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      Volume 37, Issue 4

      September 2012,   pages  579-806

    • Editorial: Green-carding the referee, and Haldane's spell

      Durgadas P Kasbekar

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    • Commentary: Monotremes and marsupials: Comparative models to better understand the function of milk

      Sanjana Kuruppath Swathi Bisana Julie A Sharp Christophe Lefevre Satish Kumar Kevin R Nicholas

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    • Making sense of ocean biota: How evolution and biodiversity of land organisms differ from that of the plankton

      Victor Smetacek

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      The oceans cover 70% of the planet’s surface, and their planktonic inhabitants generate about half the global primary production, thereby playing a key role in modulating planetary climate via the carbon cycle. The ocean biota have been under scientific scrutiny for well over a century, and yet our understanding of the processes driving natural selection in the pelagic environment – the open water inhabited by drifting plankton and free-swimming nekton – is still quite vague. Because of the fundamental differences in the physical environment, pelagic ecosystems function differently from the familiar terrestrial ecosystems of which we are a part. Natural selection creates biodiversity but understanding how this quality control of randommutations operates in the oceans − which traits are selected for under what circumstances and by which environmental factors, whether bottom-up or top-down − is currently a major challenge. Rapid advances in genomics are providing information, particularly in the prokaryotic realm, pertaining not only to the biodiversity inventory but also functional groups. This essay is dedicated to the poorly understood tribes of planktonic protists (unicellular eukaryotes) that feed the ocean’s animals and continue to run the elemental cycles of our planet. It is an attempt at developing a conceptually coherent framework to understand the course of evolution by natural selection in the plankton and contrast it with the better-known terrestrial realm. I argue that organism interactions, in particular co-evolution between predators and prey (the arms race), play a central role in driving evolution in the pelagic realm. Understanding the evolutionary forces shaping ocean biota is a prerequisite for harnessing plankton for human purposes and also for protecting the oceanic ecosystems currently under severe stress from anthropogenic pressures.

    • What history tells us XXVIII. What is really new in the current evolutionary theory of cancer?

      Michel Morange

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    • Morse potential in DNA molecule – An experiment proposal

      Slobodan Zdravković Miljko V Satarić

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      We rely on the helicoidal Peyrard-Bishop model for DNA dynamics. Interaction between nucleotides at a same site belonging to different strands is modelled by a Morse potential energy. This potential depends on two parameters that are different for AT and CG pairs, which is a possible source for inhomogeneity. It was shown recently (Zdravković and Satarić 2011) that certain values of these parameters bring about a negligible influence of inhomogeneity on the solitonic dynamics. We propose an experiment that should be carried out in order to determine the values of both of these parameters.

    • Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: A proteome-level study

      Bini Ramachandran Kanak Lata Dikshit Kuppamuthu Dharmalingam

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      Vitreoscilla haemoglobin (VHb) expression in heterologous host was shown to enhance growth and oxygen utilization capabilities under oxygen-limited conditions. The exact mechanism by which VHb enhances the oxygen utilization under oxygen-limiting conditions is still unknown. In order to understand the role of VHb in promoting oxygen utilization, changes in the total protein profile of E. coli expressing the vgb gene under its native promoter was analysed. Two-dimensional difference gel electrophoresis (2D DIGE) was employed to quantify the differentially expressed proteins under oxygen-limiting conditions. Overexpression of proteins involved in aerobic metabolic pathways and suppression of proteins involved in non-oxidative metabolic pathways shown in this study indicates that the cells expressing VHb prefer aerobic metabolic pathways even under oxygen limitation. Under these conditions, the expression levels of proteins involved in central metabolic pathways, cellular adaptation and cell division were also found to be altered. These results imply that Vitreoscilla haemoglobin expression alters aerobic metabolism specifically, in addition to altering proteins involved in other pathways, the significance of which is not clear as of now.

    • Changes in membrane lipids and carotenoids during light acclimation in a marine cyanobacterium Synechococcus sp.

      Olimpio Montero Alberto Sánchez-Guijo Luis M Lubián Gonzalo Martínez-Rodríguez

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      Time course of carotenoid and membrane lipid variation during high light (HL) acclimation (about 85 𝜇mol m−2 s−1), after transfer from low light (LL) (5–10 μmol m−2 s−1), was determined in a marine Synechococcus strain. High-performance liquid chromatography (HPLC) coupled to diode array detector (DAD) or electrospray ionization mass spectrometry (ESI-MS) was used for compound separation and detection. Myxoxanthophyll rose within a time interval of 8 h to 24 h after the onset of exposure to HL. 𝛽-carotene content started to decrease after 4 h of the onset of exposure to HL. Zeaxanthin content rose with exposure to HL, but it was only significant after 24 h of exposure. Carotenoid changes are in agreement with a coordinated activity of the enzymes of the myxoxanthophyll biosynthetic pathway, with no rate-limiting intermediate steps. Lipid analysis showed all species with a C18:3/C16:0 composition increased their content, the changes of PG(18:3/16:0) and MGDG(18:3/16:0) being primarily significant. Major lipid changes were also found to occur within 24 h. These changes might suggest reduction and reorganization of the thylakoid membrane structure. Hypotheses are also drawn on the role played by lipid molecule shape and their possible effect in membrane fluidity and protein accommodation.

    • Molecular analysis of gut microbiota in obesity among Indian individuals

      Deepak P Patil Dhiraj P Dhotre Sachin G Chavan Armiya Sultan Dhawal S Jain Vikram B Lanjekar Jayshree Gangawani Poonam S Shah Jayshree S Todkar Shashank Shah Dilip R Ranade Milind S Patole Yogesh S Shouche

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      Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR (𝑃 > 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.

    • The hnRNP A1 homolog Hrp36 is essential for normal development, female fecundity, omega speckle formation and stress tolerance in Drosophila melanogaster

      Anand K Singh Subhash C Lakhotia

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      Hrp36/Hrb87F is one of the most abundant and well-characterized hnRNP A homolog in Drosophila and is shown to have roles in regulation of alternative splicing, heterochromatin formation, neurodegeneration, etc. Yet, hrp36 null individuals were reported to be viable and without any apparent phenotype, presumably because of overlapping functions provided by Hrp38 and related proteins. Here we show that loss of both copies of hrp36 gene slows down development with significant reduction in adult life span, decreased female fecundity and high sensitivity to starvation and thermal stresses. In the absence of Hrp36, the nucleoplasmic omega speckles are nearly completely disrupted. The levels of nuclear matrix protein Megator and the chromatin remodeller ISWI are significantly elevated in principal cells of larval Malpighian tubules, which also display additional endoreplication cycles and good polytene chromosomes. We suggest that besides the non-coding hsr𝜔-n transcripts, the Hrp36 protein is also a core constituent of omega speckles. The heat-shock-induced association of other hnRNPs at the hsr𝜔 locus is affected in hrp36 null cells, which may be one of the reasons for their high sensitivity to cell stress. Therefore, in spite of the functional redundancy provided by Hrp38, Hrp36 is essential for normal development and for survival under conditions of stress.

    • Effect of chronic exposure to aspartame on oxidative stress in the brain of albino rats

      Ashok Iyyaswamy Sheeladevi Rathinasamy

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      This study was aimed at investigating the chronic effect of the artificial sweetener aspartame on oxidative stress in brain regions of Wistar strain albino rats. Many controversial reports are available on the use of aspartame as it releases methanol as one of its metabolite during metabolism. The present study proposed to investigate whether chronic aspartame (75 mg/kg) administration could release methanol and induce oxidative stress in the rat brain. To mimic the human methanol metabolism, methotrexate (MTX)-treated rats were included to study the aspartame effects. Wistar strain male albino rats were administered with aspartame orally and studied along with controls and MTX-treated controls. The blood methanol level was estimated, the animal was sacrificed and the free radical changes were observed in brain discrete regions by assessing the scavenging enzymes, reduced glutathione, lipid peroxidation (LPO) and protein thiol levels. It was observed that there was a significant increase in LPO levels, superoxide dismutase (SOD) activity, GPx levels and CAT activity with a significant decrease in GSH and protein thiol. Moreover, the increases in some of these enzymes were region specific. Chronic exposure of aspartame resulted in detectable methanol in blood. Methanol per se and its metabolites may be responsible for the generation of oxidative stress in brain regions.

    • The present Pyrenean population of bearded vulture (Gypaetus barbatus): Its genetic characteristics

      C B García J A Gil M Alcántara J González M R Cortés J I Bonafonte M V Arruga

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      The Pyrenean population of the endangered bearded vulture (Gypaetus barbatus) is the largest natural population in Europe. In this study, its current genetic variability was assessed using 110 animals of the recent population in order to know what the present situation. Sex identification by DNA methodology in the 110 bearded vultures, mitochondrial DNA (mtDNA) and eight microsatellite markers in 87 bearded vultures have been analysed. Our results for sex identification present a number of 49 males and 61 females; no significant differences for number of males and females in this population have been observed. mtDNA studies indicate that nucleotide and haplotype diversities and number of variable sites were low. Tajima’s D test and Fu and Li’s D* and F* tests suggest that mutations are selectively neutral and the population is expanding. A mean number of alleles per locus and a mean observed heterozygosity have been obtained by microsatellite analysis. FIS is not high, and inbreeding depression could be discarded in the near future. The results suggest that the Pyrenean population of bearded vultures have to be controlled in order to avoid the loss of genetic variability. This data should be taken into account when considering conservation plans for the species.

    • Enantioselective hydrolysis of epichlorohydrin using whole Aspergillus niger ZJB-09173 cells in organic solvents

      Huo-Xi Jin Zhong-Ce Hu Yu-Guo Zheng

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      The enantioselective hydrolysis of racemic epichlorohydrin for the production of enantiopure (𝑆)-epichloro-hydrin using whole cells of Aspergillus niger ZJB-09173 in organic solvents was investigated. Cyclohexane was used as the reaction medium based on the excellent enantioselectivity of epoxide hydrolase from A. niger ZJB-09173 in cyclohexane. However, cyclohexane had a negative effect on the stability of epoxide hydrolase from A. niger ZJB-09173. In the cyclohexane medium, substrate inhibition, rather than product inhibition of catalysis, was observed in the hydrolysis of racemic epichlorohydrin using A. niger ZJB-09173. The racemic epichlorohydrin concentration was markedly increased by continuous feeding of substrate without significant decline of the yield. Ultimately, 18.5% of (𝑆)-epichlorohydrin with 98% enantiomeric excess from 153.6 mM of racemic epichlorohydrin was obtained by the dry cells of A. niger ZJB-09173, which was the highest substrate concentration in the production of enantiopure (𝑆)-epichlorohydrin by epoxide hydrolases using an organic solvent medium among the known reports.

    • Oxyradicals and PSII activity in maize leaves in the absence of UV components of solar spectrum

      M B Shine K N Guruprasad

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      The regulation of oxyradicals and PSII activity by UV-B (280–315 nm) and UV-A (315–400 nm) components were investigated in the leaves of maize [Zea mays L. var: HQPM.1]. The impact of ambient UV radiation on the production of superoxide (O2˙) and hydroxyl (˙OH) radicals were analysed in the leaves of 20-day-old plants. The amount of O2˙ and ˙OH radicals and the radical scavenging activity were significantly higher in the leaves exposed to ambient UV radiation as compared to the leaves of the plants grown under UV exclusion filters. Smaller amount of oxyradicals in the leaves of UV excluded plants was accompanied by a substantial increase in quantum yield of electron transport (𝜑Eo), rate of electron transport (𝜓o) and performance index (PIABS), as indicated by chlorophyll 𝑎 fluorescence transient. Although higher amounts of oxyradicals invoked higher activity of antioxidant enzymes like superoxide dismutase and peroxidase under ambient UV, they also imposed limitation on the photosynthetic efficiency of PSII. Exclusion of UV components (UV-B 280–315 nm; UV-A 315–400 nm) translated to enhanced photosynthesis, growth and biomass. Thus, solar UV components, especially in the tropical region, could be a major limiting factor in the photosynthetic efficiency of the crop plants.

    • Ion distribution measured by electron probe X-ray microanalysis in apoplastic and symplastic pathways in root cells in sunflower plants grown in saline medium

      Reza Ebrahimi S C Bhatla

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      Little is known about how salinity affects ions distribution in root apoplast and symplast. Using x-ray microanalysis, ions distribution and the relative contribution of apoplastic and symplastic pathways for delivery of ions to root xylem were studied in sunflower plants exposed to moderate salinity (EC=6). Cortical cells provided a considerably extended Na+ and Cl storage facility. Their contents are greater in cytoplasm (root symplast) as compared to those in intercellular spaces (root apoplast). Hence, in this level of salinity, salt damage in sunflower is not dehydration due to extracellular accumulation of sodium and chloride ions, as suggested in the Oertli hypothesis. On the other hand, reduction in calcium content due to salinity in intercellular space is less than reduction in the cytoplasm of cortical cells. It seems that sodium inhibits the radial movement of calcium in symplastic pathway more than in the apoplastic pathway. The cell wall seems to have an important role in providing calcium for the apoplastic pathway. Redistribution of calcium from the cell wall to intercellular space is because of its tendency towards xylem through the apoplastic pathway. This might be a strategy to enhance loading of calcium to xylem elements and to reduce calcium deficiency in young leaves under salinity. This phenomenon may be able to increase salt tolerance in sunflower plants. Supplemental calcium has been found to be effective in reducing radial transport of Na+ across the root cells and their loading into the xylem, but not sodium absorption. Supplemental calcium enhanced Ca2+ uptake and influx into roots and transport to stele.

    • Simple luminosity normalization of greenness, yellowness and redness/greenness for comparison of leaf spectral profiles in multi-temporally acquired remote sensing images

      Ryoichi Doi

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      Observation of leaf colour (spectral profiles) through remote sensing is an effective method of identifying the spatial distribution patterns of abnormalities in leaf colour, which enables appropriate plant management measures to be taken. However, because the brightness of remote sensing images varies with acquisition time, in the observation of leaf spectral profiles in multi-temporally acquired remote sensing images, changes in brightness must be taken into account. This study identified a simple luminosity normalization technique that enables leaf colours to be compared in remote sensing images over time. The intensity values of green and yellow (green+red) exhibited strong linear relationships with luminosity (R2 > 0.926) when various invariant rooftops in Bangkok or Tokyo were spectral-profiled using remote sensing images acquired at different time points. The values of the coefficient and constant or the coefficient of the formulae describing the intensity of green or yellow were comparable among the single Bangkok site and the two Tokyo sites, indicating the technique’s general applicability. For single rooftops, the values of the coefficient of variation for green, yellow, and red/green were 16% or less (n=6−11), indicating an accuracy not less than those of well-established remote sensing measures such as the normalized difference vegetation index. After obtaining the above linear relationships, raw intensity values were normalized and a temporal comparison of the spectral profiles of the canopies of evergreen and deciduous tree species in Tokyo was made to highlight the changes in the canopies’ spectral profiles. Future aspects of this technique are discussed herein.

    • Transcriptome response to nitrogen starvation in rice

      Hongmei Cai Yongen Lu Weibo Xie Tong Zhu Xingming Lian

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      Nitrogen is an essential mineral nutrient required for plant growth and development. Insufficient nitrogen (N) supply triggers extensive physiological and biochemical changes in plants. In this study, we used Affymetrix GeneChip rice genome arrays to analyse the dynamics of rice transcriptome under N starvation. N starvation induced or suppressed transcription of 3518 genes, representing 10.88% of the genome. These changes, mostly transient, affected various cellular metabolic pathways, including stress response, primary and secondary metabolism, molecular transport, regulatory process and organismal development. 462 or 13.1% transcripts for N starvation expressed similarly in root and shoot. Comparative analysis between rice and Arabidopsis identified 73 orthologous groups that responded to N starvation, demonstrated the existence of conserved N stress coupling mechanism among plants. Additional analysis of transcription profiles of microRNAs revealed differential expression of miR399 and miR530 under N starvation, suggesting their potential roles in plant nutrient homeostasis.

    • Metabolic response to exogenous ethanol in yeast: An in vivo statistical total correlation NMR spectroscopy approach

      Maso Ricci Marianna Aggravi Claudia Bonechi Silvia Martini Anna Maria Claudio Rossi

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      In vivo NMR spectroscopy, together with selectively 13C-labelled substrates and ‘statistical total correlation spectroscopy’ analysis (STOCSY), are valuable tools to collect and interpret the metabolic responses of a living organism to external stimuli. In this study, we applied this approach to evaluate the effects of increasing concentration of exogenous ethanol on the Saccharomyces cerevisiae fermentative metabolism. We show that the STOCSY analysis correctly identifies the different types of correlations among the enriched metabolites involved in the fermentation, and that these correlations are quite stable even in presence of a stressing factor such as the exogenous ethanol.

    • Molecular characterization of `Bhut Jolokia' the hottest chilli

      J Purkayastha S I Alam H K Gogoi L Singh V Veer

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      The northeast region of India, considered as ‘hot spot’ of biodiversity, having unique ecological environment with hot and high-humidity conditions, has given rise to the world’s hottest chilli, ‘Bhut Jolokia’, which is at least two times hotter than Red Savina Habanero in terms of Scoville heat units (SHU). This study was undertaken to determine the distinctiveness of ‘Bhut Jolokia’ from Capsicum frutescens or Capsicum chinense through sequencing of the ribosomal RNA (rRNA) gene-internal transcribed (ITS) region along with its phylogenetic analysis. Although a compensatory base change (CBC) in the ITS2 region was not observed between the closely related species of C. frutescens and C. chinense when compared with Bhut Jolokia; phylogenetic analysis using ITS1, 5.8S and ITS2 sequences indicated a distinct clade for all the accessions of ‘Bhut Joloikia’, while C. frutescens and C. chinense occupied discrete lineages. Further, a unique 13-base deletion was observed in all the representative accessions of ‘Bhut Jolokia’, making it distinct from all other members within the genus and beyond. The degree of genetic variations along with its extreme pungency might be related to ambient environmental factors of northeastern India.

    • Cocos sahnii Kaul: A Cocos nucifera L.-like fruit from the Early Eocene rainforest of Rajasthan, western India

      Anumeha Shukla Rakesh C Mehrotra Jaswant S Guleria

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      Cocos sahnii Kaul, a fossil palm fruit, is validated and described from the Fuller’s earth deposits of Kapurdi village of Rajasthan considered as Early Eocene in age. The fossil best resembles the genus Cocos, particularly Cocos nucifera L., which is now a common coastal element thriving in highly moist conditions. The recovery of this coconut-like fruit, along with earlier described evergreen taxa from the same formation, suggests the existence of typical tropical, warm and humid coastal conditions during the depositional period. The present arid to semi-arid climatic conditions occurring in Rajasthan indicate drastic climate change in the region during the Cenozoic. The possible time for the onset of aridity in the region which caused the total eradication of semi-evergreen to evergreen forests is discussed, as well as the palaeobiogeography of coconuts.

    • Emergent patterns of social organization in captive Cercocebus torquatus: Testing the GrooFiWorld agent-based model

      R Dolado F S Beltran

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      We empirically applied the GrooFiWorld agent-based model (Puga-González et al. 2009) in a group of captive red-capped mangabeys (Cercocebus torquatus). We analysed several measurements related to aggression and affiliative patterns. The group adopted a combination of despotic and egalitarian behaviours resulting from the behavioural flexibility observed in the Cercopithecinae subfamily. Our study also demonstrates that the GrooFiWorld agent-based model can be extended to other members of the Cercopithecinae subfamily generating parsimonious hypotheses related to the social organization.

    • BIND – An algorithm for loss-less compression of nucleotide sequence data

      Tungadri Bose Monzoorul Haque Mohammed Anirban Dutta Sharmila S Mande

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      Recent advances in DNA sequencing technologies have enabled the current generation of life science researchers to probe deeper into the genomic blueprint. The amount of data generated by these technologies has been increasing exponentially since the last decade. Storage, archival and dissemination of such huge data sets require efficient solutions, both from the hardware as well as software perspective. The present paper describes BIND – an algorithm specialized for compressing nucleotide sequence data. By adopting a unique ‘block-length’ encoding for representing binary data (as a key step), BIND achieves significant compression gains as compared to the widely used general purpose compression algorithms (gzip, bzip2 and lzma). Moreover, in contrast to implementations of existing specialized genomic compression approaches, the implementation of BIND is enabled to handle non-ATGC and lowercase characters. This makes BIND a loss-less compression approach that is suitable for practical use. More importantly, validation results of BIND (with real-world data sets) indicate reasonable speeds of compression and decompression that can be achieved with minimal processor/memory usage. BIND is available for download at http://metagenomics.atc.tcs.com/compression/BIND. No license is required for academic or non-profit use.

    • Begomovirus research in India: A critical appraisal and the way ahead

      Basanta K Borah Indranil Dasgupta

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      Begomoviruses are a large group of whitefly-transmitted plant viruses containing single-stranded circular DNA encapsidated in geminate particles. They are responsible for significant yield losses in a wide variety of crops in India. Research on begomoviruses has focussed on the molecular characterization of the viruses, their phylogenetic analyses, infectivities on host plants, DNA replication, transgenic resistance, promoter analysis and development of virus-based gene silencing vectors. There have been a number of reports of satellite molecules associated with begomoviruses. This article aims to summarize the major developments in begomoviral research in India in the last approximately 15 years and identifies future areas that need more attention.

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