Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose

In silico approach of receptor-ligand binding and interaction: Established phytoligands from Tagetes errecta Linn. against bacterial β-glucosidase receptor

The medicinal plant, Tagetes errecta Linn. is a common ornamental plant and leaves of this plant are containing phytochemicals (volatile oil) that inhibit the growth of bacteria, fungi and known natural antimicrobial agents. The objective of the present study was to detect receptor-ligand binding energy and interaction through molecular docking for phytoligands established in the leaves of T. errecta against β-glucosidase receptor (PDB ID: 3AHZ). Molecular docking was performed by using PyRx (Version 0.8) for the structure-based virtual screening and visualized the interaction in the molecular graphic laboratory (MGL) tool (Version 1.5.6). Among 25 phytochemicals and 2 synthetic compounds (Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol), binding energy value was obtained highest in Bicyclogermacrene (-6.4 Kcal/mol) and lowest in Octanol (-4.4 Kcal/mol) and Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol showed -6.7 Kcal/mol and -3.5 Kcal/mol all of these showed no hydrogen bonding. The binding interaction of target protein with this phytocompound found binding at the mouth of the active site may be treated as competitive inhibitor. In conclusion, phytocompound Bicyclogermacrene can be alternative of synthetic fungicide as per binding energy value and interaction. It is suggesting further pharmacological and toxicological assay with this phytocompound after isolation from ornamental plant (T. errecta)

OPTIMIZATION OF PROCESS PARAMETERS FOR THE PRODUCTION OF ANTIBACTERIAL COMPOUND BY A NEWLY ISOLATED NOCARDIA CYRIACIGEORGICA, KD-15 STRAIN FROM KAZIRANGA NATIONAL PARK OF NORTH EAST INDIA

Objective: An attempt has been made to evaluate the optimal cultural conditions for obtaining high yields of bioactive metabolites.Methods: A strain of actinobacteria was isolated from the soil sample of Kaziranga National Park of Assam. Strain was identified on the basis of biochemical test as well as 16SrDNA sequence. The strain was tested for antibacterial activity using agar well diffusion method and to enhance its growth and metabolite production, the strain was cultured at different carbon and nitrogen sources and at different pH, salinity and temperature.Results: The strain was identified as Nocardia cyriacigeorgica. The secondary metabolites exhibited excellent antimicrobial activity against dreaded human pathogenic bacteria Staphylococcus aureus (MTCC 96), Bacillus subtilis (MTCC 441), Escherichia coli (MTCC 739) and Pseudomonas aeruginosa (MTCC 2453). The strain utilized glucose as good carbon source for growth and starch for metabolite production. Soybean meal and beef extract were the nitrogen sources for the elaboration of both growth and bioactive metabolites. The optimum temperature, salinity and pH for growth and bioactive metabolite production of the strain were recorded as 28±2oC, 1.5% and 7.5 respectively.Conclusion: As our results showed the potency of N. cyriacigeorgica as an antibacterial agent under these optimal conditions, so further study can be carried out in this regard. This is the first report of production of antibacterial compound from this emerging pathogenic strain N. cyriacigeorgica.Â

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Not AvailableXanthones are well recognized as chemotaxonomic markers for the plants belonging to the genus Garcinia. Xanthones have many interesting pharmacological properties. Efficient extraction and rapid liquid chromatography methods are essentially required for qualitative and quantitative determination of xanthones in their natural sources. In the present investigation, fruit rinds extracts of 8 Garcinia species from India, were prepared with solvents of varying polarity. Identification and quantification of 3 xanthones, namely, α-mangostin, β-mangostin, and γ-mangostin in these extracts were carried out using a rapid and validated ultra-high-performance liquid chromatography– photodiode array detection (UHPLC–PDA) method at 254 nm. γ-Mangostin (3.97 ± 0.05 min) was first eluted, and it was followed by α-mangostin (4.68 ± 0.03 min) and β-mangostin (5.60 ± 0.04 min). The calibration curve for α-mangostin, β-mangostin, and γ- mangostin was linear in the concentration range 0.781–100 μg/mL. α-Mangostin was quantified in all 4 extracts of Garcinia mangostana. Its content (%) in hexane, chloroform, ethyl acetate, and methanol extracts of G. mangostana was 10.36 ± 0.10, 4.88 ± 0.01, 3.98 ± 0.004, and 0.044 ± 0.002, respectively. However, the content of α-mangostin was below the limit of detection or limit of quantification in the extracts of other Garcinia species. Similarly, β-mangostin was quantified only in hexane (1.17 ± 0.01%), chloroform (0.39 ± 0.07%), and ethyl acetate (0.28 ± 0.03%) extracts of G. mangostana. γ-Mangostin was quantified in all 4 extracts of G. mangostana. Its content (%) in hexane, chloroform, ethyl acetate, and methanol extracts of G. mangostana was 0.84 ± 0.01, 1.04 ± 0.01, 0.63 ± 0.04, and 0.15 ± 0.01, respectively. γ-Mangostin was also quantified in hexane (0.09 ± 0.01), chloroform (0.05 ± 0.01), and ethyl acetate (0.03 ± 0.01) extracts of G. cowa, ethyl acetate extract of G. cambogia (0.02 ± 0.01), G. indica (0.03 ± 0.01), and G. loniceroides (0.07 ± 0.01). Similarly, γ-mangostin was quantified in 3 extracts of G. morella, namely, hexane (0.03 ± 0.01), chloroform (0.04 ± 0.01), and methanol (0.03 ± 0.01). In the case of G. xanthochymus, γ-mangostin was quantified in chloroform (0.03 ± 0.001) extract only. α-Mangostin and β-mangostin were not detected in any of 4 extracts of G. pedunculata.Not Availabl