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      Volume 32, Issue 6

      September 2007,   pages  1041-1220

    • Clipboard: Genes and proteins: Dogmas in decline

      Stuart A Newman Ramray Bhat

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    • Commentary: Understanding Anopheles and Plasmodium interactions: lessons from the real world

      Kaustubh Gokhale Milind Patole Yogesh S Shouche

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    • Commentary: Prediction and validation of microRNA targets in animal genomes

      Grace Martin Katherine Schouest Prasad Kovvuru Charles Spillane

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    • Commentary: Circadian rhythm in the pink–orange bread mould Neurospora crassa: for what?

      Ramesh Maheshwari

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    • Peanut lectin crystallography and macromolecular structural studies in India

      M Vijayan

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    • Living in a physical world XII. Keeping up upward and down downward

      Steven Vogel

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    • What history tells us X. Fifty years ago: the beginnings of exobiology

      Michel Morange

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    • Multiplicity of carbohydrate-binding sites in 𝛽-prism fold lectins: occurrence and possible evolutionary implications

      Alok Sharma Divya Chandran Desh D Singh M Vijayan

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      The 𝛽-prism II fold lectins of known structure, all from monocots, invariably have three carbohydrate-binding sites in each subunit/domain. Until recently, 𝛽-prism I fold lectins of known structure were all from dicots and they exhibited one carbohydrate-binding site per subunit/domain. However, the recently determined structure of the 𝛽-prism fold I lectin from banana, a monocot, has two very similar carbohydrate-binding sites. This prompted a detailed analysis of all the sequences appropriate for two-lectin folds and which carry one or more relevant carbohydrate-binding motifs. The very recent observation of a 𝛽-prism I fold lectin, griffithsin, with three binding sites in each domain further confirmed the need for such an analysis. The analysis demonstrates substantial diversity in the number of binding sites unrelated to the taxonomical position of the plant source. However, the number of binding sites and the symmetry within the sequence exhibit reasonable correlation. The distribution of the two families of 𝛽-prism fold lectins among plants and the number of binding sites in them, appear to suggest that both of them arose through successive gene duplication, fusion and divergent evolution of the same primitive carbohydrate-binding motif involving a Greek key. Analysis with sequences in individual Greek keys as independent units lends further support to this conclusion. It would seem that the preponderance of three carbohydrate-binding sites per domain in monocot lectins, particularly those with the 𝛽-prism II fold, is related to the role of plant lectins in defence.

    • Human cytomegalovirus UL145 gene is highly conserved among clinical strains

      Zhengrong Sun Ying Lu Qiang Ruan Yaohua Ji Rong He Ying Qi Yanping Ma Yujing Huang

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      Human cytomegalovirus (HCMV), a ubiquitous human pathogen, is the leading cause of birth defects in newborns. A region (referred to as UL/b′) present in the Toledo strain of HCMV and low-passage clinical isolates) contains 22 additional genes, which are absent in the highly passaged laboratory strain AD169. One of these genes, UL145 open reading frame (ORF), is located between the highly variable genes UL144 and UL146. To assess the structure of the UL145 gene, the UL145 ORF was amplified by PCR and sequenced from 16 low-passage clinical isolates and 15 non-passage strains from suspected congenitally infected infants. Nine UL145 sequences previously published in the GenBank were used for sequence comparison. The identities of the gene and the similarities of its putative protein among all strains were 95.9–100% and 96.6–100%, respectively. The post-translational modification motifs of the UL145 putative protein in clinical strains were conserved, comprising the protein kinase C phosphorylation motif (PKC) and casein kinase II phosphorylation site (CK-II). We conclude that the structure of the UL145 gene and its putative protein are relatively conserved among clinical strains, irrespective of whether the strains come from patients with different manifestations, from different areas of the world, or were passaged or not in human embryonic lung fibroblast (HELF) cells.

    • Productivity and biochemical properties of green tea in response to full-length and functional fragments of HpaGXooc, a harpin protein from the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

      Xiaojing Wu Tingquan Wu Juying Long Qian Yin Yong Zhang Lei Chen Ruoxue Liu Tongchun Gao Hansong Dong

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      Harpin proteins from plant pathogenic bacteria can stimulate hypersensitive cell death (HCD), drought tolerance, defence responses against pathogens and insects in plants, as well as enhance plant growth. Recently, we identified nine functional fragments of HpaGXooc, a harpin protein from Xanthomonas oryzae pv. oryzicola, the pathogen that causes bacterial leaf streak in rice. Fragments HpaG1–94, HpaG10–42, and HpaG62–138, which contain the HpaGXooc regions of the amino acid sequence as indicated by the number spans, exceed the parent protein in promoting growth, pathogen defence and HCD in plants. Here we report improved productivity and biochemical properties of green tea (Camellia sinensis) in response to the fragments tested in comparison with HpaGXooc and an inactive protein control. Field tests suggested that the four proteins markedly increased the growth and yield of green tea, and increased the leaf content of tea catechols, a group of compounds that have relevance in the prevention and treatment of human diseases. In particular, HpaG1–94 was more active than HpaGXooc in expediting the growth of juvenile buds and leaves used as green tea material and increased the catechol content of processed teas. When tea shrubs were treated with HpaHXooc and HpaG1–94 compared with a control, green tea yields were over 55% and 39% greater, and leaf catechols were increased by more than 64% and 72%, respectively. The expression of three homologues of the expansin genes, which regulate plant cell growth, and the CsCHS gene encoding a tea chalcone synthase, which critically regulates the biosynthesis of catechols, were induced in germinal leaves of tea plants following treatment with HpaG1–94 or HpaGXooc. Higher levels of gene expression were induced by the application of HpaG1–94 than HpaGXooc. Our results suggest that the harpin protein, especially the functional fragment HpaG1–94, can be used to effectively increase the yield and improve the biochemical properties of green tea, a drink with medicinal properties.

    • Cullin4B/E3-ubiquitin ligase negatively regulates 𝛽-catenin

      Rachana Tripathi Satya Keerthi Kota Usha K Srinivas

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      𝛽-catenin is the key transducer of Wingless-type MMTV integration site family member (Wnt) signalling, upregulation of which is the cause of cancer of the colon and other tissues. In the absence of Wnt signals, 𝛽-catenin is targeted to ubiquitin–proteasome-mediated degradation. Here we present the functional characterization of E3-ubiquitin ligase encoded by cul4B. RNAi-mediated knock-down of Cul4B in a mouse cell line C3H T10 (1/2) results in an increase in 𝛽-catenin levels. Loss-of-function mutation in Drosophila cul4 also shows increased 𝛽-catenin/Armadillo levels in developing embryos and displays a characteristic naked-cuticle phenotype. Immunoprecipitation experiments suggest that Cul4B and 𝛽-catenin are part of a signal complex in Drosophila, mouse and human. These preliminary results suggest a conserved role for Cul4B in the regulation of 𝛽-catenin levels.

    • Age-dependent increase in green autofluorescence of blood erythrocytes

      Sanjay Khandelwal Rajiv K Saxena

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      Green auto-fluorescence (GAF) of different age groups of mouse blood erythrocytes was determined by using a double in vivo biotinylation (DIB) technique that enables delineation of circulating erythrocytes of different age groups. A significant increase in GAF was seen for erythrocytes of old age group (age in circulation > 40 days) as compared to young erythrocytes (age < 15 days). Erythrocytes are removed from blood circulation by macrophages in the reticulo-endothelial system and depletion of macrophages results in an increased proportion of aged erythrocytes in the blood. When mice were depleted of macrophages for 7 days by administration of clodronate loaded liposomes, the overall GAF of erythrocytes increased significantly and this increase could be ascribed to an increase in GAF of the oldest population of erythrocytes. Using the DIB technique, the GAF of a cohort of blood erythrocyte generated during a 5 day window was tracked in vivo. GAF of the defined cohort of erythrocytes remained low till 40 days of age in circulation and then increased steeply till the end of the life span of erythrocytes. Taken together our results provide evidence for an age dependent increase in the GAF of blood erythrocytes that is accentuated by depletion of macrophages. Kinetics of changes in GAF of circulating erythrocytes with age has also been defined.

    • Spectrin interactions with globin chains in the presence of phosphate metabolites and hydrogen peroxide: implications for thalassaemia

      Poppy Datta Sudipa Chakrabarty Amit Chakrabarty Abhijit Chakrabarti

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      We have shown the differential interactions of the erythroid skeletal protein spectrin with the globin subunits of adult haemoglobin (HbA); these indicate a preference for 𝛼-globin over that for 𝛽-globin and intact HbA in an adenosine 5′-triphosphate (ATP)-dependent manner. The presence of Mg/ATP led to an appreciable decrease in the binding affinity of the 𝛼-globin chain to spectrin and the overall yield of globin–spectrin cross-linked complexes formed in the presence of hydrogen peroxide. Similar effects were also seen in the presence of 2-,3-diphosphoglycerate (2,3 DPG), the other important phosphate metabolite of erythrocytes. The binding affinity and yield of cross-linked high molecular weight complexes (HMWCs) formed under oxidative conditions were significantly higher in 𝛼-globin compared with intact haemoglobin, HbA and the 𝛽-globin chain. The results of this study indicate a possible correlation of the preferential spectrin binding of the 𝛼-globin chain over that of the 𝛽-globin in the haemoglobin disorder 𝛽-thalassaemia.

    • An Na+/H+ antiporter gene from wheat plays an important role in stress tolerance

      Jia Ning Yu Jian Huang Zi Ning Wang Jin Song Zhang Shou Yi Chen

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      A vacuole Na+/H+ antiporter gene TaNHX2 was obtained by screening the wheat cDNA library and by the 5′-RACE method. The expression of TaNHX2 was induced in roots and leaves by treatment with NaCl, polyethylene glycol (PEG), cold and abscisic acid (ABA). When expressed in a yeast mutant (𝛥nhx1), TaNHX2 suppressed the salt sensitivity of the mutant, which was deficient in vacuolar Na+/H+ antiporter, and caused partial recovery of growth of 𝛥nhx1 in NaCl and LiCl media. The survival rate of yeast cells was improved by overexpressing the TaNHX2 gene under NaCl, KCl, sorbitol and freezing stresses when compared with the control. The results imply that TaNHX2 might play an important role in salt and osmotic stress tolerance in plant cells.

    • Link between the early calcium deposition in placenta and nanobaсterial-like infection

      R M Agababov T N Abashina N E Suzina M B Vainshtein P M Schwartsburd

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      The placenta is a vitally important organ in the regulation of embryonic development. That is why extensive calcium deposition [also named as pathological placental calcification (PPC)] could have serious negative consequences for the adequate growth of embryos. The nature and mechanism of PPC development has not been defined as yet. In the present investigation, we have tested the hypothesis that the molecular basis of PPC development consists of nanobacteria-induced calcification in infected female placenta. Electron microscopy findings support this hypothesis. The initial stage of micro-calcification may originate from the external surface of individual nanobacteria-like particles found mainly in placental extracellular matrix, where initial calcium deposition occurs as a needle surface deposition or as an amorphous-like surface precipitate. Further calcific propagation in placenta takes place in the newly formed macro-cavities, which are characterized by low electron density, possibly reflecting its liquid content around calcium deposition. The micro-cavities contain free nanobacterial-like particles, which may relate to atypical Gram-negative bacteria but not to apoptotic bodies by morphological characters and DNA/RNA distribution. We hypothesize that the increased placental calcification might be caused, at least in part, by nanobacterial infection.

    • In silico comparison of bacterial strains using mutual information

      D Swati

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      Fast-sequencing throughput methods have increased the number of completely sequenced bacterial genomes to about 400 by December 2006, with the number increasing rapidly. These include several strains. In silico methods of comparative genomics are of use in categorizing and phylogenetically sorting these bacteria. Various word-based tools have been used for quantifying the similarities and differences between entire genomes. The simple di-nucleotide frequency comparison, codon specificity and k-mer repeat detection are among some of the well-known methods.

      In this paper, we show that the Mutual Information function, which is a measure of correlations and a concept from Information Theory, is very effective in determining the similarities and differences among genome sequences of various strains of bacteria such as the plant pathogen Xylella fastidiosa, marine Cyanobacteria Prochlorococcus marinus or animal and human pathogens such as species of Ehrlichia and Legionella. The short-range three-base periodicity, small sequence repeats and long-range correlations taken together constitute a genome signature that can be used as a technique for identifying new bacterial strains with the help of strains already catalogued in the database.

      There have been several applications of using the Mutual Information function as a measure of correlations in genomics but this is the first whole genome analysis done to detect strain similarities and differences.

    • Effect of the human follicle-stimulating hormone-binding inhibitor and its N-terminal fragment on follicle-stimulating hormone-induced progesterone secretion by granulosa cells in vitro

      Perinaaz R Wadia Smita D Mahale Tarala D Nandedkar

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      Intrafollicular factors play an important role in folliculogenesis. The follicle-stimulating hormone (FSH)-binding inhibitor (FSHBI), purified by our laboratory from human ovarian follicular fluid, has been shown to suppress ovulation and induce follicular atresia/apoptosis in mice as well as impair fertility in marmosets, the new world monkeys. The octapeptide, a peptide corresponding to the N-terminal region of human FSHBI (hFSHBI), has been synthesized and also shows FSHBI activity in vitro. In the present study, we have attempted to identify the mechanism of action of the peptide in granulosa cell cultures. Rat granulosa cell cultures were treated with varying concentrations of the octapeptide or partially purified hFSHBI (gel chromatography fraction hGF2) in the presence or absence of human FSH (hFSH) and the amount of progesterone (P4) secreted in the culture supernatants after 3 h/48 h was estimated. Both hGF2 and the octapeptide failed to alter basal levels as well as 8-bromo cAMP-induced P4 production, while FSH-induced P4 secretion was inhibited in a dose-dependent manner. These studies reveal that the octapeptide, a fragment of FSHBI, and the native protein have similar activity in vitro and both compounds alter FSH action at the receptor level upstream of cAMP formation.

    • Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate

      Dhirendra K Simanshu Sagar Chittori H S Savithri M R N Murthy

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      In Escherichia coli and Salmonella typhimurium, L-threonine is cleaved non-oxidatively to propionate via 2-ketobutyrate by biodegradative threonine deaminase, 2-ketobutyrate formate-lyase (or pyruvate formate-lyase), phosphotransacetylase and propionate kinase. In the anaerobic condition, L-threonine is converted to the energy-rich keto acid and this is subsequently catabolised to produce ATP via substrate-level phosphorylation, providing a source of energy to the cells. Most of the enzymes involved in the degradation of L-threonine to propionate are encoded by the anaerobically regulated tdc operon. In the recent past, extensive structural and biochemical studies have been carried out on these enzymes by various groups. Besides detailed structural and functional insights, these studies have also shown the similarities and differences between the other related enzymes present in the metabolic network. In this paper, we review the structural and biochemical studies carried out on these enzymes.

    • Sphingosine 1-phosphate as a novel immune regulator of dendritic cells

      Angelo Martino

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      Although originally described as an intracellular second messenger, sphingosine 1-phosphate (S1P) has recently been shown to be involved in several physiological and pathological functions as an extracellular mediator. S1P receptors are widely expressed and thought to regulate important functions in cell signalling. Recently, the role of S1P on the immune system has evoked great interest. In particular, several aspects of the effects on antigen-presenting cells (APCs) as dendritic cells (DC) in mice and humans have been reported. In this review, we focus on the role played by S1P on the DC system and its effects in immune-related pathological states.

    • Maternally derived egg yolk steroid hormones and sex determination: Review of a paradox in reptiles

      Rajkumar S Radder

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      During the past decade, maternally derived steroid hormones in the egg yolk of oviparous vertebrates have been the focus of attention for their possible role in sex determination and hence, information on the consequences of maternal egg yolk steroids on sex determination has accumulated rapidly in reptiles and birds. Until recently, the observations were dominated by the idea that yolk steroids of maternal origin play an important role in sex determination of oviparous vertebrates. However, more recent studies have cast significant doubt on the above conclusion. These studies suggest instead that steroids may be present in the yolk simply as the byproduct of passive uptake during yolk formation or observed correlations might reflect embryonically produced rather than maternally derived steroids. Thus, the objective of the present review is

      1. to provide an overview of such paradoxical observations on the role of maternal yolk steroids in sex determination of reptiles,
      2. to identify and provide brief explanations for the observed paradoxical results, and
      3. to provide some future research directions.
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