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      Volume 34, Issue 2

      June 2009,   pages  161-331

    • Clipboard: mGluR5 is a central regulator of synaptic function and plasticity in the developing mouse barrel cortex

      Liisa A Tremere Raphael Pinaud

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    • Clipboard: Snakes and ladders: the ups and downs of animal segmentation

      Ramray Bhat Stuart A Newman

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    • Commentary: Insufficient regulatory supervision prior to release of genetically modified crops for commercial cultivation in India

      Pushpa Mittra Bhargava

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    • Commentary: Green fluorescent protein: a molecular lantern that illuminates the cellular interior

      Sourav Haldar Amitabha Chattopadhyay

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    • Commentary: Why Darwin rejected intelligent design

      Frank J Sulloway

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    • The history of vitamin C research in India

      I B Chatterjee

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    • What history tells us XVII. Conrad Waddington and The nature of life

      Michel Morange

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    • Inactivation of a transgene due to transposition of insertion sequence (IS136) of Agrobacterium tumefaciens

      Preeti Rawat Sanjeev Kumar Deepak Pental Pradeep Kumar Burma

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      Agrobacterium strains harbour insertion sequences, which are known to transpose into genomes as well as into Ti plasmids. In this study we report the inactivation of a transgene due to transposition of the A. tumefaciens insertion sequence IS136. The transposition was discovered following transformation of plant tissues, although the fidelity of the binary vector was confirmed following transformation into Agrobacterium. Such transpositions are rare but can occur and it is thus important to check the fidelity of the binary vector at different times of Agrobacterium growth in order to avoid failure in achieving transgene expression.

    • Functional role of EF-hands 3 and 4 in membrane-binding of KChIP1

      Yan-Shun Liao Ku-Chung Chen Long-Sen Chang

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      The aim of the present study is to explore whether membrane targeting of K+ channel-interacting protein 1 (KChIP1) is associated with its EF-hand motifs and varies with specific phospholipids. Truncated KChIP1, in which the EF-hands 3 and 4 were deleted, retained the 𝛼-helix structure, indicating that the N-terminal half of KChIP1 could fold appropriately. Compared with wild-type KChIP1, truncated KChIP1 exhibited lower lipid-binding capability. Compared with wild-type KChIP1, increasing membrane permeability by the use of digitonin caused a marked loss of truncated KChIP1, suggesting that intact EF-hands 3 and 4 were crucial for the anchorage of KChIP1 on membrane. KChIP1 showed a higher binding capability with phosphatidylserine (PS) than truncated KChIP1. Unlike that of truncated KChIP1, the binding of wild-type KChIP1 with membrane was enhanced by increasing the PS content. Moreover, the binding of KChIP1 with phospholipid vesicles induced a change in the structure of KChIP1 in the presence of PS. Taken together, our data suggest that EF-hands 3 and 4 of KChIP1 are functionally involved in a specific association with PS on the membrane.

    • Identification of binding peptides of the ADAM15 disintegrin domain using phage display

      Jing Wu Min-Chen Wu Lian-Fen Zhang Jian-Yong Lei Lei Feng Jian Jin

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      ADAM15 plays an important role in tumour development by interacting with integrins. In this study, we investigated the target peptides of the ADAM15 disintegrin domain. First, we successfully produced the recombinant human ADAM15 disintegrin domain (RADD) that could inhibit melanoma cell adhesion by using Escherichia coli. Second, four specific binding peptides (peptides A, B, C, and D) were selected using a phage display 12-mer peptide library. The screening protocol involved 4 rounds of positive panning on RADD and 2 rounds of subtractive selection with streptavidin. By using the BLAST software and a relevant protein database, integrin 𝛼v𝛽3 was found to be homologous to peptide A. Synthetic peptide A had a highly inhibitory effect on RADD–integrin 𝛼v𝛽3 binding. The results demonstrate the potential application of short peptides for disrupting high-affinity ADAM–integrin interactions.

    • Selection of scFvs specific for the HepG2 cell line using ribosome display

      Lei Zhou Wei-Ping Mao Juan Fen Hong-Yun Liu Chuan-Jing Wei Wen-Xiu Li Feng-Yun Zhou

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      The aim of this study was to construct a ribosome display library of single chain variable fragments (scFvs) associated with hepatocarcinoma and screen such a library for hepatocarcinoma-binding scFvs. mRNA was isolated from the spleens of mice immunized with hepatocellular carcinoma cell line HepG2. Heavy and k chain genes (VH and k) were amplified separately by RT-PCR, and an anti-HepG2 VH/k chain ribosome display library was constructed by assembling VH and k into the VH/k chain with a specially constructed linker by SOE-PCR. The VH/k chain library was transcribed and translated in vitro using a rabbit reticulocyte lysate system. In order to isolate specific scFvs, recognizing HepG2 negative selection on a normal hepatocyte line WRL-68 was carried out before three rounds of positive selection on HepG2. After three rounds of panning, cell enzyme-linked immunosorbent assay (ELISA) showed that one of the scFvs had high affinity for the HepG2 cell and lower affinity for the WRL-68 cell. In this study, we successfully constructed a native ribosome display library. Such a library would prove useful for direct intact cell panning using ribosome display technology. The selected scFv had a potential value for hepatocarcinoma treatment.

    • Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L.

      Meng-Jun Li Ai-Qin Li Han Xia Chuan-Zhi Zhao Chang-Sheng Li Shu-Bo Wan Yu-Ping Bi Xing-Jun Wang

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      The cultivated peanut is a valuable source of dietary oil and ranks fifth among the world oil crops. Plant fatty acid biosynthesis is catalysed by type II fatty acid synthase (FAS) in plastids and mitochondria. By constructing a full-length cDNA library derived from immature peanut seeds and homology-based cloning, candidate genes of acyl carrier protein (ACP), malonyl-CoA:ACP transacylase, 𝛽-ketoacyl-ACP synthase (I, II, III), 𝛽-ketoacyl-ACP reductase, 𝛽-hydroxyacyl-ACP dehydrase and enoyl-ACP reductase were isolated. Sequence alignments revealed that primary structures of type II FAS enzymes were highly conserved in higher plants and the catalytic residues were strictly conserved in Escherichia coli and higher plants. Homologue numbers of each type II FAS gene expressing in developing peanut seeds varied from 1 in KASII, KASIII and HD to 5 in ENR. The number of single-nucleotide polymorphisms (SNPs) was quite different in each gene. Peanut type II FAS genes were predicted to target plastids except ACP2 and ACP3. The results suggested that peanut may contain two type II FAS systems in plastids and mitochondria. The type II FAS enzymes in higher plants may have similar functions as those in E. coli.

    • Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes

      Chandrasekaran Sivakamasundari Ramakrishnan Nagaraj

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      We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from –1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide–membrane interactions.

    • Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

      Irfan A Ghazi Prem S Srivastava Vivek Dalal Kishor Gaikwad Ashok K Singh Tilak R Sharma Nagendra K Singh Trilochan Mohapatra

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      Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

    • Variations in morphological and life-history traits under extreme temperatures in Drosophila ananassae

      Seema Sisodia B N Singh

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      Using half-sib analysis, we analysed the consequences of extreme rearing temperatures on genetic and phenotypic variations in the morphological and life-history traits of Drosophila ananassae. Paternal half-sib covariance contains a relatively small proportion of the epistatic variance and lacks the dominance variance and variance due to maternal effect, which provides more reliable estimates of additive genetic variance. Experiments were performed on a mass culture population of D. ananassae collected from Kanniyakumari (India). Two extremely stressful temperatures (18°C and 32°C) and one standard temperature (25°C) were used to examine the effect of stressful and non-stressful environments on the morphological and life-history traits in males and females. Mean values of various morphological traits differed significantly among different temperature regimens in both males and females. Rearing at 18°C and 32°C resulted in decreased thorax length, wing-to-thorax (w/t) ratio, sternopleural bristle number, ovariole number, sex comb-tooth number and testis length. Phenotypic variances increased under stressful temperatures in comparison with non-stressful temperatures. Heritability and evolvability based on among-sires (males), among-dams (females), and the sum of the two components (sire + dam) showed higher values at both the stressful temperatures than at the non-stressful temperature. These differences reflect changes in additive genetic variance. Viability was greater at the high than the low extreme temperature. As viability is an indicator of stress, we can assume that stress was greater at 18°C than at 32°C in D. ananassae. The genetic variations for all the quantitative and life-history traits were higher at low temperature. Variation in sexual traits was more pronounced as compared with other morphometric traits, which shows that sexual traits are more prone to thermal stress. Our results agree with the hypothesis that genetic variation is increased in stressful environments.

    • Effect of directional selection for body size on fluctuating asymmetry in certain morphological traits in Drosophila ananassae

      C Vishalakshi B N Singh

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      Variation in the subtle differences between the right and left sides of bilateral characters or fluctuating asymmetry (FA) has been considered as an indicator of an organism’s ability to cope with genetic and environmental stresses during development. However, due to inconsistency in the results of empirical studies, the relationship between FA and stress has been the subject of intense debate. In this study, we investigated whether stress caused by artificial bidirectional selection for body size has any effect on the levels of FA of different morphological traits in Drosophila ananassae. The realised heritability (h2) was higher in low-line females and high-line males, which suggests an asymmetrical response to selection for body size. Further, the levels of FA were compared across 10 generations of selection in different selection lines in both sexes for sternopleural bristle number, wing length, wing-to-thorax ratio, sex combtooth number and ovariole number. The levels of FA differed significantly among generations and selection lines but did not change markedly with directional selection. However, the levels of FA were higher in the G10 generation (at the end of selection) than G0 (at the start of selection) but lower than the G5 generation in different selection lines, suggesting that the levels of FA are not affected by the inbreeding generated during the course of selection. Also, the levels of FA in the hybrids of high and low lines were significantly lower than the parental selection lines, suggesting that FA is influenced by hybridisation. These results are discussed in the framework of the literature available on FA and its relationship with stress.

    • Bioluminescence emissions of the firefly Luciola praeusta Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae)

      A Gohain Barua S Hazarika N M Saikia G D Baruah

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      We recorded the in vivo emission and time-resolved spectra of the firefly Luciola praeusta Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae). The emission spectrum shows that the full width at half maximum (FWHM) value for this particular species is 55 nm, which is significantly narrower than the in vivo half-widths reported till now. The time-resolved spectrum reveals that a flash of about 100 ms duration is, in fact, composed of a number of microsecond pulses. This suggests that the speed of the enzyme-catalysed chemiluminescence reaction in the firefly for the emission of light is much faster than was previously believed.

    • Rapid aggregation and assembly in aqueous solution of A𝛽 (25-35) peptide

      Lia Millucci Roberto Raggiaschi Davide Franceschini Georg Terstappen Annalisa Santucci

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      The highly toxic A𝛽(25-35) is a peculiar peptide that differs from all the other commonly studied 𝛽-amyloid peptides because of its extremely rapid aggregation properties and enhanced neurotoxicity. We investigated A𝛽(25-35) aggregation in H2O at pH 3.0 and at pH 7.4 by means of in-solution analyses. Adopting UV spectroscopy, Congo red spectrophotometry and thioflavin T fluorimetry, we were able to quantify, in water, the very fast assembling time necessary for A𝛽(25-35) to form stable insoluble aggregates and their ability to seed or not seed fibril growth. Our quantitative results, which confirm a very rapid assembly leading to stable insoluble aggregates of A𝛽(25-35) only when incubated at pH 7.4, might be helpful for designing novel aggregation inhibitors and to shed light on the in vivo environment in which fibril formation takes place.

    • Retinoblastoma protein: a central processing unit

      M Poznic

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      The retinoblastoma protein (pRb) is one of the key cell-cycle regulating proteins and its inactivation leads to neoplastic transformation and carcinogenesis. This protein regulates critical G1-to-S phase transition through interaction with the E2F family of cell-cycle transcription factors repressing transcription of genes required for this cell-cycle check-point transition. Its activity is regulated through network sensing intracellular and extracellular signals which block or permit phosphorylation (inactivation) of the Rb protein. Mechanisms of Rb-dependent cell-cycle control have been widely studied over the past couple of decades. However, recently it was found that pRb also regulates apoptosis through the same interaction with E2F transcription factors and that Rb–E2F complexes play a role in regulating the transcription of genes involved in differentiation and development.

    • MMP-1 polymorphism and its relationship to pathological processes

      P A Arakaki M R Marques M C L G Santos

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      Matrix metalloproteinases (MMPs) are a family of zinc (Zn)-dependent endopeptidases that are collectively capable of cleaving virtually all extracellular matrix (ECM) substrates and play an important role in diverse physiological and pathological processes. The activity of MMPs is regulated at multiple levels. The transcriptional regulation of MMP appears to represent the key step in MMP regulation. There are diverse types of MMPs that differ structural and functionally. MMP-1 is the most ubiquitously expressed interstitial collagenase and has a prominent role in initial cleavage of the ECM. The level of MMP-1 expression can be influenced by different single-nucleotide polymorphisms (SNPs) in the promoter region. A functional polymorphism at position –1607 has been shown to alter the transcriptional activity of MMP-1 and was associated with diverse pathological processes. The aim of our review was to discuss some topics related to MMP in physiological and pathological processes, with a focus on MMP-1 polymorphism.

    • Living with urea stress

      Laishram R Singh Tanveer Ali Dar Faizan Ahmad

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      Intracellular organic osmolytes are present in certain organisms adapted to harsh environments. These osmolytes protect intracellular macromolecules against denaturing environmental stress. In contrast to the usually benign effects of most organic osmolytes, the waste product urea is a well-known perturbant of macromolecules. Although urea is a perturbing solute which inhibits enzyme activity and stability, it is employed by some species as a major osmolyte. The answer to this paradox was believed to be the discovery of protective osmolytes (methylamines). We review the current state of knowledge on the various ways of counteracting the harmful effects of urea in nature and the mechanisms for this. This review ends with the mechanistic idea that cellular salt (KCl/NaCl) plays a crucial role in counteracting the effects of urea, either by inducing required chaperones or methylamines, or by thermodynamic interactions with urea-destabilised proteins. We also propose future opportunities and challenges in the field.

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