Biophysical characterization of double-stranded oligonucleotides using ETBR and isothermal fluorescence spectroscopy: implication for SNP genotyping

The UV-absorption, fluorescence and CD spectra of aps 23 bp oligoduplexes were performed for potential diagnostic purpose. These oligonucleotide sequences were mimicked from natural mutations (mitochondrial genome) of human population (unpublished). This work was designed on the basis of hybridization of non-self complementary oligoduplexes (aps) containing no mismatch, one-mismatch and two-mismatches. Since melting temperature™ is dependent on concentration of the oligoduplex, various concentrations were used in this study protocol. The thermal spectra profiles (UV absorbance and fluorescence) of these oligoduplexes (aps) are different for a particular concentration, and can be implicated for mutations. − dF/dT (or dA/dT) vs T, lnK (or RlnK) vs T_M, ΔG vs T_M, ΔS vs T_M and ΔH vs T_M are also variable for those sequences. All these thermodynamic data were calculated from absorbance (at 260 nm) data. On the contrary to the 23 bp oligoduplexes (aps), the PCR products of 97 bp and 256 bp length were genotyped with ETBR (excitation 530 nm, emission 600 nm) fluorimetrically. But our attempts to genotype these PCR sequences with isothermal UV absorbance spectroscopy were unsuccessful. Isothermal UV absorbance spectra has a limitation of sequence length. However, the structural conformation (all B-type) of the oligoduplexes (aps) was determined using CD. The minor discrepancy in CD spectra of these oligoduplexes are not significant for mutational analysis. 97 bp nested PCR product was an amplicon having either GcT or AcC mutation of mitochondria of normal human population, whereas 256 bp PCR product was an amplicon of human BRCA2 gene (NCBI Accession No. AY151039) of chromosome 13 having either A or G mutation at position − 26.     

Effect of host framework on the diffusion process in microporous material: a molecular dynamics simulation investigation

One of the central assumptions when a particle moves through a window in microporous materials is that interaction of the diffusing particle with the silicon (Si) and aluminum (Al) atoms of the framework can be neglected, as the presence of bulkier oxygen in the host structure is thought to hinder close proximity of the diffusing particle to Si and Al. We examine this assumption, exploring the diffusion path and cross-checking the bottleneck associated with the diffusion process. Our study reveals that short-range interactions between the diffusing species and Si/Al of the host have a significant effect on the diffusion process. Guest–host interaction energy increases significantly if interaction between Si and Al atoms with the diffusing species is considered. The self-diffusion coefficient (D) decreases significantly in the linear regime, whereas in the anomalous regime, surprisingly, D increases. The increase in D is due to a decrease in the activation energy in the anomalous regime, whereas in the linear regime, activation energy increases, thus D decreases.

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Graphical abstract a Interaction energies (E _a) for different LJ potential for guest–guest interactions (σ_gg) along the diffusion path; b correspondingdiffusivity values

     

Molecular assessment of diversity among endophytic diazotrophs isolated from subtropical Indian sugarcane

Twenty-two endophytic bacterial isolates from the roots of sugarcane were compared morphologically, biochemically and genetically. Gram staining, colony pigment, texture and other cultural characteristics were taken for morphological characterization. Oxidation-fermentation tests for D-glucose and D-sucrose, production of acid and hydrogen from different carbon source, oxidase activity, antibiotic and drug resistance patterns were chosen as the biochemical and physiological criteria. Twelve random decamer primers were used to analyze and compare these isolates through RAPD among themselves as well as with known standard diazotrophic strains. The isolates were compared through dendrograms constructed on the basis of similarity patterns obtained from biochemical and RAPD analysis. The estimated diversity through RAPD analysis was more evident than the diversity on the basis of morphological and biochemical characters. Within Acetobacter group, the isolates showed substantial genetic diversity for future exploitation as PGPRs and diazotrophic associative endophytes.     

Step-up/step-down perfusion approach for increased mAb 520C9 production by a hybridoma cell line

The hybridoma cell line, HB-8696, produces a monoclonal antibody, 520C9 (mouse IgG₁) that recognizes the breast cancer oncoprotein, c-erbB2. The effect of perfusion rate (volume of fresh feed/working volume of reactor/day) on cell growth and mAb production was investigated but perfusion at a constant rate and at an arbitrarily increased rate could not maintain exponential cell growth or a higher specific mAb production rate. An optimum step-up/step-down perfusion strategy is therefore proposed for maintaining a steady state production phase at high cell density for ten days. The optimum step-up perfusion could achieve fast cell growth by avoiding any nutrient limited condition and the following optimum step-down perfusion could potentially maintain high live cell density and reduced product dilution as well. The maximum viable cell achieved under optimum perfusion strategy was 2.3 × 10⁷ cells/ml which was 19-fold higher than in optimum batch culture. The mAb yield and volumetric productivity were significantly improved to 52 and 50 mg/l day compared to 25 and 3.8 mg/l day in optimum batch, respectively, and could be maintained for up to ten days.     

Two selective novel triterpene glycosides from sea cucumber,Telenata Ananas: inhibitors of chemokine receptor-5

The aqueous methanolic extract of a sea cucumber was found to contain two triterpene glycosides 1 and 2. The structures of 1 and 2 were established based on high-resolution NMR studies. Compounds 1 and 2 exhibited inhibitory activity (K(i)) of 30 and 5microM, respectively, in a chemokine receptor subtype 5 (CCR5) assay. Both compounds did not show any significant inhibition in a CXCR2 assay at 50microM, suggesting their selectivity for the CCR5 receptor.     

Rap1a null mice have altered myeloid cell functions suggesting distinct roles for the closely related Rap1a and 1b proteins

The Ras-related GTPases Rap1a and 1b have been implicated in multiple biological events including cell adhesion, free radical production, and cancer. To gain a better understanding of Rap1 function in mammalian physiology, we deleted the Rap1a gene. Although loss of Rap1a expression did not initially affect mouse size or viability, upon backcross into C57BL/6J mice some Rap1a-/- embryos died in utero. T cell, B cell, or myeloid cell development was not disrupted in Rap1a-/- mice. However, macrophages from Rap1a null mice exhibited increased haptotaxis on fibronectin and vitronectin matrices that correlated with decreased adhesion. Chemotaxis of lymphoid and myeloid cells in response to CXCL12 or CCL21 was significantly reduced. In contrast, an increase in FcR-mediated phagocytosis was observed. Because Rap1a was previously copurified with the human neutrophil NADPH oxidase, we addressed whether GTPase loss affected superoxide production. Neutrophils from Rap1a-/- mice had reduced fMLP-stimulated superoxide production as well as a weaker initial response to phorbol ester. These results suggest that, despite 95% amino acid sequence identity, similar intracellular distribution, and broad tissue distribution, Rap1a and 1b are not functionally redundant but rather differentially regulate certain cellular events.     

Sunlight-mediated activation of an inert polymer surface for covalent immobilization of a protein

Polystyrene, polypropylene, and polyethylene surfaces were activated by exposing 1-fluoro-2-nitro-4-azidobenzene coated surface to sunlight. Sunlight intensity of 26,300 lux was found optimum beyond which no appreciable increase in activation was observed. Five-minutes sunlight exposure gave better activated surface than 5 min 365-nm UV light exposure. The efficacy of sunlight-mediated activated surfaces was demonstrated by covalently immobilizing proteins onto them. Horseradish peroxidase when immobilized onto the sunlight-activated surfaces showed more than twofold increase in immobilization than the surface without activation. Thus, sunlight being a versatile, eco-friendly, and clean energy source can be a potential alternative for activation of inert surface for covalent attachment of biomolecule such as protein, DNA, or carbohydrate.     

Syntheses, structures, and properties of Co(III) complexes derived from polypyridine ligands containing one carboxamido nitrogen donor

Four cobalt(III) complexes containing the polypyridine pentadentate ligands N,N-bis(2-pyridylmethyl)amine-N′-ethyl-2-pyridine-2-carboxamide (PaPy₃H), N,N-bis(2-pyridylmethyl)amine-N′-[1-(2-pyridylethyl)acetamide (MePcPy₃H), and N,N-bis(2-pyridylmethyl)amine-N′-(2-pyridylmethyl)acetamide (PcPy₃H), have been synthesized. All three ligands bind the Co(III) center in the same fashion with the exception of loss of conjugation between the carboxamide moiety and the pyridine ring in the latter two. The structures of [(PaPy₃)Co(OH)][(PaPy₃)Co(H₂O)](ClO₄)₃ · 3H₂O (1), [(PaPy₃)Co(NO₂)](ClO₄) · 2MeCN (2), [(MePcPy₃)Co(MeCN)](ClO₄)₂ · 0.5MeCN (3), and [(PcPy₃)Co(Cl)](ClO₄) · 2MeCN (4) have been determined. These ligands with strong-field carboxamido N donor stabilize the +3 oxidation state of the Co center as demonstrated by the facile oxidation of the corresponding Co(II) complexes (prepared in situ) by H₂O₂, [Fe(Cp)₂](BF₄), or nitric oxide (NO). The Co-N_amido bond distances of 1-4 lie in the narrow range of 1.853-1.898 Å. ¹H NMR spectra of these complexes confirm the low-spin d⁶ ground states of the metal centers.