Authors’ affiliation: ¹Microbiology Laboratory, Department of Life Science, Assam University, Silchar-788011, Assam, India.

²Microbiology Laboratory, Department of Botany, Gurucharan College, Silchar-788004, Assam, India.

Email: b_deb_roy@sify.com

Dates: Received on: 17 July 2010, Accepted on: 09 August 2010, Published on 11 August 2010

Article type: Review

Abstract

Nitrogen is an essential plant nutrient, widely applied as N-fertilizer to improve yield of agriculturally important crops. An interesting alternative to avoid or reduce the use of N-fertilizers could be the exploitation of plant growth-promoting bacteria (PGPB), capable of enhancing growth and yield of many plant species, several of agronomic and ecological significance. PGPB belong to diverse genera, including Azospirillum, Azotobacter, Herbaspirillum, Bacillus, Burkholderia, Pseudomonas, Rhizobium, and Gluconacetobacter, among others. They are capable of promoting plant growth through different mechanisms including (in some cases), the biological nitrogen fixation (BNF), the enzymatic reduction of the atmospheric dinitrogen (N2) to ammonia, catalyzed by nitrogenase. Aerobic bacteria able to oxidize ethanol to acetic acid in neutral or acid media are candidates of belonging to the family Acetobacteraceae. At present, this family has been divided into ten genera: Acetobacter, Gluconacetobacter, Gluconobacter, Acidomonas, Asaia, Kozakia, Saccharibacter, Swaminathania, Neoasaia, and Granulibacter. Among them, only three genera include N2-fixing species: Gluconacetobacter, Swaminathania and Acetobacter. The first N2-fixing acetic acid bacterium (AAB) was described in Brazil. It was found inside tissues of the sugarcane plant, and first named as Acetobacter diazotrophicus, but then renamed as Gluconacetobacter diazotrophicus. Later, two new species within the genus Gluconacetobacter, associated to coffee plants, were described in Mexico: G. johannae and G. azotocaptans. A salt-tolerant bacterium named Swaminathania salitolerans was found associated to wild rice plants. N2-fixing Acetobacter peroxydans and Acetobacter nitrogenifigens, associated with rice plants and Kombucha tea, respectively, were described in India. Recently, Gluconacetobacter liquefaciens, a N2-fixing bacterium of family Acetobacteraceae was found associated in the rhizosphere of tropical rainfed acidic rice fields of South Assam, India. In this paper, recent advances involving nitrogen-fixing AAB are presented. Their natural habitats, physiological and genetic aspects, as well as their association with different plants and contribution through BNF are described as an overview.

Citation

(Review)Role of Acetic Acid Bacteria in Biological Nitrogen Fixation. Deb Roy,B. Deb, G. D. Sharma, Biofrontiers (2010) vol.1, Issue.2: Pg 83-98

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Author affiliation: ¹Regional Plant Resource Center, Nayapalli, Bhubaneswar, Orissa, India

²Department of Botany, B.J.B (A) College, Bhubaneswar-751014, Orissa, India

³Department of bioinformatics, B.J.B (A) College, Bhubaneswar, Orissa, India

Email: debyani.samantray@gmail.com

Supervisors: R.K.Sahu

Supervisors affiliation: Department of Botany, B.J.B (A) College, Bhubaneswar-751014, Orissa, India

Dates: Received on: 24 April 2010, Accepted on: 20 July 2010, Published on 10 August 2010

Article type: Biotechnology

Abstract

Children are most susceptible to acquire infection because of lack of immunity and high exposure to infective larvae of the nematode Wuchereria bancrofti which is the causative agent of filarial in an endemic region .The age specific prevalence of antigenemia among children living in India has not been studied. More emphasis has been given in the adulthood and the children are neglected.  In this dissertation work, the severity of infection among the children living in a filarial endemic region of Orissa in Eastern India has been discussed. The circulating filarial antigen (CFA) was detected in finger prick blood sample collected in filter paper disc from 610 children below 15 years of age using Og4C3 test kit (JCU Trop,BIO,Queensland,Australia) according to manufacture’s instruction. The sample from each individual was tested in duplicate and the mean optical density values were used to determine the antigen concentration in units from standard curve made earlier with the seven standard antigen supplied in the kit. Individuals with an antigen units of 128(>titer of standard no 3) considered to be CFA positive. The result of this research work was that the filarial antigenemia increased marginally with the age in the children i.e. 28.26% in less than 5years, 31.45% in less than 6years, 35.18% in less than 11-15years age groups indicating adult worm burden were similar among the children of different age group. This result, in endemic regions, suggests that the filarial infections are acquired early below 5 years of age and become the source of future disease in the later part of life

Citation

Yogamaya dhal,Debyani Samantray, Gayatri Nahak, Bandita Deo and R.K.Sahu. Antigenemia in Children (according to gender) Wuchereria bancrofti living in endemic areas of Orissa, India. Biofrontiers (2010) vol.1, Issue.2: Pg 75-82

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Author affiliation: Microbiology Laboratory, Department of Life Science, Assam University, Silchar-788011, Assam, India.

Email: : b_deb_roy@sify.com

Supervisors: B. Deb ¹ and G. D. Sharma ²

Supervisors affiliation: 1 Microbiology Laboratory, Department of Life Science, Assam University, Silchar-788011, Assam, India.

2 Microbiology Laboratory, Department of Botany, Gurucharan College, Silchar-788004, Assam, India.

Dates: 18 May 2010, Accepted on: 2 June 2010, Published on 13 July 2010

Article type: Biotechnology

Abstract

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria that colonize plant roots and enhance plant growth by a wide variety of mechanisms. The use of PGPR is steadily increasing in agriculture and offers an attractive way to replace chemical N fertilizers. Here, one native strain of Azotobacter chroococcum of South Assam, India was used as biofertilizer for summer (ahu) rice cv. IR-36 with different locally available carrier materials to chalk out the best carrier in terms of improving the growth and yield of rice and better survival of the inoculant bacteria.  Among different carrier materials used, vermicompost was the best carrier material for the survival of Azotobacter chroococcum as evident from its higher cell count for a period of six months in vermicompost based inoculant. In field level evaluation of carrier based inoculants it was observed that vermicompost based inoculant of Azotobacter chroococcum cells has the most significant effect on improving the growth and yield parameters of summer (ahu) rice cv. IR-36 over the control in acidic soils under water logged condition.

Citation

B. Deb Roy, B. Deb and G. D. Sharma, Evaluation of carrier based inoculant of Azotobacter chroococcum strain SDSA-I12/2 in improving growth and yield of summer (ahu) rice cv. IR-36. Biofrontiers (2010) vol.1, Issue.2: Pg 68-74

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Author affiliation: Department of Biotechnology, Sarhad University of Science and Information Technology, Peshawar, Pakistan

Email: bdlazeem@gmail.com

Supervisors: Ihsan Ullah¹, Muhammad Ali¹, Akram Khan ¹, Jehan Bakht²

Supervisors affiliation: ¹ Department of Biotechnology, Sarhad University of Science and Information Technology, Peshawar, Pakistan.

²Institute of biotechnology and Genetic Engineering NWFP, Agricultural University Peshawar, Pakistan

Dates: Received on: 11 February 2010, Accepted on: 20 February 2010, Published on 2 April 2010

Article type: Biotechnology

Abstract

In our study an attempt has been made to analyze the effects of different sterilents on the survival rate of tobacco seeds (Nicotiana tabacum L) and the role of different growth hormones on callogenesis. The seeds of tobacco were surface disinfected with two different types of sterilents, Calcium Hypo Chloride (CaOCl₂) (2.0% and 4.0%) and Mercuric Chloride (HgCl₂) (0.2% and 0.05%) for a particular time interval. The maximum survival percentages (93.33%) of seeds obtained at 0.2% Mercuric Chloride (HgCl₂)_. While in the second half of the study, frequencies of callus formation under the influence of various growth hormones were analyzed in tobacco. In this regard, the Murashige and Skoog (MS) media were supplemented with different hormones; glutamine at 200 mgl^-1 and 250 mgl^-1, 6-Benzyle amino purine (BAP) at 1mgl^-1 and 2,4-Dichlorophenoxy acetic acid (2,4D) at 2 mgl^-1 and 3 mgl^-1 respectively. Frequency of callus formation was observed and compared with control treatment. The maximum (81.7%) callusing was observed using 2, 4D at 3 mgl^-1, with vigorous and green spots

Citation

Syed Abdul Azeem, Ihsan Ullah, Muhammad Ali, Akram Khan, Jehan Bakht, Effects of different sterilents on seeds and Callusing frequency as effected by hormones in Nicotiana tabacum L. Biofrontiers (2010) vol.1, Issue.2: Pg 62-67

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Authors affiliation: 1. ACS- Bioinformatics, Biotech Park, Lucknow, India. 2.Amity Institute of Biotechnology, Amity University, Lucknow, India.

Email: srs14_02@hotmail.com

Supervisor: Daya S. Srivastava

Supervisor affiliation: Central Drug Research Institute, Lucknow, India

Dates: Received on: 6 February 2010, Accepted on: 7 March  2010, Published on 27 March 2010

Article type: Bioinformatics

Abstract

In order to analyze binding of imidazole inhibitors with CYP2B4 enzyme, molecular docking and dynamics study was performed using AutoDock4 and Gromacs. Twenty seven imidazole inhibitors were selected on the basis of structural similarity and were docked to the crystal structure of the enzyme (PDB ID: 2BDM). Molecular dynamics studies were then performed to find out the stability of selected imidazole-CYP2B4 complexes. Our docking results indicated that residues THR302, GLY299, GLU301 construct the active pocket of CYP2B4 by forming hydrogen bonds to cause inhibitory behavior. On the basis of binding energies, compounds flutrimazole, sertaconazole, isoconazole, miconazole were selected which give better binding energies and inhibition constants than the reference bifonazole. In addition to this, compounds sertaconazole and isoconazole showed hydrogen bond with Thr-302 active site. Molecular dynamics simulation, based on the docking results, implies that the orientation of imidazole in the active pocket show different stabilities when performed for a time period of 70ps. Orientation of bifonazole, sertaconazole, and flutrimazole demonstrated hydrogen bond with residue THR-302 and gradually reach dynamic equilibrium resulting in stable dynamic complex. While the two imidazole-CYP2B4 complex (isoconazole- CYP2B4, miconazole- CYP2B4 complex) reveals an unstable binding mode with CYP 2B4, as they induced conformation strains in the enzyme during the dynamic simulation.

Citation

Siddharth Sinha1, Arpit Tandon, Daya S. Srivastava, Inhibitory activity of Imidazole with Cytochrome P450 2B4: A Docking and Molecular Dynamics Study, Biofrontiers (2010) vol.1, Issue.2: Pg 48-61

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Authors affiliation: Department of Pharmacology & Therapeutics, Chhatrapati Shahuji Maharaj Medical University, Lucknow, Uttar Pradesh, India.

²Bioinformatics Centre, Biotech Park, Lucknow, India.

Email: saritasingh.bi@gmail.com

Supervisors: Anuradaha Nischal ¹, Sanjay Khattri ¹, Rajendra Nath ¹, Prahlad Kishore Seth ² , Kamlesh Kumar Pant ¹

Supervisors affiliation:¹Department of Pharmacology & Therapeutics, Chhatrapati Shahuji Maharaj Medical University, Lucknow, Uttar Pradesh, India.

²Bioinformatics Centre, Biotech Park, Lucknow, India.

Article Type: Bioinformatics

Date: Received on: 30 December 2009, Accepted on: 19 January2010, Published on 2 February 2010

Abstract

Background and aims

RNA viruses are responsible for a variety of human diseases, and the pathogenicity of RNA viruses is often attributed to a high rate of mutation. Delta Hepatitis most commonly occurs in Mediterranean countries, sub-Saharan Africa, the Middle East and in the northern part of South America. In all, about 20 million people have been reported to be infected with Hepatitis Delta Virus (HDV). In the absence of any effective handling of the disease, there is an urgent need to find suitable methods for its diagnosis and treatment.

Methods

Delta antigen protein of HDV has immense role in viral replication; therefore it may be a precious target for diseases diagnosis. Antigen protein coding regions of HDV in various genome isolates were used as target for designing the primers using computational methods. Alignment of 93 genomic isolates were executed nation wise and delta antigen protein coding RNA sequence has been forecasted from conserved genomic isolate by open reading frame.

Result and conclusion

In an attempt to identify potential target for molecular diagnosis of HDV, Twenty six primer pairs were identified and validated. Absence of any reactivity with other viruses of these primers indicates their specificity and suitability as target for molecular diagnosis. Clinical validation would eventually establish their sensitivity, accuracy and reliability in detecting HDV infection.

Citation

Sarita Singh, Sunil Kumar Gupta, Anuradaha Nischal , Sanjay Khattri , Rajendra Nath , Prahlad Kishore Seth , Kamlesh Kumar Pant,  Primer designing for conserved genome isolates of Hepatitis Delta Virus for Molecular Diagnosis of Delta Hepatitis , Biofrontiers (2009) vol.1, Issue.2: Pg 35-47

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Author affiliation:Center of Bioinformatics, Nehru Science Center, IIDS, University of Allahabad

Email: dhruvbhu@gmail.com

Supervisor: Prof.D.K.Gupta

Supervisor affiliation:Center of Bioinformatics, Nehru Science Center, IIDS, University of Allahabad.

Article Type: Bioinformatics

Date: Received on: 26 November 2009, Accepted on: 20 December2009, Published on 20 January 2010

Abstract

HIV-1 proteases are an enzyme inside HIV which is responsible for the cleavage of long HIV polyprotein into small functional peptide fragment. These small fragments again terminate into HIV. Inhibition of cleavage of poly protein into small peptide fragment could prevent regeneration of HIV. This work describes a computational protein-ligand docking approach for stop the cleavage of polyprotein. Computational approaches were used to dock ligand (cyclic urea inhibitors) with HIV-1 proteases to stop cleavage. ADME Toxicity properties of drug show that best candidate drug against HIV-1 proteases. Cyclic Urea Inhibitors are seven-member ring structure of cyclic urea compound. It incorporates the hydrogen-bonding equivalents of an enzyme-bound water molecule into a low molecular weight. Our result suggest that some of derivatives of Cyclic urea inhibitors binds with HIV-1 proteases, which can be stop the fuction of HIV-1 proteases(cleavage of long protein chain to small peptide fragment).

Citation

Dhruv kumar & D.K.Gupta, Insilico Analysis of Interaction between HIV-1 Proteases and Derivatives of Cyclic Urea Inhibitor and Its ADME Toxicity Properties , Biofrontiers (2009) vol.1, Issue.2: Pg 24-34

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Author affiliation: center for Bioinformatics MMV , BHU, Varanasi, India.

Email: krisiids@gmail.com

Supervisor: Dr. swati

Supervisor affiliation: Dept of Physics MMV, BHU, Varanasi, India.

Article Type: Bioinformatics

Date: Received on: 8 October 2009, Accepted on: 11 November 2009, Published on 14 November 2009

Abstract

The genome of any organism is the culmination of long history of growth and evolution that extend back to the origin of life. How much about this history can we learn from the present state of the genome? When genome is viewed as a text composed of four letters [A C G T] it essentially a random text. However frequency of occurrence of oligonucleotides k-mer (k=4 to 6 bp long oligonucleotide) shows a specific pattern. Here I have analyzed the genome sequences of Staphylococcus aureus, Yersinia pestis, pyrochlorococcus marinus and Haemophylus influenza For the k-mer (4-6) oligonucleotide frequency distribution and found that Almost all the genome follow the same pattern of graph plotted between the copy number versus the frequency of the oligonucleotide. I have given a simple model of genome evolution in which I have created a DNA string duplication and deletion and then analyzed its behavior. My analysis shows that segmental duplication followed by deletion was the main factor behind the genome evolution.

Citation

Krishna Kumar Ojha, Stochastic Modeling of Genome Evolution, Biofrontiers (2009) vol.1, Issue.2: Pg 17-23

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Email: pranay.dogra@gmail.com

Author affiliation: Hislop School of Biotechnology, Hislop College, Civil Lines, Nagpur 440001 (MS) INDIA

Supervisors: Dr. AvinashUpadhyay, Dr. Jaishree Rudra, Mrs. Pise Mashitha, Mr. Deovrat Begde, Mrs. Sunita Bundale, Mr. Jinu Jhon

Supervisors affiliation: Hislop School of Biotechnology, Hislop College, Civil Lines, Nagpur 440001 (MS) INDIA

Article type: Biotechnology

Date: Received on: 24 October 2009, Accepted on: 2 November 2009, Published on 5 November 2009

Abstract

In the current study four trifoliate plants Glycine max (control), Cajanus cajans, Phaseolus vulgaris, Tecoma stans of the region were evaluated for their bioactivities. Plant leaf extracts were prepared by Soxhelltion, using petroleum ether, chloroform, methanol and water as solvents. The antibacterial activity of the extracts was evaluated against seven bacterial strains Bacillus subtilis (MTCC 441), Escherichia coli (MTCC 1652), Staphylococcus aureus (MTCC 740), Proteus mirabilis (MTCC 425), Proteus vulgaris (MTCC 426), Pseudomonas aeruginosa (MTCC 441), and Salmonella typhi (Clinical Sample), by agar well diffusion method. The anticancer activity was evaluated against MCF7 and HeLa cancer cell lines first by visual examination followed MTT based Cytotoxicity assay and Cell Viability Count. The extracts demonstrated antibacterial activity against both gram positive and gram negative bacteria. Chloroform extracts showed the best activity. Peusdomonas aeruginosa was the most susceptible to the extracts. The extracts of Cajanus cajans were the most potent. Methanol extracts of all the selected plants demonstrated the best anticancer activity. Tecoma stans exhibited anticancer activity over a range of solvents fractions. The extracts however do not show any activity against HeLa cells. It was concluded that plants can be used as a source to extract potential antibacterial and anticancer compounds.

Citation

Pranay Dogra, Jaishree Rudra, Pise Mashitha, Deovrat Begde, Sunita Bundale, Jinu John, Avinash Upadhyay. Study of Antibacterial and Anticancer Activity of Selected Trifoliate Plants. Biofrontiers (2009), Volume 1, Issue 2, November 2009, Pg 11-16

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Authors  affiliation: Sai Bioinfosys Institute of Bioinformatics Research Raghuji Nagar, Nagpur,  Maharshtra, India.

G.H.Raisoni Institute of Interdisciplinary Sciences B-37 Shraddha Park, Hingna MIDC Nagpur, Maharashtra, India.

Email : acmedilip4u@yahoo.com

Supervisor : Dr. Shubhash Ghire, Sai Bioinfosys Institute of Bioinformatics Research Raghuji Nagar, Nagpur, Maharshtra, India.

Article Type: Bioinformatics

Date: Received on: 8 october 2009, Accepted on: 27 october 2009, Published on 1 November 2009.

Abstract:

The severity of drug resistant Shigella increasing every year, causing millions of deaths. Genome marking has revealed many uncharacterized proteins (Hypothetical proteins) available in Shigella flexneri. The probable enzymatic function prediction was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching Sequence Databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. Web tools predicted 128 enzymatic hypothetical proteins while their 3D structures were constructed using PS² server for 111 sequences. This study revealed many uncharacterized proteins, whose roles are yet to discover in Shigella flexneri. These newly predicted enzymatic functions in hypothetical proteins can make them the future drug targets for Insilico drug designing to control Shigellosis.

Citation:Dilip Gore. In silico Prediction of Structure and Enzymatic Activity for Hypothetical Proteins of Shigella flexneri. Biofrontiers (2009) vol.1, Issue.2: Pg 1-10

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Supplementary Material