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      Volume 35, Issue 2

      June 2010,   pages  163-325

    • Clipboard: Heat shock protein 90: a capacitor or a mutator?

      Ritwick Sawarkar Renato Paro

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    • Clipboard: The small subunit of geranyl diphosphate synthase: a tool to improve aroma and flavour by metabolic engineering

      Dinesh A Nagegowda

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    • Commentary: Wolbachia and termite association: present status and future implications

      Bipinchandra K Salunke Rahul C Salunkhe Milind S Patole Yogesh S Shouche

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    • What history tells us XXI. Apoptosis and programmed cell death: when biological categories are blurred

      Michel Morange

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    • The light of the firefly under the influence of ethyl acetate

      Anurup Gohain Barua Subhash Rajbongshi

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      When a firefly is made to inhale ethyl acetate vapour, a constant glow appears after a few minutes from its abdominal lantern. This control experiment has been performed by a few workers to record the emission spectrum of the firefly. However, a time-resolved experiment performed by us on this continuous light emitted by the species Luciola praeusta Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae) reveals that it is composed of a continuous train of tiny pulses! The nature of the pulses suggests that an oscillatory chemical reaction continues in the microsecond time scale in the lantern of the anaesthetized firefly.

    • Spectrum of CREBBP mutations in Indian patients with Rubinstein–Taybi syndrome

      Neeti Sharma Avinash M Mali Sharmila A Bapat

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      Rubinstein–Taybi syndrome (RSTS), a developmental disorder comprising abnormalities that include mental retardation, an unusual facial appearance, broad thumbs and big toes is frequently associated with molecular lesions in the CREB-binding protein gene, CREBBP. The objective of the present study was to identify and analyse CREBBP mutations in Indian RSTS patients on which there are no data. Direct sequencing of CREBBP performed in 13 RSTS patients identified the three zinc fingers (CH1, CH2, CH3) and HAT domain as mutational hotspots in which ten novel pathogenic mutations were localized. Functional analysis revealed that three of these mutations affecting amino acids Glu1459, Leu1668 and Glu1724 were critical for histone acetyltransferase activity. Twenty-eight novel CREBBP single-nucleotide polymorphisms (SNPs) were also identified in the Indian population. Linkage disequilibrium studies revealed associations between

      1. SNP (rs129974/c.3836-206G > C) and mutation (p.Asp1340Ala);
      2. (rs130002) with mutation (p.Asn435Lys) and
      3. SNPs rs129974, rs130002 and SNP (c.3836-206G > C) signifying a disease affection status.

      In conclusion, the present study reports the highest detection rate of CREBBP mutations (76.9%) in RSTS patients to date, of which ten are predicted to be pathogenic and three critical for histone acetyltransferase activity. Moreover, identification of the association of CREBBP polymorphisms with disease susceptibility could be an important risk factor for the pathogenesis of RSTS.

    • Tumour bed irradiation of human tumour xenografts in a nude rat model using a common X-ray tube

      S V Tokalov W Enghardt N Abolmaali

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      Studies that investigate the radiation of human tumour xenografts require an appropriate radiation source and highly standardized conditions during radiation. This work reports on the design of a standardized irradiation device using a commercially available X-ray tube with a custom constructed lead collimator with two circular apertures and an animal bed plate, permitting synchronous irradiation of two animals. Dosimetry and the corresponding methodology for radiotherapy of human non-small cell lung cancer xenograft tumours transplanted to and growing subcutaneously on the right lower limb in a nude rat model were investigated. Procedures and results described herein prove the feasibility of use of the device, which is applicable for any investigation involving irradiation of non-tumorous and tumorous lesions in small animals.

    • Inhibition of human lung adenocarcinoma growth using survivint34a by low-dose systematic administration

      Yan Shan Chunting Wang Li Yang Li Juan Chen Hong Xin Deng Han Shuo Yang Zhimian Li Zhiyong Li Li Pan Fei Leng Yuquan Wei

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      Anti-apoptosis plays an important role in tumour formation and development. Survivin is a member of the inhibitor of apoptosis (IAP) family, which is a target for anti-cancer drug exploitation was replaced as development. We investigated the role of the homo dominant-negative mutant Survivin-T34A in suppressing human lung adenocarcinomas (A549). The anti-tumour activity of HSurvivinT34A plasmid was evaluated in the A549 cell line and nude mice bearing A549 subcutaneous tumours. Low-dose systemic administration was continuously used. The HSurvivinT34A plasmid (5 𝜇g/one) complexed with a cationic liposome (DOTAP/Chol) significantly inhibited tumour growth in our model. We observed microvessel density degradation by CD31 immunohistochemistry and apoptotic cell increase by TUNEL assay, PI staining and flow cytometric analysis in the treated group. The present findings suggest that the HSurvivinT34A plasmid complexed with a cationic liposome may provide an effective approach to inhibit the growth of human lung adenocarcinomas in vitro and in vivo.

    • Activated charcoal filter effectively reduces p-benzosemiquinone from the mainstream cigarette smoke and prevents emphysema

      Neekkan Dey Archita Das Arunava Ghosh Indu B Chatterjee

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      In this paper, we have made a comparative evaluation of the cytotoxicity and pathophysiological effects of mainstream smoke from cellulose acetate (CA)-filtered cigarettes with that of charcoal-filtered cigarettes developed in our laboratory. Previously, we had demonstrated that the mainstream smoke from an Indian CA-filtered commercial cigarette contains p-benzosemiquinone (p-BSQ), a major, highly toxic, long-lived water-soluble radical. Here, we have examined 16 brands of different CA-filtered cigarettes including Kentucky research cigarettes, and observed that mainstream smoke from all the cigarettes contains substantial amounts of p-BSQ (100–200 𝜇g/cigarette). We also show that when the CA filter is replaced by a charcoal filter, the amount of p-BSQ in the mainstream smoke is reduced by 73–80%, which is accompanied by a reduction of carbonyl formation in bovine serum albumin to the extent of 70–90%. The charcoal filter also prevented cytotoxicity in A549 cells as evidenced by MTT assay, apoptosis as evidenced by FACS analysis, TUNEL assay, overexpression of Bax, activation of p53 and caspase 3, as well as emphysematous lung damage in a guinea pig model as seen by histology and morphometric analysis. The results indicate that the charcoal filter developed in our laboratory may protect smokers from cigarette smoke-induced cytotoxity, protein modification, apoptosis and emphysema.

    • Antimicrobial, antioxidant, cytotoxicity and platelet aggregation inhibitory activity of a novel molecule isolated and characterized from mango ginger (Curcuma amada Roxb.) rhizome

      R S Policegoudra K Rehna L Jaganmohan Rao S M Aradhya

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      Mango ginger (Curcuma amada Roxb.) rhizome is used in the manufacture of pickles and other food preparations due to its unique raw mango flavour. The chloroform extract of mango ginger rhizome was subjected to antibacterial activity-guided purification by repeated silica gel column chromatography to obtain a pure compound. The structure of the isolated compound was deduced by analysing UV, IR, LC-MS and 2D-HMQCT NMR spectral data, and named it as amadaldehyde, a novel compound. It exhibited a wide range of antibacterial activity with potential bactericidal activity against several bacteria. The purified compound also exhibited antioxidant activity, cytotoxicity and platelet aggregation inhibitory activities.

    • Characterization of Helicobacter pylori adhesin thiol peroxidase (HP0390) purified from Escherichia coli

      Huyen Thi Minh Nguyen Kwang-Ho Nam Yasar Saleem Key-Sun Kim

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      The antioxidant protein, adhesin thiol peroxidase (HpTpx or HP0390), plays an important role in enabling Helicobacter pylori to survive gastric oxidative stress. The bacterium colonizes the host stomach and produces gastric cancer. However, little information is available about the biochemical characteristics of HpTpx. We expressed recombinant HpTpx in Escherichia coli, purified to homogeneity, and characterized it. The results showed that HpTpx existed in a monomeric hydrodynamic form and the enzyme fully retained its peroxidase and antioxidant activities. The catalytic reaction of the enzyme was similar to an atypical 2-cysteine peroxiredoxin (Prx). The conformation of the enzyme was observed in the presence and absence of dithiothreitol (DTT); similar to other known thiol peroxidases, conformational change was observed in HpTpx by the addition of DTT.

    • Morphological changes in the cephalic salivary glands of females and males of Apis mellifera and Scaptotrigona postica (Hymenoptera, Apidae)

      Silvana Beani Poiani Carminda Da Cruz-Landim

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      The cephalic salivary glands of some species of bees are exclusive and well developed only in Apinae. These glands were studied with light and scanning electron microscopy in workers, queens and males from the honey bee Apis mellifera, and the stingless bee Scaptotrigona postica in different life phases. The results show that the cephalic salivary glands are present in females of both the species, and in males of S. postica. Nevertheless, they are poorly developed in young males of A. mellifera. In both species, gland growth is progressive from the time of emergence to the oldest age but, in A. mellifera males, the gland degenerates with age. Scanning electron microscopy shows that the secretory units of newly emerged workers are collapsed while in older workers they are turgid. Some pits on the surface of the secretory units correspond to open intercellular spaces. The possible functions of these glands in females and males of both species are discussed.

    • Unusual allometry for sexual size dimorphism in a cichlid where males are extremely larger than females

      Kazutaka Ota Masanori Kohda Tetsu Sato

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      When males are the larger sex, a positive allometric relationship between male and female sizes is often found across populations of a single species (i.e. Rensch’s rule). This pattern is typically explained by a sexual selection pressure on males. Here, we report that the allometric relationship was negative across populations of a shell-brooding cichlid fish Lamprologus callipterus, although males are extremely larger than females. Male L. callipterus collect and defend empty snail shells in each of which a female breeds. We found that, across six populations, male and female sizes are positively correlated with not only sexual and fecundity selection indices, but also with shell sizes. Given their different reproductive behaviours, these correlations mean that males are required to be more powerful, and thus larger, to transport larger shells, while female bodies are reduced to the shell size to enable them to enter the shells. Among the three size selections (sexual selection, fecundity selection and shell size), shell size explained the allometry, suggesting that females are more strongly subject to size selection associated with shell size availability than males. However, the allometry was violated when considering an additional population where size-selection regimes of males differed from that of other populations. Therefore, sexual size allometry will be violated by body size divergence induced by multiple selection regimes.

    • Genetic and clonal diversity of the endemic ant-plant Humboldtia brunonis (Fabaceae) in the Western Ghats of India

      Suma A Dev Megha Shenoy Renee M Borges

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      Humboldtia brunonis (Fabaceae, Caesalpinioideae) is a dominant self-incompatible ant-plant or myrmecophyte, growing as an understorey tree in high-density patches. It is endemic to the biodiversity hotspot of the southern Western Ghats of India and, besides ants, harbours many endemic invertebrate taxa, such as bees that pollinate it as well as arboreal earthworms, within swollen hollow stem internodes called domatia. Using inter simple sequence repeat (ISSR) markers, three geographically separated populations were found to be multiclonal, characterized by high levels of clonal diversity. Values for the Simpson diversity index ranged between 0.764 and 0.964, and for Fager’s evenness index between 0.00 and 0.036 for neighbourhoods within populations. This myrmecophyte was found to combine sexual recruitment (66.7%) and clonal production (33.3%) as methods of reproduction. Moderate amounts of genetic diversity at the species level were observed, with 52.63% polymorphism, and moderate values of Shannon’s diversity index (0.1895) as well as of Nei’s gene diversity (0.1186). In each population, observed genotypic diversity was significantly lower than expected, indicating significant genetic structure. Neighbour-joining trees demonstrated that Agumbe, which is the most northern population examined and geographically twice as far away from the other two populations, grouped separately and with larger bootstrap support from a larger cluster consisting of the Sampaji and Solaikolli populations, which are closer to each other geographically. Some neighbourhoods within each population showed spatial genetic structure even at small spatial scales of < 5 m. A combination of clonality and short-distance pollen movement by small pollinating bees (Braunsapis puangensis) coupled with primary ballistic seed dispersal, and possible secondary seed dispersal by rodents, may contribute to spatial genetic structure at such small scales. The clonality of H. brunonis may be a factor that contributes to its dominance in Western Ghat forests where it supports a rich diversity of invertebrate fauna.

    • An insight into the sequential, structural and phylogenetic properties of banana 1-aminocyclopropane-1-carboxylate synthase 1 and study of its interaction with pyridoxal-5'-phosphate and aminoethoxyvinylglycine

      Swarup Roy Choudhury Sanjay Kumar Singh Sujit Roy Dibyendu N Sengupta

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      In banana, ethylene production for ripening is accompanied by a dramatic increase in 1-aminocyclopropane-1-carboxylate (ACC) content, transcript level of Musa acuminata ACC synthase 1 (MA-ACS1) and the enzymatic activity of ACC synthase 1 at the onset of the climacteric period. MA-ACS1 catalyses the conversion of 𝑆-adenosyl-L-methionine (SAM) to ACC, the key regulatory step in ethylene biosynthesis. Multiple sequence alignments of 1-aminocyclopropane-1-carboxylate synthase (ACS) amino acid sequences based on database searches have indicated that MA-ACS1 is a highly conserved protein across the plant kingdom. This report describes an in silico analysis to provide the first important insightful information about the sequential, structural and phylogenetic characteristics of MA-ACS1. The three-dimensional structure of MA-ACS1, constructed based on homology modelling, in combination with the available data enabled a comparative mechanistic analysis of MA-ACS1 to explain the catalytic roles of the conserved and non-conserved active site residues. We have further demonstrated that, as in apple and tomato, banana-ACS1 (MA-ACS1) forms a homodimer and a complex with cofactor pyridoxal-5′-phosphate (PLP) and inhibitor aminoethoxyvinylglycine (AVG). We have also predicted that the residues from the PLP-binding pocket, essential for ligand binding, are mostly conserved across the MA-ACS1 structure and the competitive inhibitor AVG binds at a location adjacent to PLP.

    • Aligning protein sequence and analysing substitution pattern using a class-specific matrix

      Hai Song Xu Wen Ke Ren Xiao Hui Liu Xiao Qin Li

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      Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the ‘twilight zone’ remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, all-beta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.

    • Nuclear reprogramming and epigenetic rejuvenation

      Prim B Singh Fred Zacouto

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    • The conversion of spring wheat into winter wheat and vice versa: false claim or Lamarckian inheritance?

      Xiuju Li Yongsheng Liu

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