New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor

To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.     

Torsion pendulum automation by a single microcomputer

A new automated torsional pendulum is described. It uses a single photocell for the measurement of the period of oscillation and the logarithmic decrement. Data acquisition, data processing and temperature control are all performed by a single microcomputer. The result is that the instrument can be produced and operated more cheaply than before.The principles behind the design, the method of determining the shape factor, the calibration procedure and the software are discussed. Examples are given to illustrate the use of this instrument. A practical limitation is that the loss tangent should not exceed about 3.     

Luminescence properties of Tb(3+)-doped CaMoO(4) nanoparticles: annealing effect, polar medium dispersible, polymer film and core-shell formation

Tb(3+)-doped CaMoO(4) (Tb(3+) = 1, 3, 5, 7, 10, 15 and 20 atom%) core and core-shell nanoparticles have been prepared by urea hydrolysis in ethylene glycol (EG) as capping agent as well as reaction medium at low temperature ～150 °C. As-prepared samples were annealed at 500 and 900 °C for 4 h to eliminate unwanted hydrocarbons and/or H(2)O present in the sample and to improve crystallinity. The synthesised nanophosphors show tetragonal phase structure. The crystallite size of as-prepared sample is found to be ～18 nm. The luminescence intensity of the (5)D(4) → (7)F(5) transition at 547 nm of Tb(3+) is much higher than that of the (5)D(4) → (7)F(6) transition at 492 nm. 900 °C annealed samples show the highest luminescence intensity. The intensity ratio R (I[(5)D(4) → (7)F(6)]/I[(5)D(4) → (7)F(5)]) lies between 0.3-0.6 for as-prepared, 500 and 900 °C annealed samples. The luminescence decay of (5)D(4) level under 355 nm excitation shows biexponential behaviour indicating availability of Tb(3+) ions on surface and core regions of particle; whereas, contribution of Mo-O charge transfer to lifetime is obtained under 250 nm excitation. The CIE coordinates of as-prepared, 500 and 900 °C annealed 5 atom% Tb(3+)-doped CaMoO(4) samples under 250 nm excitation are (0.28, 0.32), (0.22, 0.28) and (0.25, 0.52), respectively. The dispersed particles in polar medium and its polymer film show green light emission. The luminescence intensity is improved significantly after core-shell formation due to extent of decrease of non-radiative rates arising from surface dangling bonds and capping agent. Quantum yields of as-prepared samples of 1, 5 and 7 atom% Tb(3+)-doped CaMoO(4) samples are found to be 10, 3 and 2, respectively.     

Numerical analysis of the internal flow and the mixing chamber length effects on the liquid film thickness exiting from the effervescent atomizer

Journal of Thermal Analysis and Calorimetry - Two-phase flow was simulated within the effervescent atomizer by the volume of fluid interface tracing model. Different gas-to-liquid mass ratios...     

Reply to the comment from Mamedov

Here, I present the reply to the comments from Mamedov regarding numerical solution of Bloch–Gruneisen function to determine the contribution of electron–phonon interaction in polycrystalline superconductor. Reply to the comments from Mamedov is discussed one by one.     

Development of Sustained Release Baricitinib Loaded Lipid-Polymer Hybrid Nanoparticles with Improved Oral Bioavailability

Baricitinib (BTB) is an orally administered Janus kinase inhibitor, therapeutically used for the treatment of rheumatoid arthritis. Recently it has also been approved for the treatment of COVID-19 infection. In this study, four different BTB-loaded lipids (stearin)-polymer (Poly(d,l-lactide-co-glycolide)) hybrid nanoparticles (B-PLN1 to B-PLN4) were prepared by the single-step nanoprecipitation method. Next, they were characterised in terms of physicochemical properties such as particle size, zeta potential (ζP), polydispersity index (PDI), entrapment efficiency (EE) and drug loading (DL). Based on preliminary evaluation, the B-PLN4 was regarded as the optimised formulation with particle size (272 ± 7.6 nm), PDI (0.225), ζP (−36.5 ± 3.1 mV), %EE (71.6 ± 1.5%) and %DL (2.87 ± 0.42%). This formulation (B-PLN4) was further assessed concerning morphology, in vitro release, and in vivo pharmacokinetic studies in rats. The in vitro release profile exhibited a sustained release pattern well-fitted by the Korsmeyer–Peppas kinetic model (R² = 0.879). The in vivo pharmacokinetic data showed an enhancement (2.92 times more) in bioavailability in comparison to the normal suspension of pure BTB. These data concluded that the formulated lipid-polymer hybrid nanoparticles could be a promising drug delivery option to enhance the bioavailability of BTB. Overall, this study provides a scientific basis for future studies on the entrapment efficiency of lipid-polymer hybrid systems as promising carriers for overcoming pharmacokinetic limitations.     

Electronic structures,bonding, and spin state energetics of biomimetic mononuclear and bridged dinuclear iron complexes: a computational examination

Structural Chemistry - Mononuclear and dinuclear iron complexes are found as key intermediates in many synthetic and biocatalytic reactions, since many of these species are transient and have high...     

Psychrotolerant Mesorhizobium sp. Isolated from Temperate and Cold Desert Regions Solubilizes Potassium and Produces Multiple Plant Growth Promoting Metabolites

Soil potassium (K) supplement depends intensively on the application of chemical fertilizers, which have substantial harmful environmental effects. However, some bacteria can act as inoculants by converting unavailable and insoluble K forms into plant-accessible forms. Such bacteria are an eco-friendly approach for enhancing plant K absorption and consequently reducing utilization of chemical fertilization. Therefore, the present research was undertaken to isolate, screen, and characterize the K solubilizing bacteria (KSB) from the rhizosphere soils of northern India. Overall, 110 strains were isolated, but only 13 isolates showed significant K solubilizing ability by forming a halo zone on solid media. They were further screened for K solubilizing activity at 0 °C, 1 °C, 3 °C, 5 °C, 7 °C, 15 °C, and 20 °C for 5, 10, and 20 days. All the bacterial isolates showed mineral K solubilization activity at these different temperatures. However, the content of K solubilization increased with the upsurge in temperature and period of incubation. The isolate KSB (Grz) showed the highest K solubilization index of 462.28% after 48 h of incubation at 20 °C. The maximum of 23.38 µg K/mL broth was solubilized by the isolate KSB (Grz) at 20 °C after 20 days of incubation. Based on morphological, biochemical, and molecular characterization (through the 16S rDNA approach), the isolate KSB (Grz) was identified as Mesorhizobium sp. The majority of the strains produced HCN and ammonia. The maximum indole acetic acid (IAA) (31.54 µM/mL) and cellulase (390 µM/mL) were produced by the isolate KSB (Grz). In contrast, the highest protease (525.12 µM/mL) and chitinase (5.20 µM/mL) activities were shown by standard strain Bacillus mucilaginosus and KSB (Gmr) isolate, respectively.