017522   Zhu D;Li A;Wang J;Li M;Cai T (NO, The Key Laboratory of Freshwater Ecology and Biotechnology, Institute, Wuhan 430072, China, Email: wangjg@ihb.ac.cn) : Cloning, expression and characterization of aerolysin from Aeromonas hydrophila in Escherichia coli. Indian J Biochem Biophys 2007, 44(4), 204-8.

Aerolysin is a toxin (protein in nature) secreted by the strains of Aeromonas spp. and plays an important role in the virulence of Aeromonas strains. It has also found several applications such as for detection of glycosylphosphatidylinositol (GPI)-anchored proteins etc. A. hydrophila is a ubiquitous Gram-negative bacterium which causes frequent harm to the aquaculture. To obtain a significant amount of recombinant aerolysin in the active form, in this study, we expressed the aerolysin in E. coli under the control of T7 RNase promoter. The coding region (AerA-W)of the aerA gene of A. hydrophila XS91-4-1, excluding partial coding region of the signal peptide was cloned into the vector pET32a and then transformed into E. coli bl21. After optimizing the expression conditions, the recombinant protein AerA-W was expressed in a soluble form and purified using HisBind resin affinity chromatography. Recombinant aerolysin showed hemolytic activity in the agar diffusive hemolysis test. Western blot analysis demonstrated good antigenicity of the recombinant protein.

017521   Wright J D;Lim C (NO, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC) : Mechanism of DNA-binding loss upon single-point mutation in p53. J Biosci, Bangalore 2007, 32(5), 827-39.

Over 50% of all human cancers involve p53 mutations, which occur mostly in the sequence-specifi c DNA-binding central domain (p53c), yielding little/non-detectable affi nity to the DNA consensus site. Despite our current understanding of protein-DNA recognition, the mechanism(s) underlying the loss in protein-DNA binding affinity/specificity upon single-point mutation are not well understood. The goal is to identify the common factors governing the DNA-binding loss of p53c upon substitution of Arg 273 to His or Cys, which are abundant in human tumours. By computing the free energies of wild-type and mutant p53c binding to DNA and decomposing them into contributions from individual residues, the DNA-binding loss upon charge/noncharge-conserving mutation of Arg 273 was attributed not only to the loss of DNA phosphate contacts, but also to longer-range structural changes caused by the loss of the Asp 281 salt-bridge. The results herein and in previous works suggest that Asp 281 plays a critical role in the sequence-specific DNA-binding function of p53c by) orienting Arg 273 and Arg 280 in an optimal position to interact with the phosphate and base groups of the consensus DNA, respectively, and helping to maintain the proper DNA-binding protein conformation.

5 illus, 1 table, 40 ref

017520   Vikas;Kumar R;Pundir C S (Biochemistry Research Laboratory, Biosciences Dep, M D University, Rohtak-124001) : Covalent immobilisation of lipase onto onion membrane affixed on plastic surface: Kinetic properties and application in milk fat hydrolysis. Indian J Biotechnol 2007, 6(4), 479-84.

Lipase from porcine pancreas was immobilized covalently onto onion membrane, affixed on plastic surface through non-reactive fixative, with a conjugation yield of 0.174 mg/cm² and 63.6% retention of initial activity of free enzyme. The enzyme showed no change in optimum pH 7.5 but slight change in incubation temperature from 35 to 40°C and time of linearity from 15 to 30 min after immobilization. The utility of membrane bound lipase to prepare fat free milk without degradation of other essential components and formation of unwanted by-products was tested employing commercial kit for TG determination. Thus, the use of immobilized lipase in hydrolysis of milk fats increases the digestion process with out consuming them. The immobilized enzyme was reused 100 times without considerable loss of activity, when stored at 4°C for a period of 2 months.

017519   Vibha Rani (Biotechnology Dep, Jaypee Institute of Information Technology University, A-10, Sector 62, Noida-210 307, Email: vibha.rani@jiit.ac.in) : Computational methods to dissect cis-regulatory transcriptional networks. J Biosci, Bangalore 2007, 32(7), 1325-30.

Formation of diverse cell types from an invariant set of genes is governed by biochemical and molecular processes that regulate gene activity. A complete understanding of the regulatory mechanisms of gene expression is the major function of genomics. Computational genomics is a rapidly emerging area for deciphering the regulation of metazoan genes as well as interpreting the results of high-throughput screening. The integration of computer science with biology has expedited molecular modelling and processing of large-scale data inputs such as microarrays, analysis of genomes, transcriptomes and proteomes. Many bioinformaticians have developed various algorithms for predicting transcriptional regulatory mechanisms from the sequence, gene expression and interaction data. The review contains compiled information of various computational methods adopted to dissect gene expression pathways.

54 ref

017518   Tripathi N;Singh R;Singh S K;Gupta A (NO, Central Mining Research Institute, Barva Road, Dhanbad-826 001) : Microbial treatment of municipal solid wastes for clean environment and bio-energy production. Bhartiya Vaigyanik Evam Audyogik Anusandhan Patrika 2007, 15(1), 88-91.

In India, the area available for the storage of day-by-day increasing amount of municipal solid wastes is depleting. The most important fact is that several types of organic matters, abundantly found in these municipal wastes leach down to ground water and badly affect the human kind, animals and plants by causing several dreaded diseases. The gases, such as methane, nitrogen dioxide, etc., generating from the municipal solid wastes are also directly or indirectly responsible for the global warming. All the above-mentioned problems have attracted the attention of scientists and environmentalists on a global scale to achieve the environmental and health security. The gainful and environment friendly utilization of municipal solid wastes and obtaining the economical products and production of cleaner energy therefrom not only ensures the economic development of the country, but also proves to be a harbinger of the microbial technique for the municipal solid waste treatment. Anaerobic digestion of solid organic wastes, especially municipal solid wastes is proved to be very important for the gainful utilization of municipal solid wastes. In the process of anaerobic digestion, organic matters are digested in the absence of oxygen, in which biogas (which is a mixture of 65% methane and 35% carbon dioxide), besides a little amount of microbial biomass is obtained. Therefore, a good amount of gaseous fuel can be obtained by the microbial technique, which is beneficial from two points of view. Firstly, it makes the municipal solid wastes lesser polluted and secondly bio-energy is produced, which can be used for vehicles and also as heat. The present paper focuses on the anaerobic digestion of municipal solid wastes for the production of bio-energy, such as methane and methanol which can be used as a fuel.

017517   Tongden C;Chakraborty U (Plant Bichemistry Laboratory. Botany Dep, North Bengal Univ, Raja Rammaohanpur, Siliguri-734 013, Email: chakrabortyusha@hotmail.com) : Induction of thermoprotection by salicylic acid in seedlings and callus cultures of chickpea. J Pl Biol 2007, 34(3), 213-19.

Thermoprotection provided by salicylic acid (SA) was tested in 20-day-old seedlings and callus cultures of thermotolerant (ICC C37) and heat susceptible (ICC 7344) genotypes of chickpea (Cicer arietinum L.). Heat stress was imposed by directly exposing the seedlings and callus cultures separately to lethal temperatures of 46???°C and 40???°C respectively for 2 h duration. In comparison to seedlings subjected to high temperature, those treated with SA prior to temperature treatment, exhibited higher tolerance index, membrane stability and accumulation of proline as well as lower accumulation of malondialdehyde. Activities of antioxidant enzymes like peroxidase, ascorbate peroxidase, superoxide dismutase and glutathione reductase increased remarkably in pre-treated seedlings in comparison to untreated samples. Catalase activity in contrast showed a sharp decline in activity following pre-treatment in both tolerant and susceptible genotypes. Exposure of calli grown in unamended MS medium to lethal temperature led to rapid browning of calli followed by a drastic decline in growth rate (weight) and death of calli. However, calli grown in MS medium supplemented with 10^-5and 10^-6 M SA and subjected to temperature stress showed remarkable improvement in thermotoler-ance as evidenced by lesser browning and increase in fresh weights in both tolerant and susceptible genotypes following exposure to lethal temperature.

2 illus, 2 tables, 32 ref

017516   Tendular A V;Ogunnaike B;Wangikar P P (NO, Kanwal Rekhi School of Information Technology, Indian Institute of Tec, Powai, Mumbai-400 076) : Protein local conformations arise from a mixture of Gaussian distributions. J Biosci, Bangalore 2007, 32(5), 899-908.

Local conformations are represented using Geometric Invariants, properties that remain unchanged under transformations such as translation and rotation, followed by dimension reduction via principal component analysis. The local conformations are then modeled as a mixture of Gaussian probability distribution functions (PDF). Each one of the Gaussian PDF's corresponds to a conformational class with the centroid representing the average structure of that class. Finds 46 classes when it uses an octapeptide as a unit of local conformation. The protein 3-D structure can now be described as a sequence of local conformational classes. Further, it was of interest to see whether the local conformations can be predicted from the amino acid sequences. Analyses the correlation between sequence features and the conformational classes.

7 illus, 1 table, 19 ref

017515   Srividhya K V;Krishnaswamy S (Centre of Excellence in Bioinformatics, Scholl of Biotechnology, Madurai Kamaraj University, Madurai-625 021, Email: krishna@mrna.tn.nic.in) : Sub classification and targeted characterization of prophage-encoded two-component cell lysis cassette. J Biosci, Bangalore 2007, 32(5), 979-90.

Bacteriophage induced lysis of host bacterial cell is mediated by a two component cell lysis cassette comprised of holin and lysozyme. Prophages are integrated forms of bacteriophages in bacterial genomes providing a repertoire for bacterial evolution. Analysis using the prophage database constructed showed 47 prophages were associated with putative two component cell lysis genes. These proteins cluster into four different subgroups. In this process, a putative holin (essd) and endolysin (ybcS), encoded by the defective lambdoid prophage DLP12 was found to be similar to two component cell lysis genes in functional bacteriophages like p21 and P1. The holin essd was found to have a characteristic dual start motif with two transmembrane regions and C-terminal charged residues as in class II holins. Expression of a fusion construct of essd in Escherichia coli showed slow growth. However, under appropriate conditions, this protein could be over expressed and purified for structure function studies. The second component of the cell lysis cassette, ybcS, was found to have an N-terminal SAR (Signal Arrest Release) transmembrane domain. The construct of ybcS has been over expressed in E. coli and the purified protein was functional, exhibiting lytic activity against E. coli and Salmonella typhi cell wall substrate. Such targeted sequencestructure-function characterization of proteins encoded by cryptic prophages will help understand the contribution of prophage proteins to bacterial evolution.

5 illus, 4 tables, 45 ref

017514   Siva Sankar K;Reddy N S C;Jamil K;Mohana V C (NO, Bhagwan Mahavir Medical and Research Centre, Hyderabad-500 004) : Genomic analysis of SNPs in breast cancer by using bioinformatics databases. Indian J Biotechnol 2007, 6(4), 456-62.

The role of single nucleotide polymorphs (SNPs) in genes that modulate or promote cancer process has not been fully understood. Hence, an attempt has been made to collect data from Entrez Genome View, Cancer Genome Anatomy Project (NCBI) and Online Mendelian Inheritance in Man (OMIM) databases for enumerating and locating the number of SNPs in the loci of various chromosomes involved in cancerous and non-cancerous breast tissue. DNA methylation and mutations in the hotspots of the proto-oncogenes leading to formation of carcinomas in the breast tissue have been identified and discussed. Transition in the hotspots may reflect endogenous mutations and sporadic loss of DNA repair factors. This has been related to various molecular mechanisms and gene expression variations. SNPs also play important roles in conformational changes in proteins, resulting in non-functional or truncated proteins at the post-translational levels. Although SNPs in introns may not directly result in a change in function of a gene, they may be taken as biomarkers to locate the site near genes. SNPs technology has enormous potential in clinical research and pharmacogenomics. Hence, effort has been to understand the basic difference between candidate and validated SNPs and their significance in carcinogenesis or predisposition.

017513   Siva K;Gokul K;Inamdar M S (Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO, Bangalore-560 064) : Expression of conserved signalling pathway genes during spontaneous vascular differentiation of R1 embryonic stem cells and in Py-4-1 endothelial cells. J Biosci, Bangalore 2007, 32(7), 1291-8.

Embryonic stem (ES) cells are an invaluable model for identifying subtle phenotypes as well as severe outcomes of perturbing gene function that may otherwise result in lethality. However, though ES cells of different origins are regarded as equally pluripotent, their in vitro differentiation potential varies, suggesting that their response to developmental signals is different. The R1 cell line is widely used for gene manipulation due to its good growth characteristics and highly efficient germline transmission. Analyses the expression of Notch, Wnt and Sonic Hedgehog (Shh) pathway genes during differentiation of R1 cells into early vascular lineages. Notch-, Wntand Shh-mediated signalling is important during embryonic development. Regulation of gene expression through these signalling molecules is a frequently used theme, resulting in context-dependent outcomes during development. Perturbing these pathways can result in severe and possibly lethal developmental phenotypes often due to primary cardiovascular defects. Reports that during early spontaneous differentiation of R1 cells, Notch-1 and the Wnt target Brachyury are active whereas the Shh receptor is not detected. This expression pattern is similar to that seen in a mouse endothelial cell line. This temporal study of expression of genes representative of all three pathways in ES cell differentiation will aid in further analysis of cell signalling during vascular development.

4 illus, 50 ref

017512   Sinha R K;Subrahmanyam G (Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Email: gsm@iitb.ac.in) : Type II Phosphatidylinositol 4-kinase(s) in Cell signaling Cascades. Indian J Biochem Biophys 2007, 44(5), 289-94.

Phosphorylated derivatives of phosphatidylinositol (PtdIns) are key components of many signaling cascades. Many isoforms of PtdIns kinases, PtdIns phosphate kinases and phosphatases use these lipids in amazing networks of signaling cascades that are yet to be understood fully. PtdIns 4-kinase(s) phosphorylates PtdIns at the 4th -OH position of inositol head group and are classified in to type II and III PtdIns 4-kinases. While type III PtdIns 4-kinases are implicated in vesicular trafficking, type II PtdIns 4-kinases are suggested to play a role in cell signaling, cytoskeletal rearrangements, cell motility and in microbial pathogenicity. This paper reviews the role of type II PtdIns 4-kinases in cell signaling cascades in health and disease.

017511   Sinha A;Salam N;Gupta S;Natarajan K (Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110 067, Email: natarajan@icgeb.res.in) : Mycobacterium tuberculosis and Dendritic Cells: Recognition, Activation and Functional Implications. Indian J Biochem Biophys 2007, 44(5), 279-88.

The highly complex nature of interactions of Mycobacterium tuberculosis with cells of the immune system has puzzled researchers the world-over in understanding the pathogenesis and immunology associated with tuberculosis (TB). This has contributed to the delay in development of effective vaccine(s) for TB. Several excellent studies have provided only a glimpse of the kind and degree of immune responses elicited following infection by mycobacteria. Preferred entry via respiratory route results in the capture of mycobacteria by alveolar macrophages that eventually become their long-term hosts. Since the pathogen is rarely cleared this has resulted in the human population serving as a large reservoir for mycobacteria. Owing to their unique ability to prime naive and memory T cells, dendritic cells (DCs) play important and indispensable roles in the initiation and maintenance of protective immune responses following infection. The kind of immune response initiated by DCs with respect to mycobacteria determines the character of immune responses mounted by the host against the pathogen. The profile of cytokines and chemokines secreted as a result of infection of DCs by mycobacteria further plays an important role in defining the course of infection. This mini review attempts to highlight key interactions of mycobacteria with dendritic cells. We discus the uptake of mycobacteria by DCs followed by DC activation and the spectrum of immune responses initiated by infected/activated DCs, followed by numerous ways the pathogen has devised to subvert protective responses.

017510   Siddharthan R (NO, The Institute of Mathematical Sciences, Chennai-600 113, Email: rsidd@imsc.res.in) : Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach. J Biosci, Bangalore 2007, 32(5), 863-70.

Discusses the general problem of understanding transcriptional regulation from DNA sequence and prior information. The main tasks discussed are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individual binding sites. Reviews various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that was developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.

^iia26 ref

017509   Sharma S;Thakur A K;Srivastava D K (Biotechnology Dep, Dr Y.S. parmar Univ of Horticulture and Forestry, Solan-173 230) : In vitro plant regeneration from cotyledon and hypocotyls explants of bell pepper (Capsicum Annuum L. cv. California wonder). J Hill Res 2007, 20(2), 72-4.

1 table, 14 ref

017508   Sharma A;Rastogi T;Bhartiya M;Shasany A K; Khanuja S P S (Bioinformatics Div, Central Institute of Medicinal and Aromatic Plants, PO CIMAP, Lucknow-226 015, Email: ashoksharma@cimap.res.in) : Type 2 diabetes mellitus: phylogenetic motifs for predicting protein fucntional sites. J Biosci, Bangalore 2007, 32(5), 999-1004.

Diabetes mellitus, commonly referred to as diabetes, is a medical condition associated with abnormally high levels of glucose (or sugar) in the blood. Demonstrates the phylogenetic motifs (PMs) identification in type 2 diabetes mellitus very likely corresponding to protein functional sites . Identified PMs for all the candidate genes for type 2 diabetes mellitus. Glycine 310 remains conserved for glucokinase and potassium channel KCNJ11. Isoleucine 137 was conserved for insulin receptor and regulatory subunit of a phosphorylating enzyme. Whereas residues valine, leucine, methionine were highly conserved for insulin receptor. Occurrence of proline was very high for calpain 10 gene and glucose transporter.

2 illus, 2 tables, 8 ref

017507   Shalini;Tiwari S;Gupta R K;Pabbi S;Dhar D W (Centre for Conservation and Utilisation of Blue Green Algae, IARI, New Delhi-110 012) : Protocol optimization for RAPD in cyanobacteria. Indian J Biotechnol 2007, 6(4), 549-52.

Random amplification of polymorphic DNA (RAPD) analysis using the polymerase chain reaction proved a useful technique in the biodiversity analysis of microorganisms but may lack reproducibility in the poorly standardized methodology. In the present investigation, the RAPD technique was optimized for characterizing cyanobacterial isolates in order to ensure its reproducibility and discriminatory power. Cyanobacterial isolates from the three genera, Anabaena, Nostoc and Calothrix were examined for the fragment patterns produced using different 10-mer RAPD primers and concentrations of different components (DNA template, primer and Taq polymerase) at two different annealing temperatures. It was observed that variations associated with all the parameters tested modified the fingerprinting pattern. For conditions not optimized, RAPD bands were faint and difficult to score. Therefore, a set of conditions for RAPD-PCR reaction has been defined, to ensure simple and fast reproducibility.

017506   Sengupta D;Verma D;Naik P K (Bioinformatics adn Biotechnology Dep, Jaypee University of Information Technology, Waknaghat, Solan-173 215) : Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics - generalized born/surface area and absorption, distribution, metabolisum and excretion proeperties. J Biosci, Bangalore 2007, 32(7), 1307-16.

Delvardine and its structural derivatives are important non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs). Fifteen delvardine analogues were studied. A free energy-of-binding (FEB) expression was developed in the form of an optimized linear combination of van der Waal (vdW), electrostatic, solvation and solvent-accessible surface area (SASA) energy terms. The solvation energy terms estimated by generalized born/surface area (GB/SA) play an important role in predicting the binding affinity of delvardine analogues. Out of 15 derivatives, substitution of CH₃ with H at the Y and R positions, as well as substitution of SO₂CH₃ with only CH₂ at the Z position in S2, S8 and S12 analogues, were found to be the most potent (glide score = -7.60, -8.06 and -7.44; pIC50 = 7.28, 7.37 and 7.64) in comparison with the template delvardine (which is used currently as the drug candidate). All the three analogues also passed the absorption, distribution, metabolism and excretion (ADME) screening and Lipinski's rule of 5, and have the potential to be used for second-generation drug development. The work demonstrates that dock molecular mechanics-generalized born/surface area (MM-GB/SA-ADME) is a promising approach to predict the binding activity of ligands to the receptor and further screen for a successful candidate drug in a computer-aided rational drug design.

2 illus, 6 tables, 39 ref

017505   Sen S (Biochemistry and Biotechnology Dep, Burdwan Institute of Management and Computer Science, Hatudewan, Katwa Road, Burdwan-713 101) : In vitro construction of a novel organism, Triceliophthora thermophila : producer of hyper amount of cellulase and B-Glucosidase. J mycopathol Res 2007, 45(2), 159-65.

Fungal organisms behave differentially in vitro and in vivo, particularly in culture condition. Myceliophthora thermophila D-14, ATCC 48104, is a producer of cellulase and β-glucosidase (Sen et. al., 1982). However, it encodes endo and exo glucanase with a little amount of β-glucosidase. To improve the amount of expression of these enzymes, this investigation utilizes a fusion technique. It uses a known cellulase producer, Trichoderma viride which encodes hyper amount of β-glucosidase. Protoplast fusion with two strains produced a novel mycelial organism that shows hyper expression of cellulase and β-glucosidase. Molecular cloning technique has developed a number of systems for the production of industrially important enzymes; however, cellulase is an exception. Because cellulase is a complex enzyme with multiple subunits. It remains in the cell system as cellulosome. The strain is the fusion product of protoplast of Trichoderma viride and Myceliophthora thermophila. The growth temperatures 28°C to 35°C is a significant condition that supports mycelial form with characteristics of both the strains. However, increase or decrease growth temperature causes cellular differentiation. The mycelial form differentiates into a parental strain due to temperature shock. It has been recorded that above 37°C, it starts differentiation. Moreover, the stable mycelial form obtain at temperature 20°C to 37°C. It is more stable at 28°C which is only a mycelial form. Therefore, the protoplast fusion product is an unstable mycelial organism and it is named Triceliophthora thermophila. It, thus, able to provides an essential clue to understand dikaryotic condition of a cell in fungi. It also depicts interesting understanding on the production of chimerical organisms.

1 illus, 1 table, 28 ref

017504   Sablok G;Phulwaria M;Gupta A K;Shekhawat N S (Biotechnology Centre. Botany Dep, Jai Narain Vyas Univ, Jodhpur-342 033) : Pongamia pinnata : a plant for exploitation as energy crop. Green Fmg 2008, 1(10-11), 105-6.

Bio-diesel, the renewable liquid fuel from biological raw material is the current solution to the world energy crisis. The world organizations are running in the fast lane to identify crops which can play a lead role in meeting the world energy crisis naming them as energy crops. Earlier Jatropha curcas was used to play a major role in the understanding the hub of biodiesel production. But the question which remains undigged - Is a good substitute for petroleum diesel? The potentiality of this question can be well answered in introducing Pongamia pinnata as new sort out source for the biodiesel corporations. The sources for biodiesel production is so diversified ranging from soybean in USA to rapeseed in Ireland to Pongamia pinnata in India making India in race of energy Independency. Pongamia pinnata, a nitrogen fixing tree is contrast in characters to the Jatropha curcas causing no suppression of the associated crops and a/so supports micro-organisms in nature. The present paper put forth the introduction of Pongamia pinnata as a new resource for biodiesel and its roles in carbon mitigation.

7 ref

017503   Reddy B V B;Kaznessis Y N (Bioinformatics and In Silico Drug Design Lab, Computer Science Dep, Queens College, CUNY, 65-30 Kissena Blvd, Flushing, NY 11367, USA, Email: breddy@qc.cuny.edu) : Use of secondary structural information and Cα-Cα distance restraints to model protein structures with MODELLER. J Biosci, Bangalore 2007, 32(5), 929-36.

Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins have been explored to aid in modelling protein tertiary structures. In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein structures have been used the known Q3 (alpha-helix, beta-strands and irregular turns/loops) secondary structure information, along with residue-residue contact information as restraints for MODELLER. Results of our modelling studies on 30 best resolved single domain protein structures of varied lengths has been presented. The results shows that it is very difficult to obtain useful models even with 100% accurate secondary structure predictions and accurate residue contact predictions for up to 30% of residues in a sequence. The best models that obtained for proteins of lengths 37, 70, 118, 136 and 193 amino acid residues are of RMSDs 4.17, 5.27, 9.12, 7.89 and 9.69, respectively. The results show that one can obtain better models for the proteins which have high percent of alpha-helix content. This analysis further shows that MODELLER restrain optimization program can be useful only if it has truly homologous structure(s) as a template where it derives numerous restraints, almost identical to the templates used. This analysis also clearly indicates that even if we satisfy several true residue-residue contact distances, up to 30% of their sequence length with fully known secondary structural information, we end up predicting model structures much distant from their corresponding native structures.

3 tables, 27 ref

017502   Ray S S;Bandyopadhyay S;Pal S K (Centre for Soft Computing Research, A National Facility, Indian Statistical Institute, Kolkata-700 108, Email: shubhra_r@isical.ac.in) : Gene ordering in partitive clustering using microarray expressions. J Biosci, Bangalore 2007, 32(5), 1019-25.

Central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering and ordering the genes using gene expression data into homogeneous groups was shown to be useful in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on gene ordering in hierarchical clustering framework for gene expression analysis, there is no work addressing and evaluating the importance of gene ordering in partitive clustering framework, to the best knowledge of the authors. Outside the framework of hierarchical clustering, different gene ordering algorithms are applied on the whole data set, and the domain of partitive clustering is still unexplored with gene ordering approaches. A new hybrid method is proposed for ordering genes in each of the clusters obtained from partitive clustering solution, using microarray gene expressions. Two existing algorithms for optimally ordering cities in travelling salesman problem (TSP), namely, FRAG_GALK and Concorde, are hybridized individually with self organizing MAP to show the importance of gene ordering in partitive clustering framework. Validated the hybrid approach using yeast and fibroblast data and showed that the approach improves the result quality of partitive clustering solution, by identifying subclusters within big clusters, grouping functionally correlated genes within clusters, minimization of summation of gene expression distances, and the maximization of biological gene ordering using MIPS categorization. Moreover, the new hybrid approach, finds comparable or sometimes superior biological gene order in less computation time than those obtained by optimal leaf ordering in hierarchical clustering solution.

1 illus, 4 tables, 12 ref

017501   Rangannan V;Bansal M (Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, Email: mb@mbu.iisc.ernet.in) : Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability. J Biosci, Bangalore 0000, 32(5), 851-62.

Analysis of various predicted structural properties of promoter regions in prokaryotic as well as eukaryotic genomes had earlier indicated that they have several common features, such as lower stability, higher curvature and less bendability, when compared with their neighboring regions. Based on the difference in stability between neighboring upstream and downstream regions in the vicinity of experimentally determined transcription start sites, a promoter prediction algorithm has been developed to identify prokaryotic promoter sequences in whole genomes. The average free energy (E) over known promoter sequences and the difference (D) between E and the average free energy over the entire genome (G) are used to search for promoters in the genomic sequences. Using these cutoff values to predict promoter regions across entire Escherichia coli genome, achieved a reliability of 70% when the predicted promoters were cross verified against the 960 transcription start sites (TSSs) listed in the Ecocyc database. Annotation of the whole E. coli genome for promoter region could be carried out with 49% accuracy. The method is quite general and it can be used to annotate the promoter regions of other prokaryotic genomes.

4 tables, 24 ref

017500   Ramakrishnan S;Kulandaivelu G (Plant Science Dep, Mahatma Gandhi Govt Arts College, New Mahe-673 311, Email: gkplanti@sify.com) : Induction of UV-B resistance in rice (Oryza sativa L. cv. ADT 43) through adaptive mutagenesis, I: optimization of tissue culture and UV-irradiation conditions. J Pl Biol 2007, 34(3), 205-12.

Depletion of stratospheric ozone layer by pollution created because of human activities substantially increased the level of UV-B radiation impinging on the earth surface. UV-B radiation affects numerous crop plants in various ways and rice is one among them. Rice is one of the world's most important food crops and grown mostly in tropical and subtropical countries. There is a need for developing methods to produce UV-B resistant plants for the better yield and survival of the human beings. In this study we have attempted to induce callus tissue from mature rice (Oryza sativa L. cv. ADT 43) seeds on MS medium supplemented with 2 mg l^-1 of 2, 4-dichlorophcnoxyacetic acid (2,4-D) and 0.5 mg .l^-1 of benzylamino purine (BAP) in vitro. Calli were inoculated on medium containing 5 mg l^-1 BAP and screened for regeneration in response to different doses of UV-B irradiation which was given for 30 days and formation of UV-B selected shoots. It was found that UV-B irradiation for 10 min day^-1 for 30 days induced maximum frequency of shoot regeneration from calli. UV-B selected shoots were rooted on 1 mg l^-1 indole-3-butyric acid medium. Plantlets have been hardened in vermiculite and under shade for specified period. Then the somaclones planted on pots filled with garden soil to observe their growth.

3 illus, 4 tables, 28 ref

017499   Rakesh Kumar;Bhat A;Bamezaif R N K;Shamsia M B;Kumar R;Gupta N P;Amminid A C;Aron M;Sharma R K;Dada R (Molecular Reproduction and Genetics Lab, Army Reseach and Referral Hospital, New Delhi-110 018, Email: rima_dada@rediffmail.com) : Necessity of nuclear and mitochondrial genome analysis prior to assisted reproductive techniques/intracytoplasmic sperm injection. Indian J Biochem Biophys 2007, 44(6), 437-42.

Assisted reproductive technique (ART) has revolutionized the management of severe male factor infertility and in some countries 5% babies are conceived through ART/intra cytoplasmic sperm injection (ICSI). However, the carry-home live birth rate after several ART cycles is low (18-25%) and this is financially, physically and emotionally crippling for the couples. Genetic factors could lead to pre or post-implantation failure and thus explain for low ART success rate. Thus, this study was planned to understand, if infertile men harbour genetic abnormalities which may be iatrogenically transmitted by ART and adversely affect growth potential of embryo. Ninety infertile men underwent semen, cytogenetic, Yq microdeletion and mitochondrial mutation analysis. Of these, 14.4% cases harboured cytogenetic abnormality, and 8.89% Yq microdeletions. A high frequency of mitochondrial mutations was found in 23 men with asthenospermia. It is important to understand that through ART genetic abnormalities are transmitted to offspring, resulting in impaired growth and development potential of embryo and poor take-home live birth rate. Thus, genetic analysis is strongly recommend in all men with idiopathic infertility who opt for ART to counsel couples and provide them with most adapted therapeutics.

017498   Rajore S;Batra A (Biotechnology Lab, Botany Dep, University of Rajasthan, Jaipur-302 004) : Alternative source for regenerable organogenic callus induction in Jatropha curcas L.. Indian J Biotechnol 2007, 6(4), 545-8.

Plant regeneration of Jatropha curcas was achieved through organogenesis in callus cultures. Calli were induced from leaf explants on MS basal medium supplemented with NAA (1.0 mg/L) and BAP (5.0 mg/L). Green compact nodules containing clusters of meristematic centres were induced in these calli after transfer to MS basal medium containing various concentrations of BAP/Kn (0.5-5.0 mg/L) alone or in combination with auxins. MS medium supplemented with BAP (1.5 mg/L) and IBA (0.5 mg/L) was found to be the most effective combination for shoot bud differentiation. The microshoots rooted well on MS+IBA (3.0 mg/L) medium and the plantlets successfully acclimatized in soil.

017497   Rajkumar S (Biotechnology Dep, Institute of Science, Nirma University of Science and Technology, Ahmedabad-382 481) : Pharmacogenomics: Translating functional genomics to personalized medicine. Indian J Biotechnol 2007, 6(4), 449-55.

The emergence of human genome project brings hope of personalized medicine as patients with identical clinical symptoms may respond differently to the same drug therapy. Genetic polymorphisms in drug-metabolizing enzymes, transporters, receptors and other drug targets have been linked to differences in the efficacy and toxicity of many drugs between two individuals. Pharmacogenomics is the study of genetic factors that mediate a person's drug response. Pharmacogenomic analysis promises to identify disease susceptibility genes thus discovering new drug targets. This may lead to an individualized application for drug therapy and bring new insights into disease prevention. The emerging discipline of pharmacogenomics attempts to apply the innovative technologies of genome sequencing in order to better understand drug response to produce more effective drugs with fewer side effects on the basis of individual patient's genetic make up and making personalized medicine an economically viable possibility.

017496   Rajendran A;Thirugnanam M;Thangavelu V (Biochemical Engineering Lab, Chemical Engineering Dep, Annamalai University, Annamalainagar-608 002) : Statistical evaluation of medium components by Plackett-Burman experimental design and kinetic modeling of lipase production by Pseudomonas fluorescens. Indian J Biotechnol 2007, 6(4), 469-78.

The evaluation of medium components for lipase production by Pseudomonas fluorescens in submerged batch fermentation was studied using Plackett-Burman experimental design. Twelve medium components with three dummy variables were studied in this experimental design. The most significant variables affecting lipase production were found to be glucose, olive oil, yeast extract, dipotassium hydrogen phosphate and ferrous sulphate heptahydrate. Maximum lipase activity of 3.32 U mL^-1 and maximum cell mass concentration of 2.15 g L^-1 was obtained in the 32 h of fermentation using the optimized medium under optimized conditions of 30°C, with an initial pH of 7.0 at 120 rpm. Various unstructured kinetic models were analyzed to simulate the experimental values of cell growth, lipase activity and glucose concentration. Logistic model for cell growth, Luedeking-Piret model for lipase production and modified Luedeking-Piret model for substrate utilization were found to predict the fermentation profile more accurately with high determination coefficient (R²) values of 0.9893, 0.9314 and 0.9765, respectively. The estimated values of the kinetic model parameters, α and β for lipase production clearly indicate that the lipase production by P. fluorescens is growth-associated.

017495   Rai A;Chakravarty A K (Zoology Dep, St Joseph's College, Darjeeling-734 104, Email: anuradharai62@yahoo.com) : Homing of radiolabelled recombinant interleukin-2 activated natural killer cells and their efficacy in adoptive immunotherapy against murine fibrosarcoma. J Biosci, Bangalore 2007, 32(7), 1299-1305.

Natural killer (NK) cells are spontaneously cytotoxic against tumour target cells. Their number was found to be four times more in the spleen of tumour-bearing Swiss albino mice. After activation with recombinant interleukin-2 (rIL-2), NK cells were tested and found to seek out the tumour site when injected intravenously in tumour-bearing mice. Their potential for fighting tumours in vivo was further seen following adoptive transfer of rIL-2 activated NK (A-NK) cells in tumour-bearing mice. After surgical removal of tumour load, adoptive transfer of A-NK cells inhibited tumour recurrence in 92.3% cases, thereby suggesting the use of this protocol for therapeutic purposes to obtain a better outcome.

6 illus, 26 ref

017494   Purohit S D;Raghuvanshi S;Tyagi A K (Plant Biotechnology Lab, Botany Dep, Mohanlal Sukhadia University, Udaipur-313 001) : Biolistic-mediated DNA delivery and transient expression of GUS in hypocotyls of Feronia limonia L. - a fruit tree. Indian J Biotechnol 2007, 6(4), 504-7.

Feronia limonia L. (Rutaceae) is an important fruit tree of arid horticulture. To be able to introduce genes of interest for its improvement, biolistic-mediated DNA delivery method has been standardized. The hypocotyls explants were bombarded with plasmid pBI121 having gus reporter gene driven by CaMV 35S promoter and npt II under control of nos promoter as selectable marker. The best transient expression of GUS was recorded when tungsten particles coated with DNA were bombarded at a disc pressure of 1350 and 1100 psi from a distance of 9 cm. Some of the bombarded explants are being maintained to obtain viable regenerates for their analyses.

017493   Premalatha D;Ravindra P;Venkateshwar Rao L (Microbiology Dep, University College of Science, Osmania University, Hyderabad-500 007) : Homology modeling of putative thioredoxin from Helicobacetr pylori. Indian J Biotechnol 2007, 6(4), 485-9.

The tertiary structure of putative thioredoxin (trx) of Helicobacter pylori was generated based on structural homology of the X-ray crystallographic structure of thioredoxin from Escherichia coli. Inspection of theoretically predicted structure indicates that the thioredoxin of H. pylori is similar to that of E. coli. Analysis of the structure revealed that thioredoxins have a common fold, characterized by a core of twisted β-pleated sheet flanked either side by helices. The amino terminal end of the molecule is occupied by β-α-β motif and carboxy terminal end by β-β-α motif. This molecule is characterized by five strands and four helices. Among the four helices, a₂ is the longest helix which was disrupted near proline. Proline72 is identified as cis-proline. This structure retained overall trx-fold with the conservation of global shape and the secondary structures. This work determines the structure of thioredoxin and is found to be unique for further insight into molecular characterization.

017492   Prabhakar K;Ganesh S;Baheti V;Saisivam S; Madhusudan Rao Y;Kishan V (Pharmaceutics Dep, University College of Pharmaceutical Sciences, Kakatiya University, Warangal-506 009) : Preparation and in vitro cytotoxic evaluation of taxol immunoconjugates. Indian J Biotechnol 2007, 6(4), 463-8.

The taxol (paclitaxel) immunoconjugates prepared by derivatizing the taxol at two positions and linking the Mab CIBCNSH3 against EGF receptors were tested for in vitro cytotoxicity. Succinyl derivatives of taxol at 2'-OH and 7-OH groups were prepared as per the published procedures. Both the products were purified by column chromatography. The 7-succinyl taxol and 2'-succinyl taxol immunoconjugates were prepared with CIBCNSH3, Mab against EGF receptor using a published procedure involving water soluble EDC. The unbound taxol derivatives were separated either by dialysis or centricon separators. The drug to antibody ratio was estimated by either extracting the linked drug after hydrolysis of a conjugate or simultaneous Beer's law. The Drug-immunoconjugates were tested for their in vitro cytotoxic effect on EGF receptor expressing cells either A-549 or MCF-7 and HBL-100 by using MTT protocol and the IC₅₀ values were calculated. The drug to antibody ratio was 0.45:1 for 7-succinyl taxol, and 0.38:1 for 2'-succinyl taxol. The IC₅₀ value was 78 nM on A-549 cells for 7-succinyl taxol conjugate, while for 2'-succinyl taxol conjugate the IC₅₀ values were 114.8 nM and 120.3 nM on MCF-7 and HBL-100 cells respectively. Overall, as compared to the pure antibody both taxol immunoconjugates showed more cytotoxic activity.

017491   Poddar A;Chandra N;Ganapathiraju M;Sekar K; Klein Seetharaman J;Reddy R;Balakrishnan N (Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore-560 012, Email: balki@serc.issc.ernet.in) : Evolutionary insights from suffix array-based genome sequence analysis. J Biosci, Bangalore 2007, 32(5), 871-81.

Gene and protein sequence analyses, central components of studies in modern biology are easily amenable to string matching and pattern recognition algorithms. The growing need of analysing whole genome sequences more efficiently and thoroughly, has led to the emergence of new computational methods. Suffix trees and suffix arrays are data structures, well known in many other areas and are highly suited for sequence analysis too. Reports an improvement to the design of construction of suffix arrays. Enhancement in versatility and scalability, enabled by this approach, is demonstrated through the use of real-life examples. The scalability of the algorithm to whole genomes renders it suitable to address many biologically interesting problems. One example is the evolutionary insight gained by analysing unigrams, bi-grams and higher n-grams, indicating that the genetic code has a direct influence on the overall composition of the genome. Further, different proteomes have been analysed for the coverage of the possible peptide space, which indicate that as much as a quarter of the total space at the tetra-peptide level is left un-sampled in prokaryotic organisms, although almost all tri-peptides can be seen in one protein or another in a proteome. Besides, distinct patterns begin to emerge for the counts of particular tetra and higher peptides, indicative of a `meaning' for tetra and higher n-grams. The toolkit has also been used to demonstrate the usefulness of identifying repeats in whole proteomes efficiently. As an example, 16 members of one COG, coded by the genome of Mycobacterium tuberculosis H37Rv have been found to contain a repeating sequence of 300 amino acids.

^iia6 illus, 4 tables, 29 ref

017490   Patel V K;Yadav R S S;Yadav K D S (Chemistry Dep, DDU Gorakhpur University, Gorakhpur-273 009) : Enzymatic characteristics of lignin peroxidases of indigenous lignolytic fungal strains - Part I. Indian J Biotechnol 2007, 6(4), 553-6.

Extracellular production of lignin peroxidases from six indigenous fungi, viz. Abortiporus biennis MTCC-1176, Pestalotia bicolor MTCC-372, Heterobasidium annosum MTCC-146, Pleurotus ostreatus MTCC-142, Gloephyllum striatum MTCC-1117 and Loweporus lividus MTCC-1178, in liquid culture growth medium amended with lignin-containing natural substances and their enzymatic characteristics were studied. P. ostreatus MTCC-142 was found to be the best secretor of lignin peroxidase (3.50 IU/mL) in the presence of saw dust. Moreover, the enzymatic characteristics (Km, pH and temperature optima) of the lignin peroxidases produced by indigenous fungal strains were in the same range as the enzymatic characteristics of Phanerochacte chrysosporium ATCC-24725, an American type culture collection widely used for purification of lignin peroxidase. Thus, P. ostreatus MTCC-142 has potential to be used for commercial production of lignin peroxidase.

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017489   Patel S;Chiplunkar S (Chiplunkar Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTR, Kharghar, Navi Mumbai-410 210,, Email: schiplunkar@actrec.gov.in) : Role of Cyclooxygenase-2 in Tumor Progression and Immune Regulation in Lung Cancer. Indian J Biochem Biophys 2007, 44(6), 419-28.

Lung cancer is the leading cause of cancer death all over the world. The low 5-year survival rate (under 15) has changed minimally in the last 25 years. Amongst different types of lung cancers, non-small cell lung carcinoma (NSCLC) types account 25-40%. To improve the survival of lung cancer patients, new therapeutic strategies are needed. The search for improved therapies has led to the investigation of agents that target novel pathways involved in tumor proliferation, invasion, survival and immune regulation. Cyclooxygenase-2 (COX-2) is one of the novel targets under evaluation for NSCLC therapy and chemoprevention. Although multiple genetic alterations are necessary for lung cancer invasion and metastasis, COX-2 may act as central element in orchestring these processes. COX-2 plays an important role in all aspects of tumor development and growth. It also plays a pivotal role in regulation of cytokines and immune responses in NSCLC patients. In this article, we review the experimental and clinical evidences on the possible link between COX and NSCLC.

017488   Pandeya R;Ramesh Chander;Saini K B (Radiation Biology and Health Sciences Div, Bhabha Atomic Research Centre, Trombay, Mumbai-400 085, Email: ruchipandey01@gmail.com) : Prodigiosins: a Novel Family of Immunosuppressants with Anti-cancer Activity. Indian J Biochem Biophys 2007, 44(5), 295-302.

Prodigiosins (PrGs) are a family of promising therapeutic molecules, isolated mostly from Gram-negative bacteria and characterized by a common pyrryldipyrrylmethene structure with varying side chains. They show a broad spectrum of activities such as anti-microbial, anti-malarial, anti-cancer and immunosuppressive. PrGs are attracting increasing attention due to the ongoing research for less toxic, but effective agents for cancer chemotherapy and immunosuppression for preventing allograft rejection and autoimmunity. Different analogues have been synthesized and evaluated. This review discusses the immunosuppressive and anti-cancer activities of this class of compounds, as both involve inhibition of cell proliferation. The main focus is on the in vitro and in vivo immunosuppressive activity of the different PrGs and the mechanisms involved. PrGs primarily target the T cells, though some effects are observed on other cell types also. Unlike the well-known immunosuppressant cyclosporin A, PrGs do not inhibit the secretion of IL-2 but inhibit the mitogenic signaling from IL-2, suggesting a different mechanism of action. Janus tyrosine kinase 3 (Jak3) that associates with IL-2R upon activation is considered as the molecular target for PrGs. Its restricted expression makes Jak3 as an attractive target for immunosuppressive therapy. However, the available literature suggests that some other pathways are also influenced by the PrGs. These may be important for the anti-cancer activity, as well as immunosuppressive action. Therefore, PrGs appear to be potential candidates for pharmaceutical development as immunosuppressants and also as anti-cancer agents.

017487   Nowsheen Hamid;Jain S K (Biotechnology Dep, Hamdard University, Hamdard Nagar, New Delhi-110 062, Email: skjain@jamiahamdard.ac.in) : Immunological, Cellular and Molecular Events in Typhoid Fever. Indian J Biochem Biophys 2007, 44(5), 320-30.

Salmonella, a facultative intracellular Gram-negative bacterium infects a wide range of hosts causing several gastrointestinal diseases and enteric fever in humans and certain animal species. Typhoid caused by Salmonella typhi remains a major health concern in India and worldwide. Also, with emergence of multidrug resistant strains, Salmonella has acquired increased virulence, communicability and survivability, resulting in increased morbidity and mortality. Though a number of vaccines for typhoid are available against S. typhi (or also against S. typhimurium), these have certain undesirable side effects and the search for new immunogens suitable for vaccine formulation is still continuing. The immune response to primary Salmonella infection involves both humoral and cell-mediated responses. The protective immunity against Salmonella depends on host- parasite interaction, however; the detailed mechanism of virulence, innate resistance and susceptibility of host remains unclear. This review focuses on the molecular, immunological and cellular mechanisms of pathogenesis of Salmonella infection to provide an insight to counteract bacterial infections and allow a better understanding of its clinical manifestations. It also reviews better technological possibilities combined with increased knowledge in related fields such as immunology and molecular biology and allow for new vaccination strategies. Some new approaches such as subunit and nucleic acid vaccines and recombinant antigen which are becoming increasingly important for the development of potential vaccines have also been discussed. A significant progress has been made in our understanding of Salmonella pathogenesis. Despite these efforts, however, many challenges exist, especially for investigators who aim to understand how the pathogenic mechanisms operating in vitro apply to in vivo model systems. However, unyielding work and collaborations between Salmonella researchers and clinicians worldwide have made significant contributions to understanding the interaction between virulence determinants and immunity required to stop the spread of this pathogen.

017486   Nayak L;De R K (Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata-700 108, Email: rajat@isical.ac.in) : Modularized study of human calcium signalling pathway. J Biosci, Bangalore 2007, 32(5), 1009-17.

Signalling pathways are complex biochemical networks responsible for regulation of numerous cellular functions. These networks function by serial and successive interactions among a large number of vital biomolecules and chemical compounds. For deciphering and analysing the underlying mechanism of such networks, a modularized study is quite helpful. Proposes an algorithm for modularization of calcium signalling pathway of H. sapiens. The idea that "a node whose function is dependant on maximum number of other nodes tends to be the center of a sub network" is used to divide a large signalling network into smaller sub networks. Inclusion of node(s) into sub networks(s) is dependant on the outdegree of the node(s). Here outdegree of a node refers to the number of re lations of the considered node lying outside the constructed sub network. Node(s) having more than c relations lying outside the expanding sub network have to be excluded from it. Here c is a specified variable based on user preference, which is finally fixed during adjustments of created sub networks, so that certain biological significance can be conferred on them.

7 illus, 1 table, 20 ref

017485   Narain P (NO, , 29278 Glen Oaks Blvd. W, Farmington Hills, MI 48334-2932, USA, Email: narainprem@hotmail.com) : Theoretical treatment of interval mapping of a disease gene using trnasmission disequilibrium tests. J Biosci, Bangalore 2007, 32(7), 1317-24.

Genetic basis of the transmission disequilibrium test (TDT) for two-marker loci is explored from first principles. In this case, parents doubly heterozygous for a given haplotype at the pair of marker loci that are each in linkage disequilibrium with the disease gene with the further possibility of a second-order linkage disequilibrium are considered. The number of times such parents transmit the given haplotype to their affected offspring is counted and compared with the frequencies of haplotypes that are not transmitted. This is done separately for the coupling and repulsion phases of doubly heterozygous genotypes. Expectations of the counts for each of the sixteen cells possible with four-marker gametic types (transmitted vs not transmitted) are derived. Based on a test of symmetry in a square 4 x 4 contingency table, chi-square tests are proposed for the null hypothesis of no linkage between the markers and the disease gene. The power of the tests is discussed in terms of the corresponding non-centrality parameters for the alternative hypothesis that both the markers are linked with the disease locus. The results indicate that the power increases with the decrease in recombination probability and that it is higher for a lower frequency of the disease gene. Taking a pair of markers in an interval for exploring the linkage with the disease gene seems to be more informative than the single-marker case since the values of the non-centrality parameters tend to be consistently higher than their counterparts in the single-marker case. Limitations of the proposed test are also discussed.

4 tables, 23 ref

017484   Muzammil Ahmad;Pyaram K;Mullick J;Sahu A (NO, National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune-411 007, Email: arvindsahu@nccs.res.in) : Viral complement regulators: the expert mimicking swindlers. Indian J Biochem Biophys 2007, 44(5), 331-43.

The complement system is a principal bastion of innate immunity designed to combat a myriad of existing as well as newly emerging pathogens. Since viruses are obligatory intracellular parasites, they are continuously exposed to host complement assault and, therefore, have imbibed various strategies to subvert it. One of them is molecular mimicry of the host complement regulators. Large DNA viruses such as pox and herpesviruses encode proteins that are structurally and functionally similar to human regulators of complement activation (RCA), a family of proteins that regulate complement. In this review, presents the structural and functional aspects of virally encoded RCA homologs (vRCA), in particular two highly studied vRCAs, vaccinia virus complement control protein (VCP) and Kaposi's sarcoma-associated herpesvirus complement regulator (kaposica). Importance of these evasion molecules in viral pathogenesis and their role beyond complement regulation are also discussed.

017483   Mukhopadhyay P;Basak S;Ghosh T C (Bioinformatics Centre, Bose Institute, P 1/12, CIT Scheme VII M, Kolkata-700 054, Email: tapash@boseinst.ernet.in) : Synonymous condon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC₃ rich genes towards protein stability. J Biosci, Bangalore 2007, 32(5), 947-63.

Relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However, when the genes were classified according to their GC₃ levels there was an increase in non-randomness in high GC₃ group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC₃ group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codon usage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC₃ group of genes. Biological implications of these results have been discussed.

6 tables, 31 ref

017482   Mishra P K;Choudhary S B;Tripathy P S M (Botany Dep, Vinoba Bhave University, Hazaribagh, Jharkhand) : Role of biotechnology in medicinal plant management. Bhartiya Vaigyanik Evam Audyogik Anusandhan Patrika 2007, 15(1), 92-97.

Utility of medicinal plants in the treatment of various diseases has been accepted from ancient time. Discovery of antibiotics and steroids seemed to revolutionize the medicinal world. But, as long term side effect of these compounds was experienced, people once again started reverting to medicinal plants. The importance of conservation and management of medicinal plants is clear. Biotechnology can be used in this direction successfully. Population of a large number of medicinal plants is reducing and their demand is increasing. These plants can be propagated in sufficient number with the help of tissue culture. Taxus is a slow growing plant and the compound taxol obtained from it is highly useful in treatment of cancer. This compound can be obtained in the laboratory by cell culture methods. Standardisation of medicinal plants is a big problem. This can be solved by studying active molecules of plant with the help of biotechnology. In the era of globalisation, intellectual property has become a burning subject. Other countries have already tried to obtain patent on turmeric and neem. In such conditions conservation of plants and traditional knowledge is essential. It is urgent to prepare complete data base of traditional medicines and their preparations. Biotechnology can be applied successfully in this direction.

017481   Mishra M N;Kalra R;Gupta M K (Pathology Dep, Command Hospital (SC), Pune-411 040) : Antiphospholipid antibodies in young myocardial infarction patients. Indian J Biochem Biophys 2007, 44(6), 481-84.

Myocardial infarction (MI) is a multi-factorial disease which claims many young lives. There are very few Indian studies that have investigated antiphospholipid antibodies (APLs) in MI patients. APLs have been implicated in arterial thrombosis including premature coronary artery and cerebrovascular thrombosis. In the present study, the prevalence of two clinically significant APLs - anticardiolipin antibody (ACA) and lupus anticoagulants (LA) in young MI patients was studied and compared with age- and sex-matched controls. Fifty healthy blood donors and 40 young MI patients (less than 45 yrs) diagnosed according to the American Heart Association guidelines were recruited for the study. The criteria for diagnosis were presence of atleast two of three classical findings including: clinical symptoms, diagnostic ECG, and presence of one or more cardiac biomarkers out of raised CK-MB isoform and T-troponin on serial measurement. LA and ACA were tested by lupus-sensitive activated partial thromboplastin time (aPTT) and ELISA respectively. Elevation of ACA was observed in 9 patients, while 6 were positive for LA. ACA of IgG isotype was detected in 8 patients. One patient had LA and raised ACA of IgG and IgM isotypes. Antiphospholipid antibodies were found to be significantly associated with MI in young patients, when considered together (p<60>0.05) and in coronary thrombosis, mild elevation of ACA may be considered significant.

017480   Mazumdar T;Goswami C;Talukdar N C (Soil Microbiology Laboratory, Soil Science Dep, Assam Agricultural University, Jorhat-785 013) : Charcterization and screening of beneficial bacteria obtained on King's B agar from tea rhizosphere. Indian J Biotechnol 2007, 6(4), 490-94.

Nine fluorescent Pseudomonas isolates obtained on King's B agar from rhizosphere of tea plants were studied along with a reference strain P. fluorescens MTCC-103 for their biochemical and functional characteristics. They were also tested for their ability to promote growth of tea seedlings. Intrinsic antibiotic resistance profile (IARP) and SDS-PAGE banding pattern indicated that the isolates were distinct from each other and these two properties could be used as marker for their identification. The isolates produced IAA-like substances, siderophores and soluble P in the range of 8.7-32.1, 13.6-196.3 and 1.4-15.7 μg/mL culture filtrate, respectively. Four isolates were able to utilize cellulose as C-source and another four were capable of inhibiting growth of the saprophytic Rhizoctonia solani in laboratory bioassay. The isolates Psd 11, Psd 12 and Psd 13 were found to enhance total shoot and root biomass of 1-year-old tea seedlings, grown in a fertilizer unamended soil, to significantly greater magnitude. Psd 11 and Psd 13 were identified as two different strains of Bacillus circulans. The growth parameters of tea seedlings in fertilizer P added pot was statistically at par with those of superior strain inoculated seedlings. There was no statistically significant relationship between in vitro determined functional properties observed and the growth promotion ability of the isolates. Although, the three superior isolates were found to produce higher level of soluble P and exhibited maximum in vitro biocontrol activity against R. solani.

017479   Mathur M;Jain A K;Dass S;ramawat K G (Laboratory of Bio-Molecular Technology, Botany Dep, M L Sukhadia University, Udaipur-313 001) : Optimization of guggulsterone production in callus cultures of Commiphora wightii (Arnott.) Bhandari. Indian J Biotechnol 2007, 6(4), 525-31.

Commiphora wightii (Arnott.) Bhandari is an endangered, slow growing medicinal tree. Its hypolipidemic and hypocholesterolemic activity is due to the presence of two closely related steroidal ketones guggulsterone-E and guggulsterone-Z in the resin. The callus cultures derived from zygotic embryos and leaf explants were exploited for the optimal production of these bioactive molecules. The production of guggulsterone in callus cultures was maximal during 35-d growth on modified MS medium. A correlation has been observed between guggulsterone yield in callus and in vivo in the plant. Guggulsterone content of callus was maximum during January to July, the period of gum exudation in nature. The cultures, which were grown on modified MS medium (950 mg/L KNO3, 825 mg/L NH4NO3 and 220 mg/L CaCl2.2H2O) containing 2, 4, 5-T (0.25 mg/L) and kinetin (0.1 mg/L) (referred to as CM2 medium) accumulated <126>15 æg/g guggulsterone. The optimal level of nitrogen [NH₄NO₃ (1650 mg/L), KNO₃ (475 mg/L)], CaCl2 (110 mg/L) KH₂PO₄ (170 mg/L) in different media resulted in maximum accumulation of total guggulsterone up to 19 μg/g dry weight basis. The significant increase in total guggulsterone accumulation (59 μg/g) was recorded in the tissues grown on CM2 medium containing 40 g/L maltose. Significant increase in guggulsterone content was recorded in the tissues grown on the production medium with either sucrose or maltose alone (40 g/L) or glucose:sucrose ratio (20:20 g/L). Combination of all the optimal concentrations of salts and sugars did not further increase the guggulsterone accumulation. It appears that guggulsterone production reached to its maximum possible level (<126>3 fold increase) with medium salt manipulation containing 40 g/L maltose or glucose: sucrose (<126>60 μg/g dry weight) and further increase was not possible within these conditions.

017478   Majumdar T;Datta S;Ghosh D;Dutta S; Chakraborty A;Goswami R;Mazumder S (Immunobiology Laboratory, School of Life Sciences, Visva-Bharati University, Santiniketan-731 235, Email: shibnath1@yahoo.co.in) : Role of virulence plasmid of Aeromonas hydrophila in the pathogenesis of ulcerative disease syndrome in Clarias batrachus. Indian J Biochem Biophys 2007, 44(5), 401-6.

Pathogenic Aeromonas hydrophila (strain VB21), a multiple-drug resistance strain contains a plasmid of about 21 kb. After curing of plasmid, the isolates became sensitive to antimicrobials, to which they were earlier resistant. The cured bacteria exhibited significant alterations in their surface structure, growth profile and virulence properties, and failed to cause ulcerative disease syndrome (UDS) when injected into the Indian catfish Clarias batrachus. Routine biochemical studies revealed that the plasmid curing did not alter the biochemical properties of the bacteria. After transformation of the plasmid into cured A. hydrophila the bacterium regained its virulence properties and induced all the characteristic symptoms of UDS when injected into fish. Thus, the plasmid plays a pivotal role in the phenotype, growth and virulence of A. hydrophila and pathogenesis of aeromonad UDS.

017477   Luthra A;Jha A N;Ananthasuresh G K; Vishveswara S (Biotechnology Dep, Indian Institute of Technology-Guwahati, Guwahati-781 039, Email: suresh@mecheng.iisc.ernet.in ) : Method for computing the inter-residue interaction potentials for reduced amino acid alphabet. J Biosci, Bangalore 2007, 32(5), 883-9.

Inter-residue potentials are extensively used in the design and evaluation of protein structures. Dealing with all (20x20) interactions becomes computationally difficult in extensive investigations. Hence, it is desirable to reduce the alphabet of 20 amino acids to a smaller number. Currently, several methods of reducing the residue types exist; however a critical assessment of these methods is not available. Reviews and evaluate different methods by comparing with the complete (20x20) matrix of Miyazawa-Jernigan potential, including a method of grouping adopted, based on multi dimensional scaling (MDS). The second goal is the computation of inter-residue interaction energies for the reduced amino acid alphabet, which has not been explicitly addressed in the literature until now. By using a least squares technique, a systematic method of obtaining the interaction energy values for any type of grouping scheme that reduces the amino acid alphabet has been presented This can be valuable in designing the protein structures.

2 illus, 3 tables, 28 ref

017476   Lavery R;Sacquin Mora S (NO, Institut de Biologie et Chimie des Proteines, CNRS UMR 5086, Universit, Passage du Vercors, Lyon 69367, France, Email: richard.lavery@ibcp.fr) : Protein mechanics: a route from structure to function. J Biosci, Bangalore 2007, 32(5), 891-8.

In order to better understand the mechanical properties of proteins, simulation tools which enable these properties to be analysed on a residue-by-residue basis has been developed. Although these calculations are relatively expensive with all-atom protein models, good results can be obtained much faster using coarse-grained approaches. The results show that proteins are surprisingly heterogeneous from a mechanical point of view and that functionally important residues often exhibit unusual mechanical behaviour. This finding offers a novel means for detecting functional sites and also potentially provides a route for understanding the links between structure and function in more general terms.

5 illus, 36 ref

017475   Khan N A (UPRES EA 4183 Lipides & Signalisation Cellulaire, Faculte' des Science, Universite' de Bourgogne, 6, Boulevard Gabriel, 21000 Dijon, France, Email: naim.khan@u-bourgogne.fr) : Role of T-cells in Diabetic Pregnancy and Macrosomia. Indian J Biochem Biophys 2007, 44(5), 344-9.

A number of studies have recently addressed the correlationship between diabetic pregnancy/macrosomia and differentiation of T-cells into Th1 and Th2 subsets. Diabetic pregnancy has been found to be associated with a decreased Th1 phenotype and IL-4 mRNA expression. In macrosomic offspring, high expression of IL-2 and IFN-g mRNA, but not of Th2 cytokines is observed, indicating that the Th1 phenotype is upregulated during macrosomia. T-cells of gestational diabetic rats and their macrosomic offspring seem to present a defect in signal transduction. Indeed, the recruitment of free intracellular calcium concentrations from intracellular pool in T-cells of these animals is altered. The phenotype of regulatory T-cells (T-Reg) is upregulated in diabetic pregnancy and their infants. T-cells in diabetic pregnancy and macrosomic obese offspring are in vivo activated. Adipokines and peroxisome proliferator-activated receptor-a (PPARa) also seem to modulate the pro-inflammatory cytokines in these pathologies. Hence, activation of the immune system might be considered as one of the regulatory pathways including metabolic abnormalities in these two pathologies.

017474   Kaul D (Molecular Biology Unit, Experimental Medicine & Biotechnology Dep, Postgraduate Institute of Medical Education & Research, Chandigarh-160 012, Email: dkaul_24@hotmail.com) : Cellular AATF Gene: Armour against HIV-1. Indian J Biochem Biophys 2007, 44(5), 276-78.

Outcome of HIV-1 infection at the cellular level is decided by the orchestrated balance that exists between cellular nucleic acid-based adaptive immune mechanism involving non-coding micro RNAs (miRNAs) and offensive tactics of HIV-1 to suppress this host cellular immunity. In this context, the review explains the importance of a novel miRNA encoded exclusively and conspicuously by HIV-1 genome that has the ability to specifically target cellular AATF gene recognized to play a crucial role in the maintenance of adaptive immunity at nucleic acid level against HIV-1 invasion.

017473   Karuppusamy S;Aruna V;Kiranmai C;Pullaiah T (Biotechnology Dep, Sri Krishnadevaraya University, Anantapur-515 003) : In vitro propagation of an endemic umbellifer, Hydrocotyle conferta. Indian J Biotechnol 2007, 6(4), 541-4.

A protocol for in vitro propagation of Hydrocotyle conferta Wight (Apiaceae) through axillary bud multiplication was established. Murashige and Skoog (MS) medium with 6.66 μM N⁶-benzyladenine (BA) and 5.37 μM α-naphthalenacetic acid (NAA) was best suited for axillary bud multiplication including a mean of 21 shoots/node. Excision and culture of the nodal segments from the in vitro shoots on fresh medium with same concentrations of BA and NAA facilitated development of more than 25 shoots/node. Subsequent cultures enhanced the rate of shoot proliferation. The developed shoots rooted best on half strength MS medium with 0.54 μM NAA. Plantlets established in pots exhibited 95% survival.