• Volume 30, Issue 3

      June 2005,   pages  289-405

    • Clipboard: A sword in the rosetta stone

      Imran Siddiqi

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    • Clipboard: Southward Ho!

      Partha P Majumder

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    • Commentary: On RNA interference as template immunity

      Carl T Bergstrom Rustom Antia

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    • Nikolai I Vavilov (1887–1943)

      Ilya A Zakharov

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    • Living in a physical world III. Getting up to speed

      Steven Vogel

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    • What history tells us

      Michel Morange

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      The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists – and in particular biologists – can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.

    • Detergent-resistant membranes in human erythrocytes and their connection to the membrane-skeleton

      Annarita Ciana Cesare Balduini Giampaolo Minetti

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      In cell membranes, local inhomogeneity in the lateral distribution of lipids and proteins is thought to exist in vivo in the form of lipid ‘rafts’, microdomains enriched in cholesterol and sphingolipids, and in specific classes of proteins, that appear to play specialized roles for signal transduction, cell-cell recognition, parasite or virus infection, and vesicular trafficking. These structures are operationally defined as membranes resistant to solubilization by nonionic detergents at 4°C (detergent-resistant membranes, DRMs). This definition appears to be necessary and sufficient, although additional manoeuvres, not always described with sufficient detail, may be needed to ensure isolation of DRMs, like mechanical homogenization, and changes in the pH and/or ionic strength of the solubilization medium. We show here for the human erythrocyte that the different conditions adopted may lead to the isolation of qualitatively and quantitatively different DRM fractions, thus contributing to the complexity of the notion itself of lipid raft. A significant portion of erythrocyte DRMs enriched in reported lipid raft markers, such as flotillin-1, flotillin-2 and GM1, is anchored to the spectrin membrane-skeleton via electrostatic interactions that can be disrupted by the simultaneous increase in pH and ionic strength of the solubilization medium.

    • Cloning and characterization of mouse cullin4B/E3 ubiquitin ligase

      Rachana Tripathi K Seetharama Satya Keerthi Kota Usha K Srinivas

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      Heat induced differentiation of mouse embryonal carcinoma cells PCC4 has been reported earlier. We have further characterized the phenotype of the differentiated cells and by DD-RT-PCR identified several partial cDNAs that are differentially expressed during differentiation. Nucleotide homology search revealed that the genes corresponding to some of the up-regulated partial cDNAs are indeed part of differentiation pathway. 5′ extension of an EST that has homology to one of the partial cDNAs led to the identification of mouse cullin4B. Cullin4B is coded by a separate gene and has a unique and longer amino-terminal end with a putative nuclear localization signal sequence (NLS). We have cloned, expressed and raised antibodies against the amino and carboxy-terminal halves of cullin4B. Immuno staining of differentiated PCC4 cells with N-terminal Cul4B antibody showed enhanced expression of Cul4B and its translocation into the nucleus upon differentiation. Transient transfection of a chimeric gene encoding the N-terminal part of Cul4B fused to green fluorescent protein into PCC4 cells revealed that the protein was localized in the nucleus confirming the functional significance of the putative NLS. Since cullins are involved in recognition of specific proteins for degradation, based on the evidence presented here, we hypothesize that cullin4B is probably involved in differentiation specific degradation/modification of nuclear proteins.

    • Occurrence of Cucumber mosaic virus on vanilla (Vanilla planifolia Andrews) in India

      R Madhubala V Bhadramurthy A I Bhat P S Hareesh S T Retheesh R S Bhai

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      Cucumber mosaic virus (CMV) causing mosaic, leaf distortion and stunting of vanilla (Vanilla planifolia Andrews) in India was characterized on the basis of biological and coat protein (CP) nucleotide sequence properties. In mechanical inoculation tests, the virus was found to infect members of Chenopodiaceae, Cucurbitaceae, Fabaceae and Solanaceae. Nicotiana benthamiana was found to be a suitable host for the propagation of CMV. The virus was purified from inoculated N. benthamiana plants and negatively stained purified preparations contained isometric particles of about 28 nm in diameter. The molecular weight of the viral coat protein subunits was found to be 25.0 kDa. Polyclonal antiserum was produced in New Zealand white rabbit, immunoglobulin G (IgG) was purified and conjugated with alkaline phosphatase enzyme. Double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) method was standardized for the detection of CMV infection in vanilla plants. CP gene of the virus was amplified using reverse transcriptase-polymerase chain reaction (RT-PCR), cloned and sequenced. Sequenced region contained a single open reading frame of 657 nucleotides potentially coding for 218 amino acids. Sequence analyses with other CMV isolates revealed the greatest identity with black pepper isolate of CMV (99%) and the phylogram clearly showed that CMV infecting vanilla belongs to subgroup IB. This is the first report of occurrence of CMV on V. planifolia from India.

    • Expression of a ribosome inactivating protein (curcin 2) in Jatropha curcas is induced by stress

      Wei Qin Huang Ming-Xing Xu Ying Zhang Xin-Shen Chen Fang

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      The open reading frame (ORF) encoding curcin 2 was cloned from total genomic and cDNA of Jatropha curcas leaves, which were treated by drought, temperature stress and fungal infection, by polymerase chain reaction (PCR) and reverse transcriptase (RT)-PCR amplification. The ORF has 927 bp that encodes a precursor protein of 309 amino acid residues. There are high similarities with curcin and the conserved domain of ribosome inactivating proteins (RIPs). Antiserum to curcin recognized one band of 32 kDa on Western blot of the leaves treated by temperature stresses at 4°C and 50°C and by fungal infections of Pestalotia funerea, Curvularia lunata (Walk) Boed, Gibberelle zeae (Schw.) Petch. Two bands of 32 kDa and 65 kDa were recognized on Western blot of the leaves treated by 10%–40% polyethylene glycol (PEG). In addition, the 32 kDa band is nearly the molecular weight of curcin 2. This finding suggests that the protein of 32 kDa should be related to curcin 2. The presence of this protein molecular marker under stresses may provide an experimental foundation to study the stress proteins in J. curcas.

    • Epitope mapping from real time kinetic studies – Role of cross-linked disulphides and incidental interacting regions in affinity measurements: Study with human chorionic gonadotropin and monoclonal antibodies

      Nonavinakere Seetharam Srilatha P Tamil Selvi Gundlupet Satyanarayana Murthy

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      Real time kinetic studies were used to map conformational epitopes in human chorionic gonadotropin (hCG) for two monoclonal antibodies (MAbs). The epitopes were identified in the regions (𝛼5–14 and 𝛼55–62). The association rate constant (𝑘+1) was found to be altered by chemical modification of hCG, and the ionic strength of the reaction medium. Based on these changes, we propose the presence of additional interactions away from the epitope-paratope region in the hCG-MAb reaction. We have identified such incidental interacting regions (IIRs) in hCG to be the loop region 𝛼35–47 and 𝛼60–84. The IIRs contribute significantly towards the 𝐾𝐴 of the interaction. Therefore, in a macromolecular interaction of hCG and its MAb, 𝐾𝐴 is determined not only by epitopeparatope interaction but also by the interaction of the nonepitopic-nonparatopic IIRs. However, the specificity of the interaction resides exclusively with the epitope-paratope pair.

    • Type 1 (11; 22)(q24: q12) translocation is common in Ewing's sarcoma/peripheral neuroectodermal tumour in south Indian patients

      T Parija S Shirley S Uma K R Rajalekshmy S Ayyappan T Rajkumar

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      The Ewing’s sarcoma family can present diagnostic difficulties. In the past the basis of diagnosis has been a exclusion. Identification of a specific translocation especially t(11; 22) (EWS-FLI 1 fusion gene), which is seen in nearly 85% of Ewing’s sarcoma cases can help in precise diagnosis. We have carried out a study on twenty patient samples diagnosed to have Ewing’s sarcoma/peripheral neuroectodermal tumour (PNET)/small round cell malignant tumour. The study involved RT-PCR analysis for the fusion transcript, followed by sequencing to identify the specific type of fusion. Ninety percent (18/20) of the samples tested were found to be t(11; 22) translocations involving EWS-FLI 1 genes. Sixty-one percent (11/18) were found to be type 1 fusion and seven were type 2 (39%). This is the first study in India with quantitative information about the types of EWS-FLI 1 translocations present in Ewing’s family of tumours in south Indian patients.

    • Bilaterally symmetric Fourier approximations of the skull outlines of temnospondyl amphibians and their bearing on shape comparison

      Dhurjati P Sengupta Debapriya Sengupta Parthasarathi Ghosh

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      Present work illustrates a scheme of quantitative description of the shape of the skull outlines of temnospondyl amphibians using bilaterally symmetric closed Fourier curves. Some special points have been identified on the Fourier fits of the skull outlines, which are the local maxima, or minima of the distances from the centroid of the points at the skull outline. These points denotes break in curvature of the outline and their positions can be compared to differentiate the skull shapes. The ratios of arc-lengths of the posterior and lateral outline of 58 temnospondyl skulls have been plotted to generate a triaguarity series of the skulls. This series grades different families, some of their genera and species as well as some individuals according to their posterior and lateral skull length ratios. This model while comparing different taxa, takes into account the entire arc-length of the outline of the temnospondyl skulls, and does not depend on few geometric or biological points used by earlier workers for comparing skull shapes.

    • Molecular mechanisms of HIV-1 associated neurodegeneration

      Hakan Ozdener

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      Since identification of the human immunodeficiency virus-1 (HIV-1), numerous studies suggest a link between neurological impairments, in particular dementia, with acquired immunodeficiency syndrome (AIDS) with alarming occurrence worldwide. Approximately, 60% of HIV-infected people show some form of neurological impairment, and neuropathological changes are found in 90% of autopsied cases. Approximately 30% of untreated HIV-infected persons may develop dementia. The mechanisms behind these pathological changes are still not understood. Mounting data obtained by in vivo and in vitro experiments suggest that neuronal apoptosis is a major feature of HIV associated dementia (HAD), which can occur in the absence of direct infection of neurons. The major pathway of neuronal apoptosis occurs indirectly through release of neurotoxins by activated cells in the central nervous system (CNS) involving the induction of excitotoxicity and oxidative stress. In addition a direct mechanism induced by viral proteins in the pathogenesis of HAD may also play a role. This review focuses on the molecular mechanisms of HIV-associated dementia and possible therapeutic strategies.

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