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VOLUME 43

NUMBER 4

AUGUST 2006

 

CONTENTS

 

Minireview
Hydrogen production by photosynthetic green algae	201
Maria L Ghirardi
Papers
Iterative ACORN as a high throughput tool in structural genomics	211
S Selvanayagam , D Velmurugan* and T Yamane
Correlation between biochemical properties and adaptive diversity of skeletal muscle myofibrils and myosin of some air-breathing teleosts	217
Riaz Ahmad and Absar-ul Hasnain*
Physical, X-ray diffraction and scanning electron microscopic studies of uroliths	226
Naveen Kumar*, Praveen Singh and Satish Kumar
Evaluation of water binding, seed coat permeability and germination characteristics of wheat seeds equilibrated at different relative humidities	233
Nabamita Chatterjee and Shantha Nagarajan*
Notes
Purification of a peroxidase from Solanum melongena fruit juice	239
S K Vernwal, R S S Yadav and K D S Yadav*
Isolation of stress responsive Psb A gene from rice (Oryza sativa L) using differential display	244
Aruna Tyagi* and Arti Chandra
A p53-like protein from a freshwater mollusc Lamellidens corrianus	247
B P Mohanty*
Nitric oxide levels during erythroid differentiation in K562 cell line	251
B Küçükkaya, G Öztürk and L Yalçıntepe
Preparation of prospective plant oil derived micro-emulsion vehicles for drug delivery	254
Syamasri Gupta*, S K Sanyal, S Datta and S P Moulik
Instructions to Authors	258

 

 

 

 

________________

*Author for correspondence

 

 

 

 

  

Minireview

  

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 201-210

  

Hydrogen production by photosynthetic green algae

Maria L Ghirardi

National Renewable Energy Laboratory, Golden, CO 80401, USA

E-mail: maria_ghirardi@nrel.gov

Received 29 March 2006; revised 28 June 2006

Oxygenic photosynthetic organisms such as cyanobacteria, green algae and diatoms are capable of absorbing light and storing up to 10-13% of its energy into the H-H bond of hydrogen gas. This process, which takes advantage of the photosynthetic apparatus of these organisms to convert sunlight into chemical energy, could conceivably be harnessed for production of significant amounts of energy from a renewable resource, water. The harnessed energy could then be coupled to a fuel cell for electricity generation and recycling of water molecules. In this review, current biochemical understanding of this reaction in green algae, and some of the major challenges facing the development of future commercial algal photobiological systems for H₂ production have been discussed.

Keywords: Green algae, Hydrogen production, Algal hydrogenases

 

 

Papers

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp 211-216

 

Iterative ACORN as a high throughput tool in structural genomics

S Selvanayagam ^a, D Velmurugan^a†and T Yamane^b

^aDepartment of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India

^bDepartment of Biotechnology and Biomaterial Science, Graduate School of Engineering, Nagoya University,
Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Japan

Received 21 October 2005; revised 15 May 2006

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: 1is3) and catalase (PDB-ID: 1gwe) for which models are available.

Keywords: ACORN, Congerin, Catalase

^†E-mail: d_velu@yahoo.com

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 217-225

 

 

 

Correlation between biochemical properties and adaptive diversity of skeletal muscle myofibrils and myosin of some air-breathing teleosts

 

Riaz Ahmad and Absar-ul Hasnain*

Laboratory of Biochemical Genetics, Department of Zoology, Aligarh Muslim University, Aligarh 202 002, India

Received 3 November 2005; revised 22 June 2006

Functional properties of myofibrils and relative stability of myosin of five teleosts Channa punctata, Clarias batrachus, Mastacembalus armatus, Labeo rohita and Catla catla adapted to different breathing modes were compared. Myofibrillar contractility and m-ATPase of air-breathing organ (ABO) possessing C. punctata and C. batrachus were low and least affected by pH in the range of 7.1-8.5. However, their myosin isoforms were relatively thermostable, more soluble at sub-neutral pH values, between 0.1 to 0.15 M KCl concentrations and less susceptible to α-chymotryptic digestion. In contrast, myofibrils and myosin of water-breather major carps L. rohita and C. catla were more contractile and susceptible to pH and salt concentrations. Thus, correlation between catalytic efficiency and relative stability of myofibrils and myosin of ABO-possessing teleosts was of reverse order and magnitude, as compared to water-breathers. Interestingly, myofibrils and myosin of the behavioral air-breather M. armatus showed intermediate properties. The specific levels of m-ATPase of all the five teleosts were in conformity with the levels of metabolic marker, the lactate dehydrogenase. The effect of chymotryptic cleavage of 94 and 173 kDa domains on ATPase, individuality of peptide maps of MyHC isomers and perturbation of phenylalanine residues by urea implicated hydrophobic residues in stabilizing myosin structure in these fish. The present study suggests two apparent evolutionary modifications of myofibrils and myosin in ABO-possessing teleosts: (i), ‘down-regulation’ of ATPase that explains sluggishness of such species and, (ii), more stable molecular structure to support stress of air-breathing modes of life.

Keywords:      Air-breathing teleosts, Chymotryptic Peptide maps, Difference spectra, Hydrophobic interactions, m-ATPase, Muscle-type specificity, MyHC isoforms/isomers, SDS-PAGE, Structural plasticity

 

*E-mail: absarhb@yahoo.com

 

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 226-232

 

 

Physical, X-ray diffraction and scanning electron microscopic studies of uroliths

Naveen Kumar*, Praveen Singh¹⁺ and Satish Kumar²

Division of Surgery, ¹Biophysics and Electron Microscopy Section,

²Central Instrumentation Facilities, National Biotechnology Center,

Indian Veterinary Research Institute, Izatnagar (U.P.) 243 122, India

Received 2 January 2006; revised 15 May 2006

Identification of chemical constituents of calculus is important in the diagnosis and management of urolithiasis. The compositional variability of uroliths has different etiologies and requires various modes of treatment and prophylaxis. In the present study, we report the chemical compositional analyses of calculi recovered from buck and bullock by X-ray diffraction (XRD) and energy dispersive X-ray (EDX) techniques and ultra-structure examination by scanning electron microscopy (SEM). XRD and EDX investigations conclusively established the chemical compositions of urinary calculi under investigation. The calculus from buck (sample I) had calcium oxalate monohydrate, a dominant salt phase and magnesium compound in significant amount. The calculus from bullock (sample II) had magnesium ammonium phosphate phase, with significant amount of calcium in apatite form and K⁺ ions. SEM study at higher magnification (X1000) showed bipyramidal crystals in external zones of urolith (sample I). The struvite apatite calculus showed that basic unit of structure was lamination and the laminitis appeared to be made up of fine granules and high porosity. The bio-mineralization process of calculus formation was also studied, with a view to take preventive and therapeutic measures for amelioration of urinary stone diseases in animals and humans.

Keywords: Urinary calculi, Scanning electron microscopy, X-ray diffraction, Energy dispersive X-ray spectroscopy

*Email: naveen@ivri.up.nic.in

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 233-238

 

Evaluation of water binding, seed coat permeability and germination characteristics of wheat seeds equilibrated at different relative humidities

Nabamita Chatterjee¹ and Shantha Nagarajan^2*

¹Division of Agricultural Physics and ²Nuclear Research Laboratory, Indian Agricultural Research Institute, New Delhi 110 012, India

Received 29 June 2005; revised 26 June 2006

The relative binding of seed water and seed coat membrane stability were measured in two contrasting wheat (Triticum aestivum L) varieties, HDR 77 (drought-tolerant) and HD 2009 (susceptible) using seed water sorption isotherms, electrical conductivity (EC) of leachates and desorption-absorption isotherms. Analysis of sorption isotherm at 25°C showed that the seeds of HDR 77 had significantly higher number of strong binding sites, with correspondingly greater amount of seed water as strongly bound water, as compared to HD 2009. Total number of binding sites was also higher in HDR 77 than HD 2009, which explained the better desiccation tolerance and higher capacity to bind water in seeds of HDR 77. EC of seed leachate in both varieties did not change with respect to change in equilibrium relative humidity (RH), indicating the general seed coat membrane stability of wheat seeds. However, absolute conductivity values were higher for HD 2009, showing its relatively porous seed coat membrane. Significantly lower area enclosed by the desorption-absorption isotherm loop in HDR 77, as compared to HD 2009 also indicated the greater membrane integrity of HDR 77. Germination and seedling vigour of HD 2009 were reduced when equilibrated over very low and very high RH. In contrast, germination and vigour in HDR 77 were maintained high, except at very high RH, indicating again its desiccation tolerance. Thus, the study demonstrated the relative drought tolerance of HDR 77, on the basis of seed water-binding characteristics and seed membrane stability. Seed membrane stability as measured by seed leachate conductivity or as area under dehydration-rehydration loop may be used as a preliminary screening test for drought tolerance in wheat.

Keywords: Seed water binding, Desiccation tolerance, Sorption isotherms, Triticum aestivum L, Wheat seeds

 

^*E-mail: shantha@iari.res.in

 

 

                                                    NOTES

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 239-243

 

 

Purification of a peroxidase from Solanum melongena fruit juice

S K Vernwal, R S S Yadav and K D S Yadav*

Department of Chemistry, D D U Gorakhpur University, Gorakhpur 273 009, India

Received 29 September 2005; revised 3 July 2006

Solanum melongena fruit juice contains peroxidase activity of the order of 0×125 IU/mL. A method for the 11-fold purification of the enzyme was developed. The K_m values of the peroxidase for the substrates guaiacol and hydrogen peroxide were 6×5 mM and 0×33 mM, respectively. The pH and temperature optima were 5×5 and 84°C, respectively using guaiacol as the substrate. Sodium azide and phenyl hydrazine inhibited the enzyme competitively.

Keywords: Peroxidase, Solanum melongena, fruit

 

*E-mail: kds_chemistry@rediffmail.com

 

 

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 244-246

 

  

 

Isolation of stress responsive Psb A gene from rice (Oryza sativa L.) using
differential display

 

Aruna Tyagi* and Arti Chandra

Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110 012

Received 15 January 2006; revised 12 July 2006

Differential display (DD) experiments were performed on drought-tolerant rice (Oryza sativa L.) genotype N22 to identify both upregulated and downregulated partial cDNAs with respect to moisture stress. DNA polymorphism was detected between drought-stressed and control leaf tissues on the DD gels. A partial cDNA showing differential expression, with respect to moisture stress was isolated from the gel. Northern blotting analysis was performed using this cDNA as a probe and it was observed that mRNA corresponding to this transcript was accumulated to high level in rice leaves under water deficit stress. At the DNA sequence level, the partial cDNA showed homology with psb A gene encoding for D1 protein.

Keywords: Gene, Drought stress, Rice, Oryza sativa L.

 

*E mail: at_bio@iari.res.in

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 247-250

 

 

A p53-like protein from a freshwater mollusc Lamellidens corrianus

B P Mohanty*

Biochemistry and Biotechnology Lab, Riverine Fisheries Division,
Central Inland Fisheries Research Institute,
24 Panna Lal Road, Allahabad 211 002, India

Received 27 December 2005; revised 12 June 2006

p53 is the most frequently mutated protein in human cancers and the accumulation of its high levels is a potential novel marker for malignancy. Recently, its homologues such as p63 and p73 have been reported in human, mice and fish. Environmentally induced alterations in p53 protein have been reported to contribute to pathogenesis of leukemia in soft-shell clam Mya arenaria inhabiting polluted water, suggesting that p53 proteins can also be used as pollution markers. In the present study, the presence of p53 protein or its homologues was investigated in tissues of bivalve molluscs Lamellidens corrianus that are predominant in the freshwater riverine environment and are well suited to act as test organisms for evaluation of habitat degradation. The molluscs were collected live from the river Ganga at three sampling sites viz., Kanpur, Allahabad and Varanasi and different tissues (foot, gill and mantle) were collected. Proteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). On immunoblot analysis, a 45 kDa protein (p45) was recognized by the monoclonal anti-p53 antibody in the molluscan tissues. The p45 showed immunoreactivity in all the three tissues of molluscs collected at Kanpur, in foot and gill tissues in those collected at Allahabad, and in foot tissue only, in those collected at Varanasi. Since monoclonal anti-p53 recognizes a denaturation-resistant epitope on the p53 (53 kDa) nuclear protein and does not react with other cellular proteins, the molluscan p45 is a p53-homologue or p53-like protein. Further, the differential expression of p45 in the different organs might serve as a useful biomarker that would help in establishing pollution gradient for environmental monitoring in the large aquatic ecosystems.

Keywords: p53, p53-Homologue, p53-like protein, Bivalve mollusc, Biomarker, Aquatic pollution

 

E-mail: bimal.mohanty@abdn.ac.uk; bimalmohanty12@rediffmail.com

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 251-253

 

 

Nitric oxide levels during erythroid differentiation in K562 cell line

B Küçükkaya¹, G Öztürk² and L Yalçıntepe³

¹Department of Biophysics and ²Department of Physiology, Faculty of Medicine, Maltepe University, Feyzullah Cad. No: 39, Maltepe/Istanbul, Turkey

³Department of Biophysics, Faculty of Medicine, Istanbul University, Çapa/Istanbul, Turkey

Received 20 September 2005; revised 29 June 2006

Nitric oxide (NO) is endogenous mediator of numerous physiological processes that range from regulation of cardiovascular function and neurotransmission to antipathogenic and tumoricidal responses. This study was designed to investigate the possible role of NO during erythroid differentiation in K562 erythroleukemia cells. The chronic myelogenous leukemia (K562) cell line can be triggered in culture to differentiate along the erythrocytic pathway, in response to a variety of stimulatory agents. In this study, K562 cells were induced to synthesize hemoglobin by hemin. We investigated NOx (nitrate+nitrite) levels in uninduced (control) and hemin-induced K562 cell lysates during erythroid differentiation. Our results showed that NO levels decreased significantly on fourth and sixth day both in hemin-induced and control cells; the decrease was, however, more in hemin-induced group than in control group.

Keywords:   Nitric oxide, Erythroid differentiation, Hemin, K562       cell line

¹Email: bahire2002@yahoo.com

 

 

 

 

Indian Journal of Biochemistry & Biophysics

Vol. 43, August 2006, pp. 254-257

 

 

 

Preparation of prospective plant oil derived micro-emulsion vehicles for drug delivery

Syamasri Gupta^a*, S K Sanyal^b, S Datta^b and S P Moulik^a

^aCentre for Surface Science, Department of Chemistry,
Jadavpur University, Kolkata 700 032, India

^bDepartment of Chemical Engineering, Jadavpur University, Kolkata 700032, India

Received 4 August 2005; revised 12 June 2006

Biocompatible oil-in-water (o/w) micro-emulsions can be prospective drug delivery vehicles for their capability to solubilize lipophilic (oil soluble) drugs in the dispersed oil. Plant oils are considered suitable for such a purpose. In this study, we have attempted to examine the dispersion of corn, cottonseed, clove, orange and peppermint oils, as well as isopropyl myristate (IPM) in water continuum in presence of surfactants Tween-20, Brij-30 and Brij-92 and co-surfactants ethanol (EtOH) and isopropyl alcohol (iPrOH). Both ternary (oil/surfactant/water) and psedo-ternary (oil/surfactant + co-surfactant/water) phase diagrams were constructed. The ternary systems produced larger micro-emulsion forming zones than the psedo-ternary systems. The combinations peppermint oil/iPrOH/water, IPM/iPrOH/water and 1:1 (v/v) peppermint oil + IPM/iPrOH/water were found to form fair proportion of single-phase surfactant-less micro-emulsion. The surfactant-aided ternary systems produced larger clear micro-emulsion zones, compared to pseudo-ternary systems, while the behaviour of surfactant-less systems was intermediate. The prepared systems had shelf life of 1 year and they withstood temperature variations in the range of 4-40°C.

Keywords: Drug delivery system, Micro-emulsion, Surfactant, Co-surfactant, Plant oils.

*E-mail: syamasri@yahoo.com

 

 

 

 

 

 

Announcements

 

The 13^th Meeting of TRendys in Biochemistry to be held at National Institute of Nutrition, Hyderabad during August 18-19, 2006

 

TRendys in Biochemistry is an informal national forum devoted to promote discussions on the newly emerging areas in the general field of Biochemistry and Molecular Biology. About 10-12 persons are invited to speak in these meetings on a topic of their choice, which should be more in the nature of a concept, or a thought or a breakaway idea. The presentation could also be an integrated and critical review of a new development in a well-defined area that could be related to the area of interest of the speaker, but this forum is not intended for presenting data of one's own research findings. All the invitees are expected to find their own travel money. The organizers would provide local hospitality.

        The 13^th TRendys Meeting will be held at National Institute of Nutrition (NIN), Hyderabad during Aug 18-19, 2006 under the joint sponsorship of NIN and University of Hyderabad. The participants for this meeting include Drs. Seyed E Hasnain, P Balaram, A Surolia,
J Gowrishankar, V Prakash, apart from the other core members of the TRendys. Beginning from 1994 at University of Hyderabad, these meetings are held every year and Indian Journal of Biochemistry and Biophysics (IJBB) covers the summary of the proceedings of these meetings. The report of the 12^th TRendys Meeting held at IICB, Kolkata in Dec. 2005 can be seen in June 2006 issue of IJBB.

        Scientists, research scholars and postgraduate students interested to participate in this kind of activity may please contact Prof. K Subba Rao, Department of Biochemistry, University of Hyderabad, Hyderabad 500 046. Tel: 23010451(O); 23112619®; FAX; 23010451. Cell: 9440734284 E-mail: ksrsl@uohyd.ernet.in OR Dr. M Raghunath, Deputy Director, NIN, Hyderabad-500 007., Tel: 27018909/235 (O); 27202225 ® Fax: 27019074; Cell: 9440618118.
E-mail: manchalar@yahoo.com.  Registration, which is free, to attend this meeting is mandatory.

 

  

 

ICMR AWARDS and PRIZES 2004 and 2005   The Indian Council of Medical Research invites nominations/applications from Indian Scientists for ICMR awards and prizes for the years 2004 and 2005 in various fields of Biomedical Sciences.       For details and application format, kindly log on to ICMR website:     htpp://www.icmr.nic.in ·     Last Date of receipt of nominations/applications is August 31, 2006 ·     A candidate can only apply for one award in a given year   Correspondence address: International Health Division, Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, Post Box 4911, New Delhi 110029. Telefax: 91-11-26589492, Email address: ihd@icmr.org.in

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Author Index