Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

X–H rotational-echo double-resonance NMR for torsion angle determination of peptides

C–H and N–H rotational-echo double-resonance (REDOR) NMR is developed for determining torsion angles in peptides. The distance between an X spin such as ¹³C or ¹⁵N and a proton is measured by evolving the proton magnetization under REDOR-recoupled X–H dipolar interaction. The proton of interest is selected through its directly bonded heteronuclear spin Y. The sidechain torsion angle χ₁ is extracted from a ¹³Cβ-detected Hβ–N distance, while the backbone torsion angle φ is extracted from an ¹⁵N-detected H^N–C^′ distance. The approach is demonstrated on three model peptides with known crystal structures to illustrate its utility.     

Separation of lead sulphate from barium sulphate in their determination in glass

The conventional method for separation of lead from a combined lead and barium sulphate precipitate by extraction with ammonium acetate has been critically studied. The results show that quantitative separation of lead is possible only when the molar concentration ratio of barium to lead is 4.2 or above, but at ratios below 4.2 the method fails because of the formation of a solid solution of lead and barium sulphates which is maximal at initial mole-ratio 0.42. The lead in the solid solution, however, forms a strong soluble complex with EDTA and can be quantitatively separated. Based on this, a gravimetric method has been worked out for determination of lead and barium in glass.     

Estimation of underground water radon danger in Bakreswar and Tantloi Geothermal Region,India

The main aim of the study is to present an evaluation of radon concentration in underground water of Bakreswar and Tantloi geothermal region which is mainly used for drinking purposes of the local people. Water samples were collected from tube-wells at 173 different locations. The radon (²²²Rn) concentration level was observed to fluctuate widely between 3.3 and 803.8 Bq/l with an average of 106.8 Bq/l. Nearly 42% of the samples had radon concentration above the safe limit of 100 Bq/l recommended by World Health Organisation (WHO) and European Union Commission (EU). Considering the WHO and International Commission on Radiological Protection recommended water consumption rate for adults (730 l/year) the corresponding total annual effective dose of the samples were estimated to assess the probable health risk. Total annual effective dose of the samples were varied between 16.72 and 4079.47 µSv/year with an average value of 541.92 µSv/year. About 95% samples exceed the WHO and EU Commission proposed safe limit of 100 µSv/year.     

New chemical constituents from the Piper betle Linn. (Piperaceae)

The phytochemical investigation of chloroform extract from Piper betle var. haldia, Piperaceae, leaves has resulted in the isolation of two new chemical constituents which were identified as 1-n-dodecanyloxy resorcinol (H1) and desmethylenesqualenyl deoxy-cepharadione-A (H4), on the basis of spectroscopic data 1D NMR (¹H and ¹³C) and 2D NMR (¹H-¹H COSY and HMBC) as well as ESI-MS, FT-IR and HR-ESI-MS analyses. Compounds H1 and H4 showed excellent antioxidant DPPH free radical scavenging activity with IC₅₀ values of 7.14 μg/mL and 8.08 μg/mL compared to ascorbic acid as a standard antioxidant drug with IC₅₀ value of 2.52 μg/mL, respectively. Evaluation of cytotoxic activity against human hepatoma cell line (PLC-PRF-5) showed moderate effect with the GI₅₀ values of 35.12 μg/mL for H1, 31.01 μg/mL for H4, compared to Doxorubicin^® as a standard cytotoxic drug with GI₅₀ value of 18.80 μg/mL.     

Experimental investigation on the flow instability behavior of a multi-channel boiling natural circulation loop at low-pressures

Natural circulation as a mode of heat removal is being considered as a prominent passive feature in the innovative nuclear reactor designs, particularly in boiling-water-reactors, due to its simplicity and economy. However, boiling natural circulation system poses many challenges to designer due to occurrence of various kinds of instabilities such as excursive instability, density wave oscillations, flow pattern transition instability, geysering and metastable states in parallel channels. This problem assumes greater significance particularly at low-pressures i.e. during startup, where there is great difference in the properties of two phases. In light of this, a parallel channel loop has been designed and installed that has a geometrical resemblance to the pressure-tube-type boiling-water-reactor, to investigate into the behavior of boiling natural circulation. The loop comprises of four identical parallel channels connected between two common plenums i.e. steam drum and header. The recirculation path is provided by a single downcomer connected between steam drum and header. Experiments have been conducted over a wide range of power and pressures (1–10 bar). Two distinct unstable zones are observed with respect to power i.e. corresponding to low power (Type-I) and high power (Type-II) with a stable zone at intermediate powers. The nature of oscillations in terms of their amplitude and frequency and their evolution for Type-I and Type-II instabilities are studied with respect to the effect of heater power and pressure. This paper discusses the evolution of unstable and stable behavior along with the nature of flow oscillation in the channels and the effect of pressure on it.     

Development of Hydroprocessing Route to Transportation Fuels from Non-Edible Plant-Oils

Catalysts with tunable porosity, crystallinity and acidity can selectively produce aviation fuels and road transportation fuels via hydroprocessing of non-edible oils. Here we discuss several catalyst supports—mesoporous alumina, silica–alumina and hierarchical mesoporous zeolites, developed and used as support for hydroprocessing catalysts (Ni–Mo, Co–Mo, Ni–W), for the selective production of transportation fuels. These developed catalysts were used for the hydroconversion of waste cooking-oil, jatropha-oil, algal-oil and their mixtures with petroleum refinery oils. The physicochemical properties of the catalyst were tuned for optimal performance on the basis of evaluation results on high pressure fixed bed microreactors and pilot scale reactors. These studies targeted the production of transportation fuels (gasoline, kerosene and diesel) by hydroprocessing (hydrotreating or hydrocracking) renewable feed stocks or co-processing with fossil based oils. Modelling and process optimization studies for prediction of kinetic rate parameters and to know the reaction pathways for the conversion of these feed stocks to various range of hydrocarbon fuels, were also carried out. These studies provided the vital information that the reaction pathways were temperature dependent.