Artificial neural networks for prediction of mycobacterial promoter sequences

A multilayered feed-forward ANN architecture trained using the error-back-propagation (EBP) algorithm has been developed for predicting whether a given nucleotide sequence is a mycobacterial promoter sequence. Owing to the high prediction capability (97%) of the developed network model, it has been further used in conjunction with the caliper randomization (CR) approach for determining the structurally/functionally important regions in the promoter sequences. The results obtained thereby indicate that: (i) upstream region of −35 box, (ii) −35 region, (iii) spacer region and, (iv) −10 box, are important for mycobacterial promoters. The CR approach also suggests that the −38 to −29 region plays a significant role in determining whether a given sequence is a mycobacterial promoter. In essence, the present study establishes ANNs as a tool for predicting mycobacterial promoter sequences and determining structurally/functionally important sub-regions therein.     

Plutonium-239+240 selectivity for pseudo-colloids of iron in subsurface aquatic environment having elevated level of dissolved organic carbon

Laboratory simulated experiments have been conducted to study the association of ^239,240Pu with pseudo-colloids of iron in groundwater samples having dissolved organic carbon (DOC) in the range of 10–60 mg L⁻¹. Ultra-filtration membranes have been used to partition colloidal components into seven different size range of <0.45 μm-1.1 nm. Elevated levels of Fe, DOC and ^239,240Pu were observed in the fractions concentrated with 1.6 nm (10,000 NMWL) and 1.1 nm (500 NMWL) compared to the other dissolved fractions. To ascertain the fact that, the formation of pseudo-colloids of Fe in the size range 1.6 nm and 1.1 nm was assisted by the presence of DOC, experiments have been conducted under similar experimental conditions with uniform Fe concentration and varying the DOC in the range of 10–60 mg L⁻¹. Seven to eight times higher concentration of Fe was observed in fractions concentrated with 1.6 nm and 1.1 nm having DOC ≥30 mg L⁻¹, whereas Fe was equally distributed in all the fractions in groundwater having DOC ≥10 mg L⁻¹. The surface morphology and composition of the residue left on the ultra-filtration membranes was examined using scanning electron microscope (SEM) coupled with energy dispersive X-ray spectrometer (EDS). The EDS results validate the observation that the residue left on filter paper membrane of 10000 and 500 NMWL with pore size 1.6 and 1.1 nm respectively, shows elevated levels of carbon and Fe contents as compared to other fractions. Understanding the association of ^239,240Pu with Fe and DOC will facilitate in predicating the long term integrity of underground waste storage facilities of alpha emitting radioactive material.     

Biophysical,spectroscopic vis-à-vis biochemical investigation on DNA–metalloprotein interaction: a model study involving cobalt(II)-glutathione complex

Abstract  The interaction of cobalt(II)-glutathione (CoGSH) with deoxyribonucleic acid (DNA) has been studied by UV–vis, fluorescence, circular dichroism (CD), thin-film infrared (IR), and viscometric techniques. From the UV-spectroscopic method, binding constant (K _b) was determined and was found to be 2.3 × 10⁶ M⁻¹. In fluorimetric analysis, the quenching of fluorescence intensity of DNA bound to ethidium bromide (EB) was investigated. The Stern–Volmer quenching constant (K _sv) was also estimated from this study and was found to be 2.8 × 10⁶ M⁻¹at 37 °C. The solution CD spectra of DNA and DNA–CoGSH indicate that in each case, DNA exists in the ‘B’ conformation and suggested an intercalative binding mode. Thin-film IR data also reveal that DNA attains the ‘B’ family of conformations after interaction with CoGSH complex. The increase in DNA viscosity in the presence of CoGSH complexes is attributed to the lengthening of DNA helix due to intercalation. Graphical Abstract  The spectrophotometric, CD, thin film IR, viscometric and fluorimetric studies on the interaction of CoGSH with DNA indicated an intercalative binding mode with the retention of ‘B’ conformation of DNA.      

Nonlinear normal modes and quanta in the β Fermi-Pasta-Ulam lattice

We enumerate simple periodic orbits for the well-known Fermi-Pasta-Ulam (FPU) problem. Using these solutions as simple modes for the problem, we construct quantum solutions of the corresponding problem. These studies present a natural generalization of the concept of phonon in the nonlinear realm.     

SOM assembly of hydroxynaphthoquinone and its oxime: polymorphic X-ray structures and EPR studies

Investigation on solvent-induced polymorphism in X-ray structures of 2-hydroxy-1,4-naphthoquinone (Lawsone) 1, is carried out. In protic methanol, 1 crystallizes in monoclinic space group P2(1)/c (1a) comprising of 2D hydrogen bonded network via cyclic dimers. In aprotic solvent such as acetone on the other hand, 1 exhibits orthorhombic space group Pna 2(1) (1b) and emerges with 1D catemeric chain. Solvent-induced topological isomerism of cyclic dimers and helical catemeric chains arising from (i) bifurcated intra- and inter molecular hydrogen bondings viz. O-H...O=C interactions between C(2) hydroxyl and C(1), C(4) carbonyls, (ii) C-H...O interactions viz. C(3)-H...O(1)C(1) have been discussed. A signal for radical in 1 at g = 2.0058 is signatured by EPR spectrum and it's oxime derivative viz. 2-hydroxy-4-naphthoquinone-1-oxime 2, in solid state shows biradical and monoradical formation with aggregation of dimer and monomer due to non-covalent hydrogen bonds. Zero field split parameters for 2 are estimated to be D = 215 G, Ex = 13 G, Ey = 47 G at 298 K. A half field signal at 77 K indicates triplet ground state. Frozen glass EPR of 2 resolves as regioregular dimeric-monomeric species showing hyperfine interactions with 1-oximino nitrogen in dimer A (14N) = 15.5 G].     

High-light-induced changes on photosynthesis, pigments, sugars, lipids and antioxidant enzymes in freshwater (Nostoc spongiaeforme) and marine (Phormidium corium) cyanobacteria

We studied the effects of high-light exposure (500 micromol m(-2) s(-1) of photosynthetic active radiation) on the cyanobacteria Nostoc spongiaeforme Agardh, a fresh-water alga, and Phormidium corium Agardh (Gomont), a marine alga, with respect to photosynthesis, pigments, sugar content, lipid peroxidation, fatty acids composition, antioxidant enzymes activity and DNA. It was seen that the ratio of variable fluorescence (Fv) to maximum fluorescence (Fm), which is indicative of photosynthetic efficiency, decreased because of the light treatment. The damage to photosynthesis occurred in the antenna system and the photosynthetic II reaction center. Photobleaching of photosynthetic pigments was also observed. High-light treatment also resulted in decreased sugar content, which was probably due to the effect on photosynthesis. Peroxidation of membrane lipids, indicating oxidative damage to lipids and a high level of unsaturation in the cell membrane, was also observed. The activity of antioxidant enzyme superoxide dismutase and ascorbate peroxidase was increased, probably as a result of oxidative damage observed in the form of lipid peroxidation. Quantitative decreases in phospholipid and glycolipid levels were also observed. The level of unsaturated fatty acids in total lipids and glycolipids remained unchanged in both species; however, the level of saturated fatty acids decreased, which slightly changed the ratio in favor of unsaturated fatty acids. Degradation of DNA was also observed in both species. There was a transient plateau 2-4 h after exposure to high-light treatment in the Fv/Fm ratio and in levels of phycobilisome pigments, sugars and antioxidant enzymes after an initial decrease 1 h after the treatment. These findings may indicate a period of partial adaptation to high light that is due to the efficiency of protective processes operational in the two species, which subsequently failed after a longer exposure duration of 4-6 h.     

Vibrational spectra of H2O and CF4 molecules using Lie algebraic approach

In this paper, we introduce one dimensional vibron model to analyze the fundamental, overtone and combination modes of CF₄ molecule and both stretching, bending vibrational mode of bent H₂O molecule up to first overtone with few algebraic parameters. Using the model Hamiltonian, we reported here better results for the vibrational spectra of H₂O. Our analysis suggests some reassignments of levels and predicts location of states in case of CF₄ molecule which was not yet observed.     

Individual and simultaneous voltammetric determination of ascorbic acid,uric acid and folic acid by using a glassy carbon electrode modified with gold nanoparticles linked to bentonite via cysteine groups

A voltammetric sensor for both the individual and the simultaneous determination of ascorbic acid (AA), uric acid (UA) and folic acid (FA) is described. It is based on a glassy carbon electrode (GCE) that was modified with bentonite (Bnt) that was first functionalized with cysteine (Cys) to which gold nanoparticles were linked. The resulting material (referred to as Au-Cys-Bnt) and the other materials were characterized by UV-vis spectroscopy, powder X-ray diffraction (XRD), scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray analysis and electrochemical methods. The XRD peak positions of bentonite and Cys-functionalized bentonite prove the incorporation of Cys into bentonite. The XPS spectrum of Au-Cys-Bnt confirms the interaction of gold nanoparticles with the thiol group of Cys. The modified GCE displays high electrocatalytic activity for the oxidation of AA, UA and FA, typically at 0.19, 0.41, and 0.73 V (vs. SCE), respectively. Differential pulse voltammetric data show a linear response that covers the 1 μM to 25 mM concentration range for AA, the 1 to 200 μM concentration range for UA, and two linear ranges for FA, one from 5 to 100 μM and one from 100 μM to 1.5 mM. The sensor was applied to the determination of AA, UA and FA in (spiked) multi-vitamin syrup, bird serum and milk samples.

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Graphical abstract Schematic of a sensor for simultaneous and individual electrochemical determination of ascorbic, uric, and folic acids in real samples. The sensor consists of a glassy carbon electrode that was modified with a nanocomposite prepared from bentonite that was first functionalized with cysteine to which gold nanoparticles were linked.

     

Design and development of bioactive α-hydroxy carboxylate group modified MnFe2O4 nanoparticle: Comparative fluorescence study,magnetism and DNA nuclease activity

Three new α-hydroxy carboxylate group functionalized MnFe₂O₄ nanoparticles (NPs) have been developed to explore the microscopic origin of ligand modified fluorescence and magnetic properties of nearly monodispersed MnFe₂O₄ NPs. The surface functionalization has been carried out with three small organic ligands (tartrate, malate, and citrate) having different number of α-hydroxy carboxylate functional group along with steric effect. Detailed study unveils that α-hydroxy carboxylate moiety of the ligands plays key role to generate intrinsic fluorescence in functionalized MnFe₂O₄ NPs through the activation of ligand to metal charge transfer transitions, associated with ligand–Mn²⁺/Fe³⁺ interactions along with d–d transition corresponding to d–orbital energy level splitting of Fe³⁺ ions on NP surface. Further, MnFe₂O₄ NPs show a maximum 140.88% increase in coercivity and 97.95% decrease in magnetization compared to its bare one upon functionalization. The ligands that induce smallest crystal field splitting of d–orbital energy level of transition metal ions are found to result in strongest ferrimagnetic activation of the NPs. Finally, our developed tartrate functionalized MnFe₂O₄ (T-MnFe₂O₄) NPs have been utilized for studying DNA binding interaction and nuclease activity for stimulating their beneficial activities toward diverse biomedical applications. The spectroscopic measurements indicate that T-MnFe₂O₄ NPs bind calf thymus DNA by intercalative mode. The ability of T-MnFe₂O₄ NPs to induce DNA cleavage was studied by gel electrophoresis technique where the complex is found to promote the cleavage of pBR322 plasmid DNA from the super coiled form I to linear coiled form II and nicked coiled form III with good efficiency.     

CeCl3⋅7H2O-catalysed hydrophosphonylation of aldehydes and ketones: An expeditious route to α-hydroxyphosphonates under solvent-free conditions

Abstract

A cerium(III) chloride-catalysed expeditious synthesis of α-hydroxyphosphonates via a modified Abramov synthetic protocol has been developed. The scope of the current protocol is broad, with a range of aromatic, α,β-unsaturated and heterocyclic aldehydes being efficiently converted to the anticipated products in very good to excellent yields (89–96%) in 15?min using low catalytic loading. The protocol was efficiently extended to hitherto unactivated cyclic ketones such as cyclopentanone and cyclohexanone to afford the required products in excellent yields. However, the reaction with cyclohexenone delivered a Michael product instead of the anticipated α-hydroxyphosphonates. The solvent-free conditions, low catalytic loadings, avoidance of toxic reagents and good to excellent yields are significant advantages of this protocol.