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Ibioinformatics - Volume 2 - Issue 1 and 2

[<<< GO BACK ][ VOLUME 2 - ISSUE 1 AND 2 ]

Title: Insilico Structural Annotation of Human Cyclin-Dependent Kinase
Abstract :

CDK2 is a member of the cyclin-dependent protein kinase family that is ubiquitously expressed. its catalytic subunit of the cyclin-dependent protein kinase complex, whose activity is restricted to the G1-S phase, and essential for cell cycle G1/S phase transition. It is associated with and is regulated by the regulatory subunits of the complex including cyclin A or E, CDK inhibitor p21Cip1 (CDKN1A) and p27Kip1 (CDKN1B). it phosphorylates multiple cellular substrates including SMAD3 and FOXO1. Phosphorylation of FOXO1 leads to its inhibition.

Title: Mining of Expressed Sequence Ttags for Identification of ATatP Binding Ccassette Ttransporters in Human Brain
Abstract :

The general quality of expressed sequence tag (EST) sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for the study of evolutionary relationship and sequence searches. Due to emerging scope of ABC transporters in human brain diseases treatment investigations and drug resistance, here we investigate the ABC transporter ESTs present in human brain. 15 ESTs were identified and used for cluster generation to see the gaps and subjected to phylogenetic analysis to identify the evolutionary relationship and conserved structures. Investigation and clustering of human ESTs from brain allows extension of data sampling from outside of the genome project.

Title: Lead Stress-induced Changes of Antioxidant Enzymes and Biochemical Compounds in Selected Weeds and their Contribution for Phytoremediation
Abstract :

Investigation was carried out to identify tolerant plant species growing in lead contaminated soil. Lead effected Chlorophyll a, chlorophyll b and ascorbicacidoxidase. Induced malondialdehyde and starch contents with up-regulated activities of antioxidative enzymes like catalase and phenylalanineammonialyase were observed. Enzymatic activities have been enhanced in all plants taken indicating that free radical generation was accelerated due to Pb exposure. Concentrations of lead accumulated were Calotropis procera (90 mg/kg) and Bromus tectorum (77 mg/kg) are higher followed by Ipomea purpurea (72 mg/kg), Parthenium histocarpus (33 mg/kg), Anisomilius molabarica (29 mg/kg) and Eichornia fasculata (10 mg/kg). Inspite of accumulation all plants survived successfully. With our findings we can suggest these plants can be used for effective phytoremediation of lead.

Title: Genetic Diversity Analysis and RAaPD Marker Inheritance in F1 Progenies of Mulberry (Morus spp.)
Abstract :

The present study attempts to understand the pattern of RAPD markers inheritance in the F1 progenies of a cross Mysore Local and V-1 of mulberry (Morus spp.). RAPD marker analysis was carried out using 5 decamer random primers. Out of 33 amplicons generated, 20 were of monomorphic and rest 13 were polymorphic (39:39%). The size of the amplified products ranged from 500-3200 bp. The genetic distance (GD) between the parents based on RAPD data set is 0.186, which is low in comparison with morpho-agronomical divergence. In some progenies, GD calculated was higher than the parents suggesting OPA-022900, OPA-02900, OPA-02800 RAPD markers showed expected Mendelian pattern of inheritance. Besides three other markers, OPA-041450, OPA-041000 and OPA-071000 showed Mendelian segregation pattern for 1:1 ratio. The finding proves that the dominant status of the RAPD markers may not be a limiting factor in genetical analysis of a heterozygous tree like mulberry, where F1 tends to behave like a segregating population. The polymorphic RAPD markers in parents, segregates as independent alleles in the F1 progenies and showed the heterozygotic status of mulberry varieties.

Title: Effect of gibberellin and cytokinin on Sucker Production and flowering of anthurium (Anthurium andraeanum Lind.) cv. Nitta in the Plains of West Bengal
Abstract :

Greenhouse grown Anthurium (Anthurium andraeanum Lind.) cv. Nitta plants were treated with six different levels of plant growth regulators namely BA 500 ppm, BA 1000 ppm, GA3 500 ppm, GA3 1000 ppm, BA 250 ppm + GA3 250 ppm and BA 500 ppm + GA3 500 ppm and their effect on the sucker production and flowering were compared against control (without application of plant growth regulators). Plants treated with 1000 ppm BA recorded highest number of side-shoots per plant (5.67), earliest flower bud initiation (253.83 days) and higher post-harvest life of cut flowers (12.33 days). Control plants showed the earliest spadix visibility (32.83 days) stage, longest spadix (4.17 cm) and reached the blooming stage earlier (5.83 days) along with plants treated with BA 500 ppm. GA3 500 ppm treated plants produced the highest number of flowers per plant (3.33) and spadix circumference (1.33 cm) however, the longest stalks (15.82 cm) and spathes (6.53 cm) were obtained from the plants treated with GA3 1000 ppm and BA 250 ppm + GA3 250 ppm respectively. Widest spathes (5.60 cm) and maximum in-situ longevity of flowers (36 days) were obtained from the plant growth regulator treatment BA 250 ppm + GA3 250 ppm and monthly leaf number, leaf length, leaf width and petiole lengths were fluctuated greatly with season and stage of crop growth. BA 1000 ppm and a mixture of BA (250 ppm) and GA3 (250 ppm) was found better for growth, development, flowering, post-harvest life and keeping quality of anthurium flowers.

Title: optimization of Fermentation Parameters for R3DSCc5 and R3DPMmP Strains for Ethanol Production
Abstract :

Two newly isolated strains of Saccharomyces cerevisiae - R3DPMP and R3DSC5 were subjected to optimization studies with varying inoculum size, initial glucose concentration, initial pH and temperature using yeast extract peptone dextrose medium. Both the strains accumulated peak ethanol early with higher inoculum density and exhibited similar pattern with changing initial pH. Though higher glucose tolerance was noticed, 20% g/v and 25% g/v glucose concentration were found to be optimum for R3DPMP and R3DSC5 respectively. Similar amount of ethanol was accumulated within 30-400C temperature by R3DPMP and 30-350C temperature by R3DSC5. However, based on higher temperature tolerance, sugar tolerance and peak ethanol level, R3DSC5 appears to be superior to R3DPMP. Therefore, R3DPMP strain is recommended for brewery industry whereas R3DSC5 for both brewery and very high gravity fermentation.

Title: Best Parameters for Assessment of Anti-Rheumatoid Arthritic Drugs is ECHO MoDEL (Economical, Clinical and Humanistic Outcome)
Abstract :

Physicians are always in dilemma for selection of the right parameters to assess anti-rheumatoid arthritis drugs. Any single parameter is incapable to reveal the efficacy safety and cost-effectiveness of anti-rheumatoid arthritis drugs. Therefore a group of parameters are obligatory to assessment of anti-rheumatoid arthritis drugs. Here the best parameters are mentioned in ECHO model (Economical, Clinical and Humanistic outcome) for best assessment of anti-rheumatoid arthritis drugs.

Title: characterisation of Plant Growth Promoting Endophytic Bacteria Isolated from Lens culinaris Medic with Antagonistic Potential against Fusarium Oxysporum
Abstract :

A total of 152 endophytic bacterial isolates belonging to Rhizobium, Pseudomonas and Bacillus spp. were isolated from the root nodules of Lens culinaris from seven different provinces of Uttar Pradesh (India) growing in different soil condition of varying pH 6.8-7.8. These isolates were characterized morphologically, physiologically and biochemically, and screened in vitro for their plant growth promoting traits such as production of indole acetic acid (IAA), ammonia (NH3), hydrogen cyanide (HCN), siderophore, phosphate solubilization and antifungal activity against Fusarium oxysporum. Only 27 endophytic showed positive results for all plant growth promoting attributes and antagonism against Fusarium oxysporum. All physio-biochemical characters including carbon utilization were analyzed by a Jaccard’s coefficient dendrogram, that classified the isolates into the three major groups viz., RT1, RT9-RT16, RT26 and RT27 isolates in one group, RT2-RT8, RT17-RT18, RT24 and RT25 isolates in second group, and RT19 - RT23 isolates in third group. On the basis of UPGMA cluster analysis and similarity with the standard strains these isolates were identified as Rhizobium strains RT1, RT9-RT16, RT26, RT27, Pseudomonas strains RT2-RT8, RT17-RT18, RT24 and RT25, and Bacillus strains RT19 - RT23. The strains RT1, RT2 and RT11 showed synergism among them and also found to possess plant growth promoting and antagonistic properties.

Title: Fragment based de novo Design and aDMmE/Tt Analysis of Dual Binding Site Acetylcholinesterase Inhibitors for Alzheimers Disease
Abstract :

Fragment-based de novo design has been successfully carried out to identify novel dual binding site acetylcholinesterase inhibitors. Dataset consists of 18 co-crystallized inhibitors of the acetylcholinesterase enzyme from protein data bank. They were dissected into 31 chemically diverse and commercially available fragments. The newly generated compounds have been filtered through detailed ADMET analysis followed by molecular docking experiment. Finally, synthesis accessibility of the new leads was predicted by SYLVIA software. We identified 15 potential leads from the present study. These virtual screened compounds are expected to be important leads for the search of dual binding site acetylcholinesterase inhibitors and may provide invaluable insights to further understand the structural basis of catalysis and inhibition of acetylcholinesterase enzyme.