On the Estimation of True Treatment Response when Patients Enter Staggeredly in a Clinical Trial

Due to staggered entries of patients during a clinical trial, the available exposure to observe the patients under a treatment is less and non-uniform while the patients with whom the trial is started initially are exposed to uniform exposures to the treatment. Because of this, the true response of the treatment gets masked. Here we have attempted to estimate the true response of the treatment in presence of staggered entries. Further, by Martingale approach the probability of acceptance/rejection has been worked out for both staggered and no staggered entry cases. The results are then compared with the help of a numerical example which shows that under staggered entries the treatment is rejected with higher probability.     

Search for signatures in miRNAs associated with cancer

Since the first discovery in the early 1990''s, the predicted and validated population of microRNAs (miRNAs or miRs) has grown significantly. These small (~22 nucleotides long) regulators of gene expression have been implicated and associated with several genes in the cancer pathway as well. Globally, the identification and verification of microRNAs as biomarkers for cancer cell types has been the area of thrust for most miRNA biologists. However, there has been a noticeable vacuum when it comes to identifying a common signature or trademark that could be used to demarcate a miR to be associated with the development or suppression of cancer. To answer these queries, we report an in silico study involving the identification of global signatures in experimentally validated microRNAs which have been associated with cancer. This study has thrown light on the presence of significant common signatures, viz., - sequential and hybridization, which may distinguish a miR to be associated with cancer. Based on our analysis, we suggest the utility of such signatures in the design and development of algorithms for prediction of miRs involved in the cancer pathway.     

Somatic embryogenesis in strawberry (<Emphasis Type="Italic">Fragaria</Emphasis> sp.) through callus culture

Somatic embryogenesis was achieved from callus from leaf and nodal segments of strawberry clone pbgel-2000. The highest percent of cultures with somatic embryos was achieved on MS medium supplemented with 1.0 mg/l 2,4-D, 0.5 mg/l BAP and 50% proline. Darkness was the best condition for incubation with daily light periods over 6 h reducing the frequency of embryogenesis. Regenerated plants (90–95%) were successfully transferred to soil, showed normal morphology and produced fruit four months after planting.     

Netropsin Specifically Recognizes One of the Two Conformationally Equivalent Strands of Poly (dA)·Poly (dT). One Dimensional NMR Study at 500 MHz Involving NOE Transfer Between Netropsin and DNA Protons

Abstract

Recent observations that the heteronomous structural model for poly(dA)·poly(dT) is not found in solution and that in this DNA, the two strands are conformationally equivalent (J. Biomole. Str. Dyns. 2, 1057 (1985)), has added a new dimension to the structural dynamics of DNA-netropsin complex. Does the antibiotic somehow distinguish between the two strands and specifically interact with only one of the conformationally equivalent strands?

Model-building studies suggest that netropsin can either bind to the dA-strand in the minor groove such that H-bonds are formed between the imino protons N4-H, N6-H, N8-H of netropsin and N3 atoms of A or can bind to the dT-strand in the minor groove and form H-bonds between the imino-protons N4-H, N6-H, N8-H of netropsin and O2 atoms of T. If netropsin binds to the dA-strand, AH2 atoms of poly(dA)-poly(dT) would be in closer proximity to the imino protrons N4-H, N6-H, N8-H and pyrrole ring protons C5-H, Cll-H of netropsin than they would be, if netropsin binds to the dT-strand. In order to distinguish these possibilities experiments were conducted which involved NOE energy transfer between netropsin and DNA protons in the drug-DNA complex. Difference NOE spectra of netropsin·poly(dA)-poly(dT) complex in which AH2 was irradiated indicate that dominant NOEs were observed at the imino and pyrrole ring protons of netropsin. When the netropsin pyrrole ring protons were irradiated, the magnetization transfer was at AH2 of DNA. These observations suggest that netropsin binds to the dA-strand of poly(dA)-poly(dT) even though dA/dT strands are conformationally equivalent.     

Analysis of DevR regulated genes in Mycobacterium tuberculosis

The DevRS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we propose a theoretical model to show role of binding sites in DevR mediated gene expression. Individual and collective role of binding sites in regulating DevR mediated gene expression has been shown via modeling. Objective of the present work is twofold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze behavior of the system from information theoretical point of view. Using the tools of information theory we have calculated molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.     

New 1,3,5-trioxygenated xanthones in Canscora decussata

Aerial parts of Canscora decussata have been shown to contain 1-methoxy-3,5-dihydroxyxanthone and its 3-O-rutinosyl derivative. The identity of these compounds was established by chemical transformation and spectral (UV, IR, PMR, MS) evidence of the compounds and their derivatives. This is the first demonstration of the occurrence of the two compounds in nature.     

NaCl pretreatment alleviates salt stress by enhancement of antioxidant defense system and osmolyte accumulation in mungbean (Vigna radiata L. Wilczek)

Enhancement of salt (NaCl) tolerance by pretreatment with sublethal dose (50 mM) of NaCl was investigated in V. radiata seedlings. NaCl stress caused drastic effects on roots compared to shoots. Accompanying reductions in length, number of root hairs and branches, roots became stout, brittle and brown in color. Salt stress caused gradual reduction in chlorophyll, carotenoid pigment contents and chlorophyll fluorescence intensity also. Superoxide dismutase and catechol peroxidase activities increased under stress in both roots and leaves. But catalase activity showed an increase in roots and decrease in leaves. In these seedlings, the oxidative stress has been observed under salinity stress and the level of proline, H2O2 and malondialdehyde content were increased. But pretreatment with sublethal dose of NaCl was able to overcome the adverse effects of stress imposed by NaCl to variable extents by increasing growth and photosynthetic pigments of the seedlings, modifying the activities of antioxidant enzymes, reducing malondialdehyde and H2O2 content and increasing accumulation of osmolytes like proline. Thus, mungbean plants can acclimate to lethal level of salinity by pretreatment with sublethal level of NaCl, improving their health and production under saline condition.     

{Ru-NO} and {Ru-NO} configurations in [Ru(trpy)(tmp)(NO)] (trpy = 2,2:6′,2′′-terpyridine, tmp = 3,4,7,8-tetramethyl-1,10-phenanthroline): An experimental and theoretical investigation

The ruthenium-nitrosyl complexes [Ru^II(trpy)(tmp)(NO⁺)](ClO₄)₃ ([4](ClO₄)₃) and [Ru^II(trpy)(tmp)(NO)](ClO₄)₂ ([5](ClO₄)₂) with {Ru-NO}⁶ and {Ru-NO}⁷ configurations, respectively (trpy = 2,2′:6′,2′′-terpyridine, tmp = 3,4,7,8-tetramethyl-1,10-phenanthroline) have been isotaled. The nitrosyl complexes [4]³⁺ and [5]²⁺ have been generated by following a stepwise synthetic procedure: [Ru^II(trpy)(tmp)(X)]ⁿ, X/n = Cl/+ (1⁺) → CH₃CN/2+ (2²⁺) → NO₂/+ (3⁺) → NO⁺/3+ (4³⁺) → NO/2+ (5²⁺). The single-crystal X-ray structures of two precursor complexes [1]ClO₄ and [3]ClO₄ have been determined. The DFT optimized structures of 4³⁺ and 5²⁺ suggest that the Ru-N-O geometries in the complexes are linear (177.9°) and bent (141.4°), respectively. The nitrosyl complexes with linear (4³⁺) and bent (5²⁺) geometries exhibit ν(NO) frequencies at 1935 cm⁻¹ (DFT: 1993 cm⁻¹) and 1635 cm⁻¹ (DFT: 1684 cm⁻¹), respectively. Complex 4³⁺ undergoes two successive reductions at 0.25 V (reversible) and −0.48 V (irreversible) versus SCE involving the redox active NO function, Ru^II-NO⁺ ? Ru^II-NO and Ru^II-NO → Ru^II-NO⁻, respectively, besides the reductions of trpy and tmp at more negative potentials. The DFT calculations on the optimized 4³⁺ suggest that LUMO and LUMO+1 are dominated by NO⁺ based orbitals of around 65% contribution along with partial metal contribution of ∼25% due to (dπ)Ru^II → π∗(NO⁺) back-bonding. The lowest energy transitions in 4³⁺ and 5²⁺ at 360 nm and 467 nm in CH₃CN (TD-DFT: 364 and 459 nm) have been attributed to mixed MLLCT transitions of tmp(π) → NO⁺(π∗), Ru(dπ)/tmp(π) → NO⁺(π^∗) and Ru(dπ)/NO(π) → trpy(π^∗), respectively. The paramagnetic reduced species 5²⁺ exhibits an anisotropic EPR spectrum with g₁ = 2.018, g₂ = 1.994, g₃ = 1.880 (〈g〉 = 1.965 and Δg = 0.138) in CH₃CN, along with ¹⁴N (I = 1) hyperfine coupling constant, A2 = 35 G at 110 K due to partial metal contribution in the singly occupied molecular orbital (DFT:SOMO:Ru (34%) and NO (53%)). Consequently, Mulliken spin distributions in 5²⁺ are calculated as 0.115 for Ru and 0.855 for NO (N, 0.527; O, 0.328). The reaction of moderately electrophilic nitrosyl center in 4³⁺ with the nucleophile, OH⁻ yields the nitro precursor, 3⁺ with the second-order rate constant value of 1.7 × 10⁻¹ M⁻¹ s⁻¹ at 298 K in CH₃CN-H₂O (10:1). On exposure to light (Xenon 350 W lamp) both the nitrosyl species, 4³⁺ ({Ru^II-NO⁺}) and 5²⁺ ({Ru^II-NO}) undergo photolytic Ru-NO bond cleavage process but with a widely varying k_NO, s⁻¹ (t_1/2, s) of 1.56 × 10⁻¹(4.4) and 0.011 × 10⁻¹(630), respectively.     

Development of mutants of <Emphasis Type="Italic">Melanocarpus albomyces</Emphasis> for hyperproduction of xylanase

The wild type filamentous fungus, Melanocarpus albomyces, produces many commercially valuable enzymes, including Xylanases and Xylan-debranching enzymes with low activity. In this paper, we report for the first time the development of M. albomyces mutants from vegetative spores. Profuse sporulation of M. albomyces was induced on Potato Carrot Agar medium. These spores, when subjected to chemical mutation, led to the isolation of the hyper-xylanase producing mutant, viz, M. albomyces IITD3A. Various parameters including number of spores, nitrogen source and C/N ratio of the medium were optimized for production of xylanase by the mutant in a shake flask culture. Under controlled pH at 7.8, the mutant produced highly active xylanase with 415 IU/mL after 36 h of growth on soluble alkaline lignocellulosic extract in a 14-L fermentor. The overall productivity of xylanase was 8-fold higher than the wild type culture with11, 530 IU/L/h. The enzyme can be easily stored at 37°C for 50 days by addition of a small amount of the preservative — thiomersal. Also, for long term storage, a lyophilized powder form of the enzyme can be used which retained 100% of its activity for > 50 days. When assayed at pH 7.5 and temperature 55°C, the xylanase retained 100% of its original activity, and also at pH 9.0, it retained > 50% of its activity for 2 h, which is promising for its application in the pulp and paper industry.