Comparative molecular field analysis and comparative molecular similarity indices analysis of boron-containing human thymidine kinase 1 substrates

Three-dimensional quantitative structure-activity relationship (3D-QSAR) using CoMFA and CoMSIA techniques was applied to evaluate 56 pyrimidine nucleosides as substrates of human thymidine kinase 1 (hTK1), 27 of them containing a carborane substituent either at the 3-, 5-, or 3'-position of the 2'-deoxyuridine scaffold. This is the first report describing 3D-QSAR studies of compounds containing boron atoms. Both CoMFA and CoMSIA models were derived from a training set of 47 molecules and the predictive capacity of the CoMSIA model was successfully validated by accurately calculating known phosphorylation rates of both boronated and non-boron hTK1 substrates that were not included in the training set. The optimal CoMSIA model provided the following values: q(2) 0.622, r(2) 0.983, s 0.165, and F 187.5. Contour maps obtained from the CoMSIA model were in agreement with the experimentally determined biological data.     

The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus entry into host cells

Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higher dp and sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, purified glycoprotein B shows strong binding to heparin, and desulfated heparin analogs compete poorly with heparin for gB binding. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity.     

Substitutions of 2S and 7U chromosomes of Aegilops kotschyi in wheat enhance grain iron and zinc concentration

Biofortification through genetic manipulation is the best approach for improving micronutrient content of the staple food crops to alleviate hidden hunger, namely, the deficiency of Fe and Zn affecting more than two billion people worldwide. An interspecific hybridization was made between T. aestivum line Chinese Spring (CS) and Aegilops kotschyi accession 3790 selected for high grain iron and zinc concentration. The CS × Ae. kotschyi F₁ hybrid with low chromosome pairing was highly male and female sterile. This was backcrossed with wheat cultivars to get seed set. The selfed BC₁F₁ and BC₂F₁ plants with high grain iron and zinc concentration were selected in subsequent generations. The selected derivatives showed 60–136% enhanced grain iron and zinc concentration and 50–120% increased iron and zinc content per seed as compared to the recipient wheat cultivars. Thirteen cytologically stable, fertile and agronomically superior plants with high grain iron and zinc concentrations were selected for molecular characterization. The application of anchored wheat SSR markers, transferable to Ae. kotschyi, to the high grain iron and zinc containing derivatives indicated introgression of group 2 and group 7 chromosomes of Ae. kotschyi. GISH and FISH analysis of some derivatives confirmed the substitution of chromosomes 2S and 7U for their homoeologues of the A genome, suggesting that some of the genes controlling high grain micronutrient content in the Ae. kotschyi accession are on these chromosomes.     

Antimalarial evaluation of copper(II) nanohybrid solids: inhibition of plasmepsin II, a hemoglobin-degrading malarial aspartic protease from Plasmodium falciparum

A new class of copper(II) nanohybrid solids, LCu(CH₃COO)₂ and LCuCl₂, have been synthesized and characterized by transmission electron microscopy, dynamic light scattering, and IR spectroscopy, and have been found to be capped by a bis(benzimidazole) diamide ligand (L). The particle sizes of these nanohybrid solids were found to be in the ranges 5–10 and 60–70 nm, respectively. These nanohybrid solids were evaluated for their in vitro antimalarial activity against a chloroquine-sensitive isolate of Plasmodium falciparum (MRC 2). The interactions between these nanohybrid solids and plasmepsin II (an aspartic protease and a plausible novel target for antimalarial drug development), which is believed to be essential for hemoglobin degradation by the parasite, have been assayed by UV–vis spectroscopy and inhibition kinetics using Lineweaver–Burk plots. Our results suggest that these two compounds have antimalarial activities, and the IC₅₀ values (0.025–0.032 μg/ml) are similar to the IC₅₀ value of the standard drug chloroquine used in the bioassay. Lineweaver–Burk plots for inhibition of plasmepsin II by LCu(CH₃COO)₂ and LCuCl₂ show that the inhibition is competitive with respect to the substrate. The inhibition constants of LCu(CH₃COO)₂ and LCuCl₂ were found to be 10 and 13 μM, respectively. The IC₅₀ values for inhibition of plasmepsin II by LCu(CH₃COO)₂ and LCuCl₂ were found to be 14 and 17 μM, respectively. Copper(II) metal capped by a benzimidazole group, which resembles the histidine group of copper proteins (galactose oxidase, β-hydroxylase), could provide a suitable anchoring site on the nanosurface and thus could be useful for inhibition of target enzymes via binding to the S1/S3 pocket of the enzyme hydrophobically. Both copper(II) nanohybrid solids were found to be nontoxic against human hepatocellular carcinoma cells and were highly selective for plasmepsin II versus human cathepsin D. The pivotal mechanism of antimalarial activity of these compounds via plasmepsin II inhibition in the P. falciparum malaria parasite is demonstrated.     

Effect of salt stress on cucumber: Na+–K+ ratio, osmolyte concentration, phenols and chlorophyll content

A pot experiment with 17 diverse genotypes of cucumber with four levels of salt stress viz., 0, 2, 4 and 6 dS m^?1 was carried out during 2006. ANOVA revealed significant differences amongst genotypes and genotype × salt stress interaction indicating the genetic variability and differential response of the genotypes to different salt stress levels. The salt stress adversely affected the biochemical parameters; effects were severe under 4 dS m^?1. No genotype could survive at 6 dS m^?1. Sodium content, Na⁺–K⁺ ratio, proline, reducing sugars, phenol and yield reduction (%) increased significantly as the salt stress increased. Potassium, chlorophyll, membrane stability index and fruit yield decreased significantly under salt stress in all genotypes. However, the genotypes CRC-8, CHC-2 and G-338 showed lower accumulation of sodium, lesser depletion of potassium, lower Na⁺–K⁺ ratio and higher accumulation of proline, reducing sugars, phenols, better membrane stability and lower yield reduction (%) under salt stress, while CH-20 and DC-1 were sensitive to salt stress. Thus, a combination of traits such as higher membrane stability, lower Na⁺–K⁺ ratio, higher osmotic concentration and selective uptake of useful ions and prevention of over accumulation of toxic ions contribute to salt stress tolerance in cucumber. These traits would be useful selection criteria during salt stress breeding in cucumber.     

Radioprotection of plasmid and cellular DNA and Swiss mice by silibinin

The radioprotective effect of a non-toxic bioactive component in plant milk thistle, silibinin against genotoxicity induced by γ-irradiation was investigated in vivo/in vitro. Under in vitro conditions of irradiation, silibinin protected plasmid pBR322 DNA against γ-radiation-induced strand breaks in a concentration dependent manner (0–200 μM). Under cellular conditions of radiation exposure (3 Gy), silibinin offered protection to lymphocyte DNA as evidenced from reduction in DNA damage and micronuclei formation, which showed correlation to the extent of intracellular reactive oxygen species reduction. Our extended animal studies suggest that oral administration of silibinin (70 mg/kg for 3 days) to mice prior to whole-body γ-exposure (7.5 Gy) resulted in significant protection to radiation-induced mortality and DNA damage in blood leukocytes. However, silibinin treatment after irradiation was not as effective as pre-administration. In conclusion, present study indicated that silibinin has a strong potential to prevent radiation-induced DNA damage under both in vitro and in vivo.     

A technique using reusable components for hand-infesting cornstalks with European corn borer (Lepidoptera: Crambidae) larvae

Field trials were conducted in 2005 and 2006 to evaluate the use of reusable wire nuts and nonreusable gelatin capsules for hand-infesting cornstalks with European corn borer, Ostrinia nubilalis (Hübner), (Lepidoptera: Crambidae) larvae. The reusable technique, which consists of a modified WingGard plastic wire connector (i.e., wire nut) as a containment device for larvae, was compared over three plant growth stages to a gelatin capsule technique. In 2005 and 2006, the wire nut technique resulted in significantly higher number of wire nuts still intact (i.e., undamaged, with or without a larva) on the stalk at 72 h after infestation compared with the gelatin capsule technique. In addition, the wire nut technique resulted in significantly higher number of tunnels per stalk compared with the gelatin capsule technique at all three corn growth stages during both years. In 2005, the mean +/- SEM number of tunnels per stalk was 0.53 +/- 0.03 in the wire nut technique compared with 0.13 +/- 0.03 tunnels per stalk in the gelatin capsule technique. In 2006, the mean number of tunnels per stalk was 0.45 +/- 0.03 in the wire nut technique compared with 0.08 +/- 0.02 tunnels per stalk in the gelatin capsule technique. In addition, the relative net precision in the wire-nut technique was approximately 2 times higher compared with the gelatin capsule technique.     

Photophysical Probes of the Amorphous Solid State of Proteins

The properties of amorphous solid proteins influence the texture and stability of low-moisture foods, the shelf-life of pharmaceuticals, and the viability of seeds and spores. We have investigated the relationship between molecular mobility and oxygen permeability in dry food protein films—bovine α-lactalbumin (α-La), bovine β-lactoblobulin (β-Lg), bovine serum albumin (BSA), soy 11S globulin, and porcine gelatin—using phosphorescence from the triplet probe erythrosin B. Measurements of the phosphorescence decay in the absence (nitrogen) and presence (air) of oxygen versus temperature provide estimates of the non-radiative decay rate for matrix-induced quenching (k _TS0) and oxygen quenching (k _Q[O₂]) of the triplet state. Since the oxygen quenching constant is the product of the oxygen solubility ([O₂]) and a term (k _Q) proportional to the oxygen diffusion coefficient, it is a measure of the oxygen permeability through the films. For all proteins except gelatin, Arrhenius plots of k _TS0 reveal a gradual increase of apparent activation energy across a broad temperature range starting at ∼50 °C; this suggests that there is a steady increase in the available modes of molecular motion with increasing temperature within the protein matrix. Arrhenius plots for k _Q[O₂] were linear for all proteins with activation energies ranging from 24 to 29 kJ/mol. The magnitude of the oxygen quenching constants varied in the different proteins; the rates were approximately 10-fold higher in α-La, β-Lg, and BSA than in 11S glycinin and gelatin. Although the rate of oxygen permeability was not directly affected by the increased mobility of the protein matrix, plots of k _Q[O₂] versus k _TS0 were linear over nearly three orders of magnitude in the protein films, suggesting that the matrix mobility plays a specific role in modulating oxygen permeability. This effect may reflect differences in matrix-free volume that directly influence both mobility and oxygen solubility.     

Aerosol Chemistry over a High Altitude Station at Northeastern Himalayas,India

Background

There is an urgent need for an improved understanding of the sources, distributions and properties of atmospheric aerosol in order to control the atmospheric pollution over northeastern Himalayas where rising anthropogenic interferences from rapid urbanization and development is becoming an increasing concern.

Methodology/Principal Findings

An extensive aerosol sampling program was conducted in Darjeeling (altitude ∼2200 meter above sea level (masl), latitude 27°01′N and longitude 88°15′E), a high altitude station in northeastern Himalayas, during January–December 2005. Samples were collected using a respirable dust sampler and a fine dust sampler simultaneously. Ion chromatograph was used to analyze the water soluble ionic species of aerosol. The average concentrations of fine and coarse mode aerosol were found to be 29.5±20.8 µg m⁻³ and 19.6±11.1 µg m⁻³ respectively. Fine mode aerosol dominated during dry seasons and coarse mode aerosol dominated during monsoon. Nitrate existed as NH₄NO₃ in fine mode aerosol during winter and as NaNO₃ in coarse mode aerosol during monsoon. Gas phase photochemical oxidation of SO₂ during premonsoon and aqueous phase oxidation during winter and postmonsoon were the major pathways for the formation of SO₄ ²⁻ in the atmosphere. Long range transport of dust aerosol from arid regions of western India was observed during premonsoon. The acidity of fine mode aerosol was higher in dry seasons compared to monsoon whereas the coarse mode acidity was higher in monsoon compared to dry seasons. Biomass burning, vehicular emissions and dust particles were the major types of aerosol from local and continental regions whereas sea salt particles were the major types of aerosol from marine source regions.

Conclusions/Significance

The year-long data presented in this paper provide substantial improvements to the heretofore poor knowledge regarding aerosol chemistry over northeastern Himalayas, and should be useful to policy makers in making control strategies.     

Comparative modeling of retinol-binding protein-3 and retinal S-antigen in Eales’ disease and prediction of their binding sites using computational methods

Retinal S-antigen and interphotoreceptor retinoid-binding protein-3 play a significant role in the etiopathogenesis of Eales' disease. Protein 3D structures are functionally very important and play a significant role in progression of the disease, hence these 3D structures are better target for further drug designing and relative studies. We developed 3D model structure of retinol-binding protein-3 and retinal S-antigen protein of human involved in Eales' disease. Functional site prediction is a very important and related step; hence, in the current course of analysis, we predicted putative functional site residues in the target proteins. Molecular models of these proteins of Eales' disease as documented in this study may provide a valuable aid for designing an inhibitor or better ligand against Eales' disease and could play a significant role in drug design.