Delta, T-value promotes the removal of the more strongly bound adsorbate.

International audience; SUMMARY : Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.

Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria., Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria. The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells.

Remote nano-magneto-mechanical actuation of magnetic nanoparticles (MNPs) by non-heating extremely low frequency magnetic field (ELF MF) is explored as a tool for non-invasive modification of bionanomaterials in pharmaceutical and medical applications. Here we study the effects of ELF MF (30–160 Hz, 8–120 kA/m) on the activity and release of a model enzyme, superoxide dismutase 1 (SOD1) immobilized by polyion coupling on dispersed MNPs aggregates coated with poly(L-lysine)-block-poly(ethylene glycol) block copolymer (s-MNPs). Such fields do not cause any considerable heating of MNPs but promote their rotating-oscillating mechanical motion that produces mechanical forces and deformations in adjacent materials. We observed the changes in the catalytic activity of immobilized SOD1 as well as its release from the s-MNPs/SOD1 polyion complex upon application of the ELF MF for 5 to 15 min. At longer exposures (25 min) the s-MNPs/SOD1 dispersion destabilizes. The bell-shaped effect of the field frequency with maximum at f = 50 Hz and saturation effect of field strength (between 30 kA/m and 120 kA/m at f = 50 Hz) are reported and explained. The findings are significant as one early indication of the nano-magneto-mechanical disruption by ELF MF of cooperative polyion complexes that are widely used for design of current functional healthcare bionanomaterials.

The structures and stereodynamic behavior of (O→Si)-chelate methyldifluorosilanes in solutions were studied by multinuclear (1H, 13C, 19F, 29Si) and 2D (COSY, HETCOR 1H, 13C) NMR spectroscopy. The range of studied complexes included amides RC(O)N(R')CH2SiMeF2 [R = Ph, R' = H (1a); R = R' = Me (1b); R = Me, R' = CHMePh (1c)], lactams LCH2SiMeF2 (L = 2-oxoazepan-1-yl (2a), 2,2-dimethyl-4-oxo-2H-benzo[1,3]oxazin-3-yl (2b) or 4-methyl-2-oxoquinolin-1-yl (2c)] and the six-membered imide Im6CH2 [2,6-dioxopiperidin-1-yl (3)]. The pentacoordination of silicon atoms in all studied compounds was confirmed by NMR study in solutions and single-crystal X-ray studies of complexes 1c, 2a, 2c and 3. The temperature dependency observed for the 19F NMR signals in solution was explained by the ligand exchange in the coordination environment of silicon atoms (permutational isomerization) and used for determining the activation parameters of this process by 19F DNMR. Quantum-chemical calculations for various isomers of complexes 1c, 2a, 2c and 3 suggested the "turnstile rotation" as the most likely mechanism for the observed stereodynamic processes.

Although it is well known that reactivity of α,β-unsaturated enaminoketones is closely associated with spatial and electronic structure but until now little attention was devoted to quantitative investigation of interconversion of different stereoisomeric forms of enaminoketones. In present work we studied peculiarities of kinetics of Z ⇌ E isomerization of enaminoketone 4-(N-methylamino)-1,1,1-trifluorobut-3-en-2-one F3C-CO CH CH NH(CH3) (1) in Ar-matrix exposed to UV-radiation (λ = 340 nm) with IR Fourier and 2D correlation spectroscopy and we found that Z-s-Z-s-trans isomer transforms primarily into two E-isomers, E-s-E-s-trans and E-s-Z-s-trans which further turn into the E-s-E-s-cis and E-s-Z-s-cis conformers all interconversion rate constants being comparable in magnitude. Along with this process long-term exposure to the UV-radiation results in proton transfer from nitrogen of methylamino group to carbonyl oxygen with simultaneous isomerization of ‘cyclic’ iminoenol form into ‘linear‘one. In solution of enaminoketone 4-(N-methylamino)-1,1,1-trifluoro-3-methylbut-3-en-2-one F3C-CO-C(CH3) CH-NH(CH3) (2) we observed reversed process, namely, spontaneous interconversion of the E-s-E-s-trans and E-s-Z-s-trans conformers into the Z-s-Z-trans isomer. It was found that rate constants of the dimeric forms of the E-s-E-s-trans and E-s-Z-s-trans conformers are higher than those of the monomers and are independent on total enaminoketone concentration. Addition of highly polar HMPA promotes proton transfer from nitrogen to oxygen in the Z-s-Z-s-trans isomer of 2 with subsequent isomerization into the linear imino-enol product but the rate constant of this transformation is ten-fold smaller than that for 1 in the Ar matrix exposed to UV radiation.

A simple method for the synthesis of sterically shielded pyrrolidine nitroxides, including the title compound, has been suggested. The key procedure implies assembling the pyrrolidine ring from α-amino acid, ketone, and activated alkene in a three-component domino process, followed by oxidation to nitrone and Grignard reagent addition. The new nitroxides demonstrate very high stability against reduction with ascorbate.

Magnetomechanical modulation of biochemical processes is a promising instrument for bioengineering and nanomedicine. This work demonstrates two approaches to control activity of an enzyme, α-chymotrypsin immobilized on the surface of gold-coated magnetite magnetic nanoparticles (GM-MNPs) using a nonheating low-frequency magnetic field (LF MF). The measurement of the enzyme reaction rate was carried out in situ during exposure to the magnetic field. The first approach involves α-chymotrypsin-GM-MNPs conjugates, in which the enzyme undergoes mechanical deformations with the reorientation of the MNPs under LF MF (16-410 Hz frequency, 88 mT flux density). Such mechanical deformations result in conformational changes in α-chymotrypsin structure, as confirmed by infrared spectroscopy and molecular modeling, and lead to a 63% decrease of enzyme initial activity. The second approach involves an α-chymotrypsin-GM-MNPs/trypsin inhibitor-GM-MNPs complex, in which the activity of the enzyme is partially inhibited. In this case the reorientation of MNPs in the field leads to disruption of the enzyme-inhibitor complex and an almost 2-fold increase of enzyme activity. The results further demonstrate the utility of magnetomechanical actuation at the nanoscale for the remote modulation of biochemical reactions.

Adsorptive transformation of heat is an energy and environment saving technology, which allows effective utilization of low temperature heat sources. Recently, a new adsorption cycle (the so-called “Heat from Cold” or HeCol) has been suggested for amplification of the ambient heat in cold regions up to higher temperature, suitable for heating. In this paper, at first we analyzed which adsorbent is needed for practical realization of the HeCol cycle. Then, the composite sorbent, based on LiCl and silica gel, was selected for the comprehensive study, and its sorption equilibrium with methanol was analyzed keeping in mind the requirements of the HeCol cycle. Finally, a first lab-scale HeCol prototype was tested with the LiCl/silica sorbent to evaluate the feasibility of the new cycle. The effects of the heat source temperature and the rate of heat transfer fluid on the prototype performance were studied. It was shown that at heat source temperature of 20–30 °C, the maximum temperature of the released heat reaches 34–53 °C, which is suitable for warm floor and hot water systems. The maximum specific heating power varies from 6.0 to 10.8 kW/kg and the sorbent heating capacity reaches 620 kJ/kg. The results obtained clearly demonstrate that the use of the LiCl/silica sorbent allows quite compact HeCol units to be designed.

Halogen exchange reactions between hexacoordinate tin dihalides (LnCH2)2SnX2 and (LnCH2)2SnY2 (LnCH2 = C,O-chelate n-membered lactamomethyl ligand, n = 5–7, X, Y = Cl, Br, I) produce mixed dihalides (LnCH2)2SnXY. Along with the signals of original complexes, NMR 119Sn spectra of solutions containing two different homodihalides show the third signal with a median chemical shift. The results of NMR monitoring studies, conductivity data and quantum-chemical calculations suggest that mixed dihalides readily form in solutions, although these complexes have not been isolated as individual compounds.

Adsorptive transformation of heat is an emerging technology that is especially promising for low-temperature heat sources. Recently, an adsorption cycle (the so-called “Heat from Cold” or HeCol) has been suggested for upgrading the ambient heat in cold countries. This paper addresses the selection of composite sorbents of methanol specialized for this cycle and the study of their sorption properties. First, we analyzed which adsorbent is optimal for the HeCol cycle and how its properties depend on the HeCol cycle boundary temperatures. Then, three composite sorbents, based on CaCl2, CaBr2 and their mixture confined inside the silica gel mesopores, were prepared and their sorption equilibrium with methanol was analyzed keeping in mind the HeCol cycles with various boundary temperatures. It was shown, that these composite sorbents exchange up to 0.48 g of methanol per 1 g of the composite that far exceeds this value for common activated carbons. Finally, a first lab-scale HeCol prototype was built and tested with one of the studied sorbents, namely CaClBr/SiO2, to evaluate the feasibility of the cycle.

Catalytic chemical vapor deposition (CCVD) of chlorobenzene over bulk nickel alloy (nichrome) was studied. The bulk Ni-containing samples being exposed to a contact with aggressive reaction medium undergo self-disintegration followed by growth of carbon nanofibers. This process, also known as a metal dusting, requires the simultaneous presence of chlorine and hydrogen sources in the reaction mixture. Molecule of chlorobenzene complies with these requirements. The experiments on CCVD were performed in a flow-through reactor system. The initial stages of nickel disintegration process were investigated in a closed system under Autogenic Pressure at Elevated Temperature (RAPET) conditions. Scanning and transmission electron microscopies and ferromagnetic resonance spectroscopy were applied to examine the samples after their interaction with chlorobenzene. Introduction of additional hydrogen into the flow-through system was shown to affect the morphology of grown carbon nanofibers.

Novel ZrO2/Al2O3 nanofibers with the average diameter of around 110 nm are fabricated by heat treatment of electrospun zirconium oxychloride (ZrOCl2)/aluminium nitrate (Al(NO3)3)/polyvinylpyrrolidone (PVP) composite fibers at temperature of 1200 °C. Intermediate and the final ceramic filaments are characterized by thermogravimetric analysis (TGA), differential thermal analysis (DTA), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) and X-ray diffractometry (XRD). The ZrO2/Al2O3 nanofibers contain mainly tetragonal zirconium dioxide in contrast to pure ZrO2 nanofibers consisting of monoclinic zirconia. It is revealed that Al2O3 impedes the ZrO2 grain growth and stabilizes the tetragonal phase of zirconia forming Al2O3-ZrO2 solid solution. Fabricated zirconia nanoscale filaments with varying phase composition can be considered, for instance, as promising one-dimensional high-temperature supports for heterogeneous catalysts with controlled activity and selectivity.

A novel approach to the synthesis of nitrogen-doped carbon nanofibers in a closed system at elevated pressure with the use of bulk Ni-Cr alloy as a catalyst precursor was proposed. Melamine was chosen as a substrate containing both carbon and nitrogen. Method of ferromagnetic resonance was applied for diagnostics of dispersed Ni particles appearance. The process of corrosion of a bulk alloy followed by formation of dispersed Ni particles catalyzing the growth of nitrogen-doped carbon nanofibers was found to take place at temperatures above 560 °C. The final content of nitrogen in obtained carbon nanofibers was about 10 at.%.

Catalytic chemical vapor deposition of halogenated butanes over bulk nickel-containing samples was studied. Butyl iodide and butyl bromide were used as substrates containing both hydrogen and halogen molecules. The experiments were performed in a flow reactor system as well as reaction under autogenic pressure at elevated temperature conditions. Scanning and transmission electron microscopies and ferromagnetic resonance spectroscopy were applied to examine the samples. The formation of structured particles of micron size was observed when nickel ribbon or nichrome wire was used as a bulk sample. The intermediates were shown to be stable in a narrow temperature range. The morphology of the resulting microcrystals was different depending on the metal precursor.