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The subject matter of this paper is assessment of the suitability of a dynamic cone penetrometer for determination of the state of soil. The principle of operation of the dynamic cone penetrometer, similar to commonly used DPL penetrometers, is described in the paper. Next the results of investigation conducted in Poland using a new dynamic cone penetrometer are presented. A series of measurements were performed in real field conditions. An attempt was made to correlate the results obtained with the dynamic and static cone penetrometers (CPT) respectively. These correlations were then subjected to validation to obtain a preliminary evaluation of the suitability of the dynamic cone penetrometer for determining the state of soil.

Within the INMOP 3 research project, an attempt was made to solve a number of problems associated with the methodology of modelling travel in urban areas and the application of intermodal models. One of these is the ability to describe the behaviour of transport system users, when it comes to making decisions regarding the selection of means of transport and searching for relationships between travel describing factors and the decisions made in regard of means of transport choice.

The subject of this paper is analysis of the influence of horizontal forces estimated on the basis of Eurocode on the stability of an exemplary railway embankment located in the horizontal curve. The work begins with an overview of the methods for determining the earthworks stability. The methods are presented along with a reference to the recommendations contained in Eurocode 7. On the basis of the Eurocode, the loads acting on the analyzed embankment are presented together. In addition to the standard vertical interactions (from the rolling stock, the weight of the track structure and ground), the calculations also take into account horizontal forces caused by: wind forces on rolling stock, centrifugal forces and nosing force of the rolling stock as well as thermal stresses in the rails. Next, there are 15 load combinations calculated according to the Eurocode guidelines. At the end of the work the values of safety factors of the embankment obtained by shear strength reduction method are presented. The obtained results show a significant influence of horizontal forces calculated on the basis of the Eurocode on the stability of the railway embankment analyzed in the work.

The dynamic probing methods are commonly used for the subsoil identification. For example, the relative density/density index (ID) of cohesionless soils can be determined by using appropriate correlation relationships. The results obtained by various probing methods (DPL, DPH, DPM) may vary from one to another. Thus, the field tests were conducted in order to determine how important these discrepancies are. Each of the above mentioned methods were performed 10 times at one location. The effect of the influence of the penetrometer type on the relative density estimation results was determined. Based on the analysis, it can be concluded that the results obtained by the medium and heavy penetrometers are very close to each other. On the other hand, the discrepancies between the results obtained with the light penetrometer and the other two penetrometers are greater, both in terms of mean difference and scatter.

We report biochemical and structural studies on inhibiting bacterial S -adenosyl-L-homocysteine hydrolase by transition metal cations. Our results revealed diverse molecular mechanisms of enzyme inactivation. Depending on the cation, the mechanism is based on arresting the enzyme in its closed, inactive conformation, disulfide bond formation within the active site or oxidation of the intermediate form of a cofactor.

The insect gut, which plays a role in ion and water balance, has been shown to leak solutes in the cold. Cold stress can also activate insect immune systems, but it is unknown whether the leak of the gut microbiome is a possible immune trigger in the cold. We developed a novel feeding protocol to load the gut of locusts (Locusta migratoria) with fluorescent bacteria before exposing them to -2°C for up to 48 h. No bacteria were recovered from the hemolymph of cold-exposed locusts, regardless of exposure duration. To examine this further, we used an ex vivo gut sac preparation to re-test cold-induced fluorescent FITC-dextran leak across the gut and found no increased rate of leak. These results question not only the validity of FITC-dextran as a marker of paracellular barrier permeability in the gut, but also to what extent the insect gut becomes leaky in the cold., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2023. Published by The Company of Biologists Ltd.)

Covalent triazine-based frameworks have attracted much interest recently due to their high surface area and excellent thermal and electrochemical stabilities. This study shows that covalently immobilizing triazine-based structures on spherical carbon nanostructures results in the organization of micro- and mesopores in a three-dimensional manner. We selected the nitrile-functionalized pyrrolo[3,2-b]pyrrole unit to form triazine rings to construct a covalent organic framework. Combining spherical carbon nanostructures with the triazine framework produced a material with unique physicochemical properties, exhibiting the highest specific capacitance value of 638 F g -1 in aqueous acidic solutions. This phenomenon is attributed to many factors. The material exhibits a large surface area, a high content of micropores, a high content of graphitic N, and N-sites with basicity and semi-crystalline character. Thanks to the high structural organization and reproducibility, and remarkably high specific capacitance, these systems are promising materials for use in electrochemistry. For the first time, hybrid systems containing triazine-based frameworks and carbon nano-onions were used as electrodes for supercapacitors., (© 2023. The Author(s).)

Most naturally occurring nucleotides and nucleosides are N -glycosyl derivatives of β-d-ribose. These N -ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N -ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

The self-complementary L-d(CGCGCG) 2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K + cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K + site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder., (open access.)

Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS 2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Marszalek-Zenczak, Satyr, Wojciechowski, Zenczak, Sobieszczanska, Brzezinski, Iefimenko, Figlerowicz and Zmienko.)

Objective. Verification of delivered proton therapy treatments is essential for reaping the many benefits of the modality, with the most widely proposed in vivo verification technique being the imaging of positron emitting isotopes generated in the patient during treatment using positron emission tomography (PET). The purpose of this work is to reduce the computational resources and time required for simulation of patient activation during proton therapy using the GPU accelerated Monte Carlo code FRED, and to validate the predicted activity against the widely used Monte Carlo code GATE. Approach. We implement a continuous scoring approach for the production of positron emitting isotopes within FRED version 5.59.9. We simulate treatment plans delivered to 95 head and neck patients at Centrum Cyklotronowe Bronowice using this GPU implementation, and verify the accuracy using the Monte Carlo toolkit GATE version 9.0. Main results. We report an average reduction in computational time by a factor of 50 when using a local system with 2 GPUs as opposed to a large compute cluster utilising between 200 to 700 CPU threads, enabling simulation of patient activity within an average of 2.9 min as opposed to 146 min. All simulated plans are in good agreement across the two Monte Carlo codes. The two codes agree within a maximum of 0.95 σ on a voxel-by-voxel basis for the prediction of 7 different isotopes across 472 simulated fields delivered to 95 patients, with the average deviation over all fields being 6.4 × 10 -3 σ . Significance. The implementation of activation calculations in the GPU accelerated Monte Carlo code FRED provides fast and reliable simulation of patient activation following proton therapy, allowing for research and development of clinical applications of range verification for this treatment modality using PET to proceed at a rapid pace., (Creative Commons Attribution license.)

Four new compounds, 5-hydroxy-2',6'-dimethoxyflavone ( 4 ), 5-hydroxy-2',3',6'-trimethoxyflavone ( 5 ), 5-dihydroxy-6-methoxyflavone ( 6 ), and 5,6'-dihydroxy-2',3'-dimethoxyflavone ( 7 ), and three known compounds, 1,3-diphenylpropane-1,3-dione ( 1 ), 5-hydroxyflavone ( 2 ), and 5-hydroxy-2'-methoxyflavone ( 3 ), were isolated from the aerial parts of Hottonia palustris . Their chemical structures were determined through the use of spectral, spectroscopic and crystallographic methods. The quantitative analysis of the compounds ( 1-7 ) and the zapotin ( ZAP ) in methanol ( HP1 ), petroleum ( HP6 ), and two chloroform extracts ( HP7 and HP8 ) were also determined using HPLC-PDA. The biological activity of these compounds and extracts on the oral squamous carcinoma cell (SCC-25) line was investigated by considering their cytotoxic effects using the MTT assay. Subsequently, the most active compounds and extracts were assessed for their effect on DNA biosynthesis. It was found that all tested samples during 48 h treatment of SCC-25 cells induced the DNA biosynthesis-inhibitory activity: compound 1 (IC 50 , 29.10 ± 1.45 µM), compound 7 (IC 50 , 40.60 ± 1.65 µM) and extracts ZAP (IC 50 , 20.33 ± 1.01 µM), HP6 (IC 50 , 14.90 ± 0.74 µg), HP7 (IC 50 , 16.70 ± 0.83 µg), and HP1 (IC 50 , 30.30 ± 1.15 µg). The data suggest that the novel polymethoxyflavones isolated from Hottonia palustris evoke potent DNA biosynthesis inhibitory activity that may be considered in further studies on experimental pharmacotherapy of oral squamous cell carcinoma.

The mesophilic cyanobacterium Synechocystis sp. PCC 6803 encodes an S-adenosyl-L-homocysteine hydrolase (SAHase) of archaeal origin in its genome. SAHases are essential enzymes involved in the regulation of cellular S-adenosyl-L-methionine (SAM)-dependent methylation reactions. They are usually active as homotetramers or, less commonly, as homodimers. A SAHase subunit is composed of two major domains: a cofactor (NAD + )-binding domain and a substrate (S-adenosyl-L-homocysteine)-binding domain. These are connected by a hinge element that is also a coordination site for an alkali-metal cation that influences domain movement during the catalytic cycle. Typically, the highest activity and strongest substrate binding of bacterial SAHases are observed in the presence of K + ions. The SAHase from Synechocystis (SynSAHase) is an exception in this respect. Enzymatic and isothermal titration calorimetry studies demonstrated that in contrast to K + -dependent SAHases, the activity and ligand binding of SynSAHase are not affected by the presence of any particular alkali ion. Moreover, in contrast to other SAHases, the cyanobacterial enzyme is in an equilibrium of two distinct oligomeric states corresponding to its dimeric and tetrameric forms in solution. To explain these phenomena, crystal structures of SynSAHase were determined for the enzyme crystallized in the presence of adenosine (a reaction byproduct or substrate) and sodium or rubidium cations. The structural data confirm that while SynSAHase shares common structural features with other SAHases, no alkali metal is coordinated by the cyanobacterial enzyme as a result of a different organization of the macromolecular environment of the site that is normally supposed to coordinate the metal cation. This inspired the generation of SynSAHase mutants that bind alkali-metal cations analogously to K + -dependent SAHases, as confirmed by crystallographic studies. Structural comparisons of the crystal structure of SynSAHase with other experimental models of SAHases suggest a possible explanation for the occurrence of the cyanobacterial enzyme in the tetrameric state. On the other hand, the reason for the existence of SynSAHase in the dimeric state in solution remains elusive.

This work reports the results of random mutagenesis of the Escherichia coli class 2 L-asparaginase EcAIII belonging to the Ntn-hydrolase family. New variants of EcAIII were studied using structural, biophysical and bioinformatic methods. Activity tests revealed that the L-asparaginase activity is abolished in all analyzed mutants with the absence of Arg207, but some of them retained the ability to undergo the autoproteolytic maturation process. The results of spectroscopic studies and the determined crystal structures showed that the EcAIII fold is flexible enough to accept different types of mutations; however, these mutations may have a diverse impact on the thermal stability of the protein. The conclusions from the experiments are grouped into six lessons focused on (i) the adaptation of the EcAIII fold to new substitutions, (ii) the role of Arg207 in EcAIII activity, (iii) a network of residues necessary for autoprocessing, (iv) the complexity of the autoprocessing reaction, (v) the conformational changes observed in enzymatically inactive variants and (vi) the cooperativity of the EcAIII dimer subunits. Additionally, the structural requirements (pre-maturation checkpoints) that are necessary for the initiation of the autocleavage of Ntn-hydrolases have been classified. The findings reported in this work provide useful hints that should be considered before planning enzyme-engineering experiments aimed at the design of proteins for therapeutic applications. This is especially important for L-asparaginases that can be utilized in leukemia therapy, as alternative therapeutics are urgently needed to circumvent the severe side effects associated with the currently used enzymes., (open access.)

Herein, we report the synthesis of mesoporous carbon materials from diblock star copolymers derived from polyacrylonitrile. The size of the pores was controlled by manipulating the length of the polymer blocks. Furthermore, the organization of polymers on the carbon nano-onion's surface resulted in materials of higher surface area and superficial electrochemical performance.

Derivatives based on pyridine-2-6- and furan-2,5-dicarboxamide scaffolds reveal numerous chemical properties and biological activities. This fact makes them an exciting research topic in supramolecular and coordination chemistry and in discovering new pharmacologically-active compounds. This work aimed to obtain a series of symmetrical pyridine-2-6- and furan-2,5-dicarboxamides through a condensation reaction of the appropriate acyl chlorides and aromatic amides. Successful syntheses were confirmed with NMR spectroscopy. We solved their crystal structures for seven compounds; two pyridine and five furan derivatives. Based on our crystallographic studies, we were able to indicate supramolecular features of the crystals under investigation. Additionally, Hirshfeld surface analysis allowed us to calculate a distribution of intermolecular contacts in the dicarboxamide crystals.

Sutures are fibrous joints that occur between bone elements in vertebrate skulls, where they play a variety of roles including facilitating skull growth and function. In addition, a variety of studies examining sutures from diverse perspectives in many taxa have enabled the determination of anatomical homologs. Surprisingly, one important aspect of sutures-histology-remains unknown in the key model organism of the chicken. To fill this gap in our knowledge, we generated histological sections of six different cranial sutures across a range of developmental stages in embryonic chicken. Despite having a skull that is largely co-ossified or fused as an adult, we found that the types, components, and ontogeny of sutures in chicken skulls are very similar to sutures in other vertebrates. We did, however, find a new transient stage in the ontogeny of sutures between endochondral bone elements, in which one element has ossified and one was still cartilaginous. Moreover, to better understand the morphogenetic events at the onset of suture formation, we compared the developmental histology of six sutures with that of the space between the two ossification centers of the frontal-a location expected to be void of suture structures. We found that the mesenchymal cells in sutures condense and form a middle vascular layer. This was not found to be the case in the space between the two ossifications of the frontal, where instead only osteoid occurs., (© 2021 Anatomical Society.)

Curcumin (CUR) is a natural compound that exhibits anti-inflammatory, anti-bacterial, and other biological properties. However, its application as an effective drug is problematic due to its poor oral bioavailability, solubility in water, and poor absorption from the gastrointestinal tract. The aim of this work is to synthesize monocarbonyl analogs of CUR based on the 9-methyl-9-azabicyclo[3.2.1]nonan-3-one (pseudopelletierine, granatanone) scaffold to improve its bioavailability. Granatane is a homologue of tropane, whose structure is present in numerous naturally occurring alkaloids, e.g., l-cocaine and l-scopolamine. In this study, ten new pseudopelletierine-derived monocarbonyl analogs of CUR were successfully synthesized and characterized by spectral methods and X-ray crystallography. Additionally, in vitro test of the cytotoxicity and anti-inflammatory properties of the synthesized compounds were performed.

There is a growing appreciation that insect distribution and abundance are associated with the limits of thermal tolerance, but the physiology underlying thermal tolerance remains poorly understood. Many insects, like the migratory locust ( Locusta migratoria ), suffer a loss of ion and water balance leading to hyperkalaemia (high extracellular [K + ]) in the cold that indirectly causes cell death. Cells can die in several ways under stress, and how they die is of critical importance to identifying and understanding the nature of thermal adaptation. Whether apoptotic or necrotic cell death pathways are responsible for low-temperature injury is unclear. Here, we use a caspase-3 specific assay to indirectly quantify apoptotic cell death in three locust tissues (muscle, nerves and midgut) following prolonged chilling and recovery from an injury-inducing cold exposure. Furthermore, we obtain matching measurements of injury, extracellular [K + ] and muscle caspase-3 activity in individual locusts to gain further insight into the mechanistic nature of chilling injury. We found a significant increase in muscle caspase-3 activity, but no such increase was observed in either nervous or gut tissue from the same animals, suggesting that chill injury primarily relates to muscle cell death. Levels of chilling injury measured at the whole animal level, however, were strongly correlated with the degree of haemolymph hyperkalaemia, and not apoptosis. These results support the notion that cold-induced ion balance disruption triggers cell death but also that apoptosis is not the main form of cell damage driving low-temperature injury.

S -adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S -adenosyl-l-homocysteine or adenosine and the second domain binds the NAD + cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N -glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.

Chalcones, including dibenzoylmethane, are an important subgroup of natural polyphenolic compounds that exhibit a wide spectrum of pharmacological and industrial applications. Dibenzoylmethane was isolated from Hottonia palustris L. (Primulaceae). The compound was crystallized in two polymorphic forms: in monoclinic space group P2 1 /c and orthorhombic space group Pbca. Crystal structures of the polymorphs were solved and refined against diffraction data measured at 100 and 293 K. In both crystal structures, the chalcone occurs in its keto-enol tautomeric form with the hydroxyl H atom mutually bound by two oxygen atoms rather than covalently attached to a particular oxygen atom. To explain this phenomenon in more detail, density functional theory and quantum theory of atoms in molecules based quantum chemistry calculations were applied. Additionally, high-resolution experimental data of very high quality measured for the monoclinic and orthorhombic crystals at 100 K allowed the engagement of the quantum crystallography method, based on Hirshfeld atom refinement, to determine the position of each individual H atom. It is suggested that the presence of the particular tautomeric form of dibenzoylmethane with a centred H atom position results from the π-stacking interaction between the phenyl ring and the malondialdehyde quasi-ring causes delocalization of the electron density in the latter.

The synthesis and characterization of one oxidoethoxidovanadium(V) [V V O(L 1 )(OEt)] ( 1 ) and two nonoxidovanadium(IV) complexes, [V IV (L 2-3 ) 2 ] ( 2 and 3 ), with aroylhydrazone ligands incorporating naphthalene moieties, are reported. The synthesized oxido and nonoxido vanadium complexes are characterized by various physicochemical techniques, and their molecular structures are solved by single crystal X-ray diffraction (SC-XRD). This revealed that in 1 the geometry around the vanadium atom corresponds to a distorted square pyramid, with a O 4 N coordination sphere, whereas that of the two nonoxido V IV complexes 2 and 3 corresponds to a distorted trigonal prismatic arrangement with a O 4 N 2 coordination sphere around each "bare" vanadium center. In aqueous solution, the V V O moiety of 1 undergoes a change to V V O 2 species , yielding [V V O 2 (L 1 )] - ( 1' ), while the nonoxido V IV -compounds 2 and 3 are partly converted into their corresponding V IV O complexes, [V IV O(L 2-3 )(H 2 O)] ( 2' and 3' ). Interaction of these V V O 2 , V IV O, and V IV systems with two model proteins, ubiquitin (Ub) and lysozyme (Lyz), is investigated through docking approaches, which suggest the potential binding sites: the interaction is covalent for species 2' and 3' , with the binding to Glu16, Glu18, and Asp21 for Ub, and His15 for Lyz, and it is noncovalent for species 1' , 2 , and 3 , with the surface residues of the proteins. The ligand precursors and complexes are also evaluated for their in vitro antiproliferative activity against ovarian (A2780) and prostate (PC3) human cancer cells and in normal fibroblasts (V79) to check the selectivity of the compounds for cancer cells.

Chill-susceptible insects, like the migratory locust, often die when exposed to low temperatures from an accumulation of tissue damage that is unrelated to freezing (chilling injury). Chilling injury is often associated with a loss of ion balance across the gut epithelia. It has recently been suggested that this imbalance is at least partly caused by a cold-induced disruption of epithelial barrier function. Here, we aimed to test this hypothesis in the migratory locust ( Locusta ). First, chill tolerance was quantified by exposing locusts to -2°C and recording chill coma recovery time and survival 24 h post-cold exposure. Longer exposure times significantly increased recovery time and caused injury and death. Ion-selective microelectrodes were also used to test for a loss of ion balance in the cold. We found a significant increase of haemolymph K migratoria ). First, chill tolerance was quantified by exposing locusts to -2°C and recording chill coma recovery time and survival 24 h post-cold exposure. Longer exposure times significantly increased recovery time and caused injury and death. Ion-selective microelectrodes were also used to test for a loss of ion balance in the cold. We found a significant increase of haemolymph K + and decrease of haemolymph Na + concentration over time. Next, barrier failure along the gut was tested by monitoring the movement of an epithelial barrier marker (FITC-dextran) across the gut epithelia during exposure to -2°C. We found a significant increase in haemolymph FITC-dextran concentration over time in the cold when assayed in the mucosal to serosal direction. However, when tested in the serosal to mucosal direction, we saw minimal marker movement across the gut epithelia. This suggests that while cold-induced barrier disruption is present, it is apparently unidirectional. It is important to note that these data reveal only the phenomenon itself. The location of this leak as well as the underlying mechanisms remain unclear and require further investigation., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

Two accessory loop regions that are present in numerous variants of New Delhi metallo-β-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Ω loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Ω loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Ω loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Ω loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the β-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins., Competing Interests: Declaration of competing interest None declared., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Metallophthalocyanine (MPc) and carbon nano-onion (CNO) derivatives were synthesized and characterized by using ultraviolet-visible spectroscopy, infrared and Raman spectroscopy, scanning electron microscopy with energy-dispersive X-ray spectroscopy and X-ray powder diffraction. The unmodified CNOs and MPc-CNO derivatives were used as photocatalysts for rhodamine B (RhB) degradation under visible-light irradiation. The photocatalytic studies revealed that the MPc-CNO nanostructural materials simultaneously exhibited a high absorption capacity and an excellent visible-light-driven photocatalytic activity towards RhB. These nanostructures possess great potential for use as active photocatalysts for organic pollutant degradation., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Two new dimeric Zn(II) ([{ZnL 1 (DMSO 2 )} 2 ]·DMSO (1), [{ZnL 2 Cl} 2 ] (2)) and a novel tetrameric Zn(II) complex ([(Zn 2 L 3 ) 2 (μ-OAc) 2 (μ 3 -O) 2 ] (3)), where H 2 L 1  = 4-(p-methoxyphenyl) thiosemicarbazone of o-hydroxynapthaldehyde, HL 2  = 4-(p-methoxyphenyl)thiosemicarbazone of benzoyl pyridine and H 2 L 3  = 4-(p-chlorophenyl)thiosemicarbazone of o-vanillin are reported. Ligands and their complexes were characterized by spectroscopic and single crystal X-ray diffraction techniques. In addition, the complexes exhibited good binding affinity towards HSA (10 12  M -1 ), which is supported by their ability to quench the tryptophan fluorescence emission spectra of HSA. The complexes were also screened for their DNA binding propensity through UV-vis absorption titration, circular dichroism and fluorescence spectral studies. Results show that they effectively interact with CT-DNA through an intercalative mode of binding, with binding constants ranging from 10 3 to 10 4  M -1 . Among the three complexes 1 has the highest binding affinity towards CT-DNA. Further, the phosphatase activity was evaluated using bis(2,4-dinitrophenyl)phosphate (BDNPP) as substrate, however, the complexes did not yield any measurable catalytic activity. Nevertheless the complexes showed significant cytotoxic potential against HeLa and HT-29 cancer cell lines that was assessed through MTT assay and DAPI staining. Remarkably, complex 1 showed better activity than cisplatin against HT-29 cell line., Competing Interests: Declaration of competing interest All the authors' declare no conflict of interest., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Many insects enter coma upon exposure to anoxia, a feature routinely exploited by experimentalists to handle them. But the genetic and physiological bases of anoxic coma induction and recovery are only partially understood, as are the long-term consequences for the animal's performance. We examined three populations of Drosophila melanogaster (designated B) that have been inadvertently under selection for rapid recovery from CO 2 exposure for nearly 40 years (around 1000 generations) resulting from routine maintenance practices. We contrasted CO 2 and N 2 (presumed a less reactive gas) knockdown and recovery times of these B flies with six populations of common ancestry (A and C populations) that were not exposed to CO 2 over the same period. We found that B populations showed faster and more consistent locomotor recovery than A or C populations after CO 2 knockdown, a result also observed with N 2 knockdown. A and C populations showed much higher variance in recovery time after CO 2 exposure than after N 2 exposure, suggesting gas-specific effects on pathways associated with locomotor recovery. Although these selection treatments result in considerable variation in life history attributes and body size, with the characteristic intermediacy of B populations, their superiority in resistance to gas exposure and locomotor recovery suggests that this is a direct consequence of prior repeated exposure to anoxia, broadly, and CO 2 , specifically. Hence we describe a powerful new evolutionary model for the genetic and physiological investigation of anoxic coma in insects., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K + ion and one Zn 2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K + ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn 2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K + or Rb + ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23 Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn 2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn 2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.

Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures., (Copyright © 2017 Elsevier B.V. All rights reserved.)

A series of mononuclear non-oxido vanadium(IV) [V(IV)(L(1-4))2] (1-4), oxidoethoxido vanadium(V) [V(V)O(L(1-4))(OEt)] (5-8), and dinuclear μ-oxidodioxidodivanadium(V) [V(V)2O3(L(1))2] (9) complexes with tridentate aroylazine ligands are reported [H2L(1) = 2-furoylazine of 2-hydroxy-1-acetonaphthone, H2L(2) = 2-thiophenoylazine of 2-hydroxy-1-acetonaphthone, H2L(3) = 1-naphthoylazine of 2-hydroxy-1-acetonaphthone, H2L(4) = 3-hydroxy-2-naphthoylazine of 2-hydroxy-1-acetonaphthone]. The complexes are characterized by elemental analysis, by various spectroscopic techniques, and by single-crystal X-ray diffraction (for 2, 3, 5, 6, 8, and 9). The non-oxido V(IV) complexes (1-4) are quite stable in open air as well as in solution, and DFT calculations allow predicting EPR and UV-vis spectra and the electronic structure. The solution behavior of the [V(V)O(L(1-4))(OEt)] compounds (5-8) is studied confirming the formation of at least two different types of V(V) species in solution, monomeric corresponding to 5-8, and μ-oxidodioxidodivanadium [V(V)2O3(L(1-4))2] compounds. The μ-oxidodioxidodivanadium compound [V(V)2O3(L(1))2] (9), generated from the corresponding mononuclear complex [V(V)O(L(1))(OEt)] (5), is characterized in solution and in the solid state. The single-crystal X-ray diffraction analyses of the non-oxido vanadium(IV) compounds (2 and 3) show a N2O4 binding set and a trigonal prismatic geometry, and those of the V(V)O complexes 5, 6, and 8 and the μ-oxidodioxidodivanadium(V) (9) reveal that the metal center is in a distorted square pyramidal geometry with O4N binding sets. For the μ-oxidodioxidodivanadium species in equilibrium with 5-8 in CH2Cl2, no mixed-valence complexes are detected by chronocoulometric and EPR studies. However, upon progressive transfer of two electrons, two distinct monomeric V(IV)O species are detected and characterized by EPR spectroscopy and DFT calculations.

Conventional PET systems can be augmented with additional detectors placed in close proximity of the region of interest. We developed a high resolution PET insert module to evaluate the added benefit of such a combination. The insert module consists of two back-to-back 1 mm thick silicon sensors, each segmented into 1040 1 mm 2 pads arranged in a 40 by 26 array. A set of 16 VATAGP7.1 ASICs and a custom assembled data acquisition board were used to read out the signal from the insert module. Data were acquired in slice (2D) geometry with a Jaszczak phantom (rod diameters of 1.2-4.8 mm) filled with 18 F-FDG and the images were reconstructed with ML-EM method. Both data with full and limited angular coverage from the insert module were considered and three types of coincidence events were combined. The ratio of high-resolution data that substantially improves quality of the reconstructed image for the region near the surface of the insert module was estimated to be about 4%. Results from our previous studies suggest that such ratio could be achieved at a moderate technological expense by using an equivalent of two insert modules (an effective sensor thickness of 4 mm).

Histidine-containing phosphotransfer proteins (HPts) take part in hormone signal transduction in higher plants. The overall pathway of this process is reminiscent of the two-component system initially identified in prokaryotes. HPts function in histidine-aspartate phosphorelays in which they mediate the signal from sensory kinases (usually membrane proteins) to RRs in the nucleus. Here, we report the crystal structure of an HPt protein from Medicago truncatula (MtHPt1) determined at 1.45 Å resolution and refined to an R-factor of 16.7% using low-temperature synchrotron-radiation X-ray diffraction data. There is one MtHPt1 molecule in the asymmetric unit of the crystal lattice with P2(1)2(1)2(1) symmetry. The protein fold consists of six α helices, four of which form a C-terminal helix bundle. The coiled-coil structure of the bundle is stabilized by a network of S-aromatic interactions involving highly conserved sulfur-containing residues. The structure reveals a solvent-exposed side chain of His79, which is the phosphorylation site, as demonstrated by autoradiography combined with site-directed mutation. It is surrounded by highly conserved residues present in all plant HPts. These residues form a putative docking interface for either the receiver domain of the sensory kinase, or for the RR. The biological activity of MtHPt1 was tested by autoradiography. It demonstrated phosphorylation by the intracellular kinase domain of the cytokinin receptor MtCRE1. Complex formation between MtHPt1 and the intracellular fragment of MtCRE1 was confirmed by thermophoresis, with a dissociation constant K(d) of 14 μM., (© 2013 FEBS.)