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).     

Four levels of pattern recognition

Problems of pattern recognition in chemistry and other subjects can be divided conveniently into four different types depending on the level of scope of the problem.(1) Classification into one of a number of defined classes. As an example blood samples taken from persons known to be either controls or welders are considered. The problem is whether trace element concentrations in these samples contain information on whether or not a person is a welder.(2) Level 1 plus the possibility that an object is an outlier, i.e. does not belong to any of the defined classes. As an example, the üse of ¹³C-n.m.r. data to decide whether 2-substituted norbornanes have the exo or endo structure is discussed. (2A) Level 2, asymmetric. This situation occurs when one class does not have a systematic structure, but another class is homogeneous and can be described by a level 2 model. This occurs in the classification of materials or compounds as good or bad, active or inactive, and in binary classifications. As an example the use of trace element data to classify steel samples as having good or poor properties of strength is discussed.(3) Level 2 plus the ability to relate the variables measured to external properties of continuous character. As an example, the classification of a series of chemical compounds as β -receptor blockers, β -receptor stimulants, or neither, on the basis of their structural variables is discussed. In addition, relations between these structural variables and the measured biological activity are sought within each of the two classes.(4) Level 3 with the difference that several external property variables in the objects are measured. It may be desirable to use variables of the objects both for classification and for relations to several property variables: such examples are numerous in analytical chemistry.     

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).     

Shear softening and structure in a simulated three-dimensional binary glass

Three-dimensional model binary glasses produced by quenching from a range of liquid temperatures were tested in shear over a range of strain rates using molecular-dynamics techniques. Tests were performed under constant volume and constant pressure constraints. The simulations revealed a systematic change in short-range order as a function of the thermal and strain history of the glass. While subtle signs of differences in short-range order were evident in the pair distribution function, three-body correlations were observed to be markedly more sensitive to the changes in structure. One particular structural parameter, the number of aligned three-atom clusters, was analyzed as a function of the degree of supercooling, the strain and the strain rate. The glasses quenched from the supercooled liquid regime were observed to contain an initially higher number of such clusters, and this number decreased under shear. Those quenched from high-temperature equilibrium liquids contained lower numbers of such clusters and these increased or remained constant under shear. The glasses quenched from the supercooled liquid regime showed higher strength, more marked shear softening, and an increased propensity toward shear localization. The evolution of this structural parameter depended both on its initial value and on the imposed shear rate. These results were observed to hold for simulations performed under both constant density and constant pressure boundary conditions.     

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.     

Damage spreading in a single-component irreversible reaction process: Dependence of the system's immunity on the Euclidean dimension

The spreading of a globally distributed damage, created in the stationary regime, is studied in a single-component irreversible reaction process, i.e., the BK model [Browne and Kleban,Phys. Rev. A 40, 1615 (1989)]. The BK model describes one variant of the A+AA₂ reaction process on a lattice in contact with a reservoir of A species. The BK model has a single parameter, namely the rate of arrival of A species to the lattice (Y). The model, exhibits an irreversible phase transition between a stationary reactive state with production of A₂ species and a poisoned state with the lattice fully covered by A species. The transition takes place at critical points (Y _C ) which solely depend on the Euclidean dimensiond. It is found that the system is immune ford=1 andd=2, in the sense that even 100% of initial damage is healed within a finite healing period (T _H ). Within the reactive regime,T _H diverges when approachingY _C according toT _H (Y _C –Y)^–, with 1.62 and 1.08 ford=1 andd=2, respectively. Ford=3 a frozen-chaotic transition is found close toY _s 0.4125, i.e., well inside the reactive regime 0YY _C 0.4985. Just atY _S the damageD(t) heals according toD(t) t ^–, with 0.71. For the frozen-chaotic transition atd=3 the order parameter critical exponent 0.997 is determined.