Advances in the computational analysis of SARS-COV2 genome

Nonlinear Dynamics - Given a data-set of Ribonucleic acid (RNA) sequences we can infer the phylogenetics of the samples and tackle the information for scientific purposes. Based on current data and...     

Thermal,morphostructural and spectrometric characterization of an antibacterial kaolinite-based filter modified with silver for water treatment

Journal of Thermal Analysis and Calorimetry - The aim of this work is to synthesize and characterize a new structured silver–clay dried, calcined or sintered at different temperatures...     

A novel microporous copper silicate: Na2Cu2Si4O11.2H2O

The synthesis and structural characterisation of a thermally stable novel three-dimensional microporous copper silicate open-framework are described; the material is capable of undergoing reversible zeolitic water removal without destruction of the framework.     

Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. p53C phase separated in the presence of the crowding agent polyethylene glycol (PEG). Similarly, mutant p53C (M237I and R249S) underwent PS; however, the process evolved to a solid-like phase transition faster than that in the case of wild-type p53C. The data obtained by microscopy of live cells indicated that transfection of mutant full-length p53 into the cells tended to result in PS and phase transition (PT) in the nuclear compartments, which are likely the cause of the GoF effects. Fluorescence recovery after photobleaching (FRAP) experiments revealed liquid characteristics of the condensates in the nucleus. Mutant p53 tended to undergo gel- and solid-like phase transitions in the nucleus and in nuclear bodies demonstrated by slow and incomplete recovery of fluorescence after photobleaching. Polyanions, such as heparin and RNA, were able to modulate PS and PT in vitro. Heparin apparently stabilized the condensates in a gel-like state, and RNA apparently induced a solid-like state of the protein even in the absence of PEG. Conditions that destabilize p53C into a molten globule conformation also produced liquid droplets in the absence of crowding. The disordered transactivation domain (TAD) modulated both phase separation and amyloid aggregation. In summary, our data provide mechanistic insight into the formation of p53 condensates and conditions that may result in the formation of aggregated structures, such as mutant amyloid oligomers, in cancer. The pathway of mutant p53 from liquid droplets to gel-like and solid-like (amyloid) species may be a suitable target for anticancer therapy.

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF).     

Theoretical study on the adsorption of aromatic compounds on platinum clusters

B3 LYP hybrid functional with LACVP* pseudopotential was applied for the optimization of geometries of complexes resulting from interaction of benzene, pyridine, naphthalene, and quinoline with Pt_n (n = 4, 7) clusters. For benzene‐containing complexes, the most stable form corresponds to a bridge adsorption, with benzene undergoing considerable geometric distortions, assuming a boat‐like conformation. C? H bonds are bended upward from the plane of the cluster. C? C bonds stretch, especially when they form π‐complexes with low coordinated Pt atoms. Some arrangements for pyridine complexes involving the N atom of the organic moiety undergo further distortions, apparently preserving a formal C? N π bond. Except for that distortion, the behavior of any heteroaromatic complex is similar to that of benzene in the same arrangement. The quinoline–Pt₇ complex can suitably be used for simulation of the cinchonidine (CD) anchorage over Pt. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

X-ray diffraction and solid-state NMR studies of a germanium binuclear complex

A compound formulated as (C4H12N2)[Ge2(pmida)2(OH)2] x 4 H2O (where pmida(4-) = N-(phosphonomethyl)iminodiacetate and C4H12N2(2+) = piperazinedium cation), containing the anionic [Ge2(pmida)2(OH)2]2- complex, has been synthesised by the hydrothermal approach and its structure determined by single-crystal X-ray diffraction analysis. Several high-resolution solid-state magic-angle spinning (MAS) NMR techniques, in particular two-dimensional 1H-X(13C,31P) heteronuclear correlation (HETCOR) and 1H-1H homonuclear correlation (HOMCOR) experiments incorporating a frequency-switched Lee-Goldburg (FS-LG) decoupling scheme, have been employed for the first time in such a material. Using these tools in tandem affords an excellent general approach to study the structure of other inorganic-organic hybrids. We assigned the NMR resonances with the help of C...H and P...H internuclear distances obtained through systematic statistical analyses of the crystallographic data. The compound was further characterised by powder X-ray diffraction techniques, IR and Raman spectroscopy, and by elemental and thermal analyses (thermogravimetric analysis and differential scanning calorimetry).     

Cathodic stripping voltammetry of trace Mn(II) at carbon film electrodes

A sensitive voltammetric method is presented for the determination of tract levels of Mn (II) using carbon film electrodes fabricated from carbon resistors of 2 Ω. Determination of manganese was made by square wave cathodic stripping voltammetry (CSV), with deposition of manganese as manganese dioxide. Chronoamperometric experiments were made to study MnO₂ nucleation and growth. As a result, it was found to be necessary to perform electrode conditioning at a more positive potential to initiate MnO₂ nucleation. Under optimised conditions the detection limit obtained was 4 nM and the relative standard deviation for eight measurements of 0.22 nM was 5.3%. Interferences from various metal ions on the response CSV of Mn(II) were investigated, namely Cd(II), Ni(II), Cu(II), Cr(VI), Pb(II), Zn(II) and Fe(II). Application to environmental samples was demonstrated.     

New designs for inhibitors of the NF-κB: DNA binding

We present a series of new inhibitors of the association between nuclear factor kappa B (NF-B) and the corresponding B site in DNA. They were designed using the lead compound 15-deoxy-^12,14 -prostaglandin J₂ (PGJ2), which is a natural product with demonstrated inhibitory efficiency for this system. First, the binding mode of PGJ2 to NF-B was unraveled by GOLD docking calculation. Subsequently, substitutions were made to PGJ2 to optimize its association with NF-B. Care was taken not to strongly increase the reactivity of the new compounds, and to keep the overall shape, size and hydrophilicity of the lead compound, which should render them a similar bioavailability. Molecular mechanics calculations were performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-B. Density functional theory calculations were performed also to study the overall reactivity of the substituted drugs towards NF-B. Important general conclusions were obtained, concerning the improvement of these natural inhibitors; namely, a set of rational methodologies were deduced to improve the association between the PGJ2 derivatives and NF-B, and their efficiency demonstrated by generating a set of substituted complexes, some of them with a very much increased affinity for NF-B, opening new doors to enlarge the therapeutic capabilities of this class of drugs.     

Determination of arsenic in sediments, coal and fly ash slurries after ultrasonic treatment by hydride generation atomic absorption spectrometry and trapping in an iridium-treated graphite tube

A simple and reliable method for the determination of arsenic in sediment and in coal without sample digestion, based on hydride generation from slurry samples is proposed. After grinding the samples to a particle size of 50 μm, the sample powder was mixed with aqua regia and hydrofluoric acid in an ultrasonic bath for 30 min. After diluting the mixture with hydrochloric acid, the slurry was allowed to stand for 48 h, and an aliquot was used for hydride generation with sodium borohydride. More than 80% of the arsenic was leached to the aqueous phase under these conditions, except for one sediment sample with very high silica content. The generated arsine was collected in a graphite tube, treated with 0.5 mg of iridium as a permanent modifier, and the arsenic determination was carried out by electrothermal atomic absorption spectrometry. The same tube could be used for at least 160 cycles without any re-treatment. The greatest advantage of the method was that only a minimum of reagents and sample handling were required, reducing the risks of contamination and/or analyte loss. However, the addition calibration technique had to be used in order to obtain results within the 95% confidence level for 11 certified reference materials, 5 sediments, 5 coals and one coal fly ash. One certified sediment slurry was spiked with the analyte and the resulting addition calibration curve was used for the analysis of the certified sediments. Similarly, one certified coal was used to obtain the addition calibration curve for the coal and coal fly ash samples. The recoveries of the certified values, except for one sediment, were between 91 and 115%. The limits of detection in the samples were 0.54 and 0.7 μg g⁻¹ for the coal and sediment samples, respectively, obtained for 1 ml of slurry containing 1 mg of sample.