• Issue front cover thumbnail

      Volume 43, Issue 1

      March 2018,   pages  1-223

    • How do biological systems escape ‘chaotic’ state?

      B J RAO

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    • Liberating primatology


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    • Sisyphus desperately seeking publisher


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      As a punishment for his trickery, King Sisyphus was made to endlessly roll a huge boulder up a steep hill. The maddeningnature of the punishment was reserved for King Sisyphus due to his hubristic belief that his cleverness surpassed that ofZeus himself. Today’s scientists also pay a heavy price for their hubris and narcissism. They try to trick the editors of a few

      ‘top’ journals by peppering their papers with glitter and ‘bling-bling’, making overblown promises, and giving minimalcredit to their predecessors. The editors wield their Olympian authority by making today’s scientists endlessly push theirweighty boulders up steep hills. By bowing to this implacable ritual, we scientists confer undue power to a handful ofpopular but irresponsible journals.

    • Low concentrations of ethanol during irradiation drastically reduce DNA damage caused by very high doses of ionizing radiation


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      Presence of low concentrations (1–2%) of ethanol during irradiation exhibited significant protection against DNA damagecaused by very high doses (2–12 kGy) of 60Co-gamma-rays in vitro. Radiation-induced DNA damage was substantiallyreduced in different types of DNA molecules (chromosomal DNA from Anabaena 7120 or Deinococcus radiodurans orbacteriophage Lambda, and plasmid pBluescript DNA) when irradiated in the presence of ethanol, thus indicating thegeneric nature of ethanol protection. The radioprotection appeared to be a consequence of the well known ability of ethanolto scavenge hydroxyl radicals. Addition of ethanol during 6 kGy irradiation also reduced DNA damage in vivo andimproved post-irradiation growth recovery of Anabaena 7120 cultures. To our knowledge, this is the first instance of abilityof very low ethanol concentrations to protect DNA from damage triggered by extremely high doses of 60Co-gamma rays.

    • ATR kinase regulates its attenuation via PPM1D phosphatase recruitment to chromatin during recovery from DNA replication stress signalling


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      In eukaryotes, in response to replication stress, DNA damage response kinase, ATR is activated, whose signalling abrogationleads to cell lethality due to aberrant fork remodelling and excessive origin firing. Here we report that inhibition ofATR kinase activity specifically during replication stress recovery results in persistent ATR signalling, evidenced by thepresence of ATR-dependent phosphorylation marks (cH2AX, pChk1 and pRad17) and delayed cell cycle re-entry. Further,such disruption of ATR signalling attenuation leads to double-strand breaks, fork collapse and thereby ‘replicationcatastrophe’. PPM1D phosphatase, a nucleolar localized protein, relocates to chromatin during replication stress and revertsback to nucleolus following stress recovery, under the control of ATR kinase action. Inhibition of ATR kinase activity,specifically during post replication stress, triggers dislodging of the chromatin-bound PPM1D from nucleus to cytoplasmfollowed by its degradation, thereby leading to persistence of activated ATR marks in the nuclei. Chemical inhibition ofPPM1D activity or SiRNA mediated depletion of the protein during post replication stress recovery ‘phenocopies’ ATRkinase inhibition by failing to attenuate ATR signalling. Collectively, our observations suggest a novel role of ATR kinasein mediating its own signal attenuation via PPM1D recruitment to chromatin as an essential mechanism for restarting thestalled forks, cell-cycle re-entry and cellular recovery from replication stress.

    • An individual-level selection model for the apparent altruism exhibited by cellular slime moulds


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      In Dictyostelium discoideum, cells that become part of the stalk or basal disc display behaviour that can be interpreted asaltruistic. Atzmony et al. (Curr Sci 72:142–145, 1997) had hypothesised that this behaviour could be the outcome of anadaptive strategy based on differing intrinsic quality as reflected by phenotypes that indicate differences in potential forsurvival and reproduction, followed by intercellular competition among amoebae of differing qualities. Low-qualityamoebae would have a poor chance of succeeding in the competition to form spores; they could enhance their chances ofsurvival by adopting a presumptive stalk strategy. Here we extend the hypothesis by making use of recent findings. Ourapproach is based on the view that an evolutionary explanation for the apparent altruism of stalk cells in D. discoideummust apply broadly to other cellular slime moulds (CSMs) that exhibit stalk cell death. Further, it must be capable of beingmodified to cover social behaviour in CSMs with an extracellular stalk, as well as in sorocarpic amoebae whose stalk cellsare viable. With regard to D. discoideum, we suggest that (a) differentiation-inducing factor, thought of as a signal thatinhibits amoebae from forming spores and induces them to differentiate into basal disc cells, is better viewed as a mediatorof competition among post-aggregation amoebae and (b) the products of the ‘recognition genes’, tgrB and tgrC, allow anamoeba to assess its quality relative to that of its neighbours and move to a position within the aggregate that optimises itsreproductive fitness. From this perspective, all cells behave in a manner that is ‘selfish’ rather than ‘altruistic’, albeit withdifferent expectations of success.

    • Thalassiosira malaitalic> (Bacillariophyta), a potentially harmful, marine diatom from Chilka Lake and other coastal localities of Odisha, India: Nomenclature, frustule morphology and global biogeography


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      Our examination of net phytoplankton collected from coastal localities in Odisha on the east coast of India, includingChilka Lake, Chandrabhaga Beach and Puri, in December 2015, revealed the overwhelming dominance of Thalassiosiramala, a gelatinous colony-forming, potentially harmful, marine planktonic diatom. The large numbers of cells allowed us toobserve details of the cingulum not previously reported. The epicingulum is composed of four open bands including anareolated valvocopula, an areolated copula and two non-areolated pleurae. The immature hypocingulum includes at leasttwo bands. Openings of alternate bands are arranged in a dextral pattern. Based on previous reports from the west coast andour current findings, Thalassiosira mala appears to be a common, widely distributed primary producer in Indian coastalwaters. The presence of morphologically similar species, especially those less than 20 micro-m in diameter, underscores the importanceof reliable species-level taxonomy using appropriate techniques for meaningful ecological and biogeographic considerationsand for monitoring potentially harmful algae in India’s economically important coastal waters. Published reportssuggest that Thalassiosira mala is widely distributed in temperate and tropical waters, present in 26 of 232 ecoregions and18 of 62 provinces recognized in a recent classification of coastal marine ecoregions.

    • PAX6 can substitute for LHX2 and override NFIA-induced astrogliogenesis in developing hippocampus in vivo


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      In the developing central nervous system, transcription factors play a crucial role in the regulation of cell fate.Previously we demonstrated that LHX2 is a critical regulator of the neuron-glia cell fate switch in the developingmouse hippocampus. Here, we test LHX2 target gene Pax6 for a role in this process. We report that Pax6 overexpressionis able to suppress the enhanced astrogliogenesis arising due to loss of functional LHX2. Furthermore, weshow that like Lhx2, Pax6 is also able to suppress induced astrogliogenesis caused by overexpression of progliogenicfactor Nfia. This demonstrates that overexpression of Pax6 can substitute for Lhx2 in the regulation of the neuronalversus glial cell fate in the developing hippocampus, and therefore, supports a role for PAX6 as a mediator of LHX2function in this process.

    • Acute pharmacogenetic activation of medial prefrontal cortex excitatory neurons regulates anxiety-like behaviour


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      The medial prefrontal cortex (mPFC) is implicated in anxiety-like behaviour. In rodent models, perturbations of mPFCneuronal activity through pharmacological manipulations, optogenetic activation of mPFC neurons or cell-type specificpharmacogenetic inhibition of somatostatin interneurons indicate conflicting effects on anxiety-like behaviour. In thepresent study we examined the effects of pharmacogenetic activation of Ca2?/calmodulin-dependent protein kinase a(CamKIIa)-positive excitatory neurons on anxiety-like behaviour. We used clozapine-N-oxide (CNO) to pharmacogeneticallyactivate virally delivered CamKIIa-hM3Dq-DREADD in mPFC excitatory neurons. The effects of acute CNO orvehicle treatment on anxiety-like behaviour in the open field and elevated plus maze tests were examined in rats virallyinfected with either CamKIIa-hM3Dq-DREADD or CamKIIa-GFP. In addition, the effects of acute CNO treatment on theexpression of the neuronal activity marker c-Fos were examined in the mPFC as well as downstream target neuronal circuitsusing immunohistochemistry. Acute pharmacogenetic activation of mPFC excitatory neurons evoked a significant decreasein anxiety-like behaviour selectively on the elevated plus maze task, but not the open field test. Acute CNO treatmentresulted in enhanced c-Fos-immunopositive cell number in the infralimbic, prelimbic and cingulate subdivisions of themPFC. This was also accompanied by enhanced c-Fos-immunopositive cell number in multiple downstream circuits of themPFC in CNO-treated hM3Dq animals. Acute pharmacogenetic activation of mPFC excitatory neurons reduces anxiety-likebehaviour in a task-specific fashion accompanied by enhanced c-Fos expression in the mPFC and multiple targetcircuits implicated in the regulation of anxiety-like behaviour.

    • Target-specific delivery of doxorubicin to human glioblastoma cell line via ssDNA aptamer


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      Targeted drug delivery approaches have been implementing significant therapeutic gain for cancer treatment since lastdecades. Aptamers are one of the mostly used and highly selective targeting agents for cancer cells. Herein, we address anano-sized targeted drug delivery approach adorned with A-172 glioblastoma cell-line-specific single stranded DNA(ssDNA) aptamer in which the chemotherapeutic agent Doxorubicin (DOX) had been conjugated. DNA aptamer, GMT-3,was previously selected for specific recognition of glioblastoma and represented many advantageous characteristics for drugtargeting purposes. Flow cytometry analysis proved the binding efficiency of the specific aptamer to tumour cell lines. Celltype-specific toxicity of GMT-3:DOX complex was showed by XTT assay and terminated cytotoxic effects were screenedfor both target cell and a control breast cancer cell line. The result of this contribution demonstrated the potential utility ofGMT-3 aptamer-mediated therapeutic drug transportation in the treatment of gliomas specifically. It was concluded thataptamer-mediated drug delivery can be applied successfully for clinical use.

    • Root transcripts associated with arsenic accumulation in hyperaccumulator Pteris vittata


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      Hyperaccumulation of arsenic (As) by brake fern Pteris vittata has been described as an important genetic trait that providesan option for development of a sustainable phytoremediation process for As mitigation. Accumulation of very highconcentration of arsenic in above-ground tissues may be the result of arsenic vacuole compartmentalization, but themechanism(s) of arsenic uptake and transport by underground tissues are largely unknown. In this study, we made anattempt towards understanding the molecular mechanism of As hyperaccumulation in this plant. A time-dependent Asaccumulation study indicates an exponential accumulation of As from 7 to 30 days of arsenic exposure in fronds, and day3–7 in roots. Root transcriptome analysis identified 554,973 transcripts. Further, subsets of 824 transcripts were differentiallyexpressed between treated and control samples. Many of the genes of critical As-stress response, transcriptionfactors and metal transporters, biosynthesis of chelating compounds involved in uptake and accumulation mechanisms wereidentified. The genes that were highly expressed such as cysteine-rich RLK, and ABC transporter G family member 26needs further studies along with arsenite transmembrane transporter. The analysis of generated transcriptome dataset hasprovided valuable information and platform for further functional studies.

    • Glucohexaose-induced protein phosphatase 2C regulates cell redox status of cucumber seedling


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      Protein Phosphatase 2C (PP2C) is an important phosphatase-like protein in eukaryotic organisms that can negativelyregulate protein kinase cascade abscisic acid (ABA) signal system through phosphorylation and carry out vital roles invarious cell processes. The previous study indicated that the accumulation of reactive oxygen species (ROS) is a part ofmechanism of glucohexaose-induced resistance in cucumber cotyledons, and CsPP2C80s might play a crucial role inprocesses related to ROS produce and signal transduction. To identify the mechanism of CsPP2C80s involved in glucohexaoseand ABA signaling regulating cell redox status, the effects of glucohexaose and ROS inhibitor pretreatment onendogenous ABA content and ABA signaling genes expression levels of cucumber seedlings were analysed. These resultssuggest that cucumber CsPP2C80s are involved in ROS accumulation and ABA signal transduction pathway induced byglucohexaose, CsPP2C80s play a positive regulatory role in process of ABA combined with ABA receptors (PYLs) toactivate SNF1-related protein kinases 2 (SnRK2s) and regulate NADPH oxidase to produce extracellular hydrogen peroxide(H2O2), providing unequivocal molecular evidence of PP2C-mediated ABA response mechanisms functioning in cellredox status induced by glucohexaose.

    • Blocking dephosphorylation at Serine 120 residue in t-SNARE SNAP-23 leads to massive inhibition in exocytosis from mast cells


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      Mast cells (MCs) respond to allergen challenge by release of pre-stored inflammatory mediators from their secretorygranules, on cross-linking of Fce receptor I (FceRI) receptors. The target-SNARE (t-SNARE) SNAP-23 has been shown toplay an important role in MC exocytosis and undergoes transient phosphorylation at Serine 95 (S95) and Serine 120 (S120),concomitant with mediator release. During current study we explored the importance of transient nature of phosphorylationat S120 in MC exocytosis. A phosphomimetic SNAP-23-S120D mutant of rodent SNAP-23 was cloned into EGFP vectorand its effect on the exocytosis and the mechanisms involved was studied in RBL-2H3 MC line. Secretion reporter assaywith SNAP-23-S120D transfected MCs revealed a very significant inhibition of exocytosis, and reduced ruffling inresponse to FceRI cross-linking. Further, the effect of this mutation on localization of SNAP-23 in MCs was studied.Immunofluorescence microscopy studies and membrane-cytosol fractionation of green fluorescent protein-tagged SNAP-23-S120D (GFP-SNAP-23-S120D) transfected MCs showed that a large proportion of GFP-SNAP-23-S120D was residingin cytosol unlike wild-type SNAP-23, in resting and activated MCs and even the membrane associated portion was oninternal lysosomal membranes than plasma membrane. These studies imply that dephosphorylation of S120 is important forSNAP-23 membrane association dynamics and subsequently MC degranulation.

    • Tetrahymena dynamin-related protein 6 self-assembles independent of membrane association


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      Self-assembly on target membranes is one of the important properties of all dynamin family proteins. Drp6, a dynaminrelatedprotein in Tetrahymena, controls nuclear remodelling and undergoes cycles of assembly/disassembly on the nuclearenvelope. To elucidate the mechanism of Drp6 function, we have characterized its biochemical and biophysical propertiesusing size exclusion chromatography, chemical cross-linking and electron microscopy. The results demonstrate that Drp6readily forms high-molecular-weight self-assembled structures as determined by size exclusion chromatography andchemical cross-linking. Negative stain electron microscopy revealed that Drp6 assembles into rings and spirals at physiologicalionic strength. We have also shown that the recombinant Drp6 expressed in bacteria is catalytically active and itsGTPase activity is not enhanced by low salt. These results suggest that, in contrast to dynamins but similar to MxA, Drp6self-assembles in the absence of membrane templates, and its GTPase activity is not affected by ionic strength of the buffer.We discuss the self-assembly structure of Drp6 and explain the basis for lack of membrane-stimulated GTPase activity.

    • Triacylglycerol: nourishing molecule in endurance of Mycobacterium tuberculosis


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      The ability of Mycobacterium tuberculosis (M. tuberculosis) to accumulate lipid-rich molecules as an energy sourceobtained from host cell debris remains interesting. Additionally, the potential of M. tuberculosis to survive under differentstress conditions leading to its dormant state in pathogenesis remains elusive. The exact mechanism by which these lipidbodies generated in M. tuberculosis infection and utilized by bacilli inside infected macrophage for its survival is still notunderstood. In this, during bacillary infection, many metabolic pathways are involved that influence the survival of M.tuberculosis for their own support. However, the exact energy source derived from infecting host cells remain elusive.Therefore, this study highlights several alternative energy sources in the form of triacylglycerol (TAG) and fatty acids, i.e.oleic acids accumulation, which are essential in dormancy-like state under M. tuberculosis infection. The prominent stage intuberculosis (TB) infection is re-establishment of M. tuberculosis under stress conditions and deployment of a confinedstrategy to utilize these biomolecules for its persistence survival. So, growing in our understanding of these pathways willhelp us in accelerating therapies, which could reduce TB prevalence world widely.

    • Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling


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      Protein scaffolds as essential backbones for organization of supramolecular signalling complexes are a recurrent theme inseveral model systems. Scaffold proteins preferentially employ linear peptide binding motifs for recruiting their interactionpartners. PDZ domains are one of the more commonly encountered peptide binding domains in several proteins includingthose involved in scaffolding functions. This domain is known for its promiscuity both in terms of ligand selection, mode ofinteraction with its ligands as well as its association with other protein interaction domains. PDZ domains are subject toseveral means of regulations by virtue of their functional diversity. Additionally, the PDZ domains are refractive to theeffect of mutations and maintain their three-dimensional architecture under extreme mutational load. The biochemical andbiophysical basis for this selectivity as well as promiscuity has been investigated and reviewed extensively. The presentreview focuses on the plasticity inherent in PDZ domains and its implications for modular organization as well as evolutionof cellular signalling pathways in higher eukaryotes.

    • Plant reference genes for development and stress response studies


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      Many reference genes are used by different laboratories for gene expression analyses to indicate the relative amount of inputRNA/DNA in the experiment. These reference genes are supposed to show least variation among the treatments and withthe control sets in a given experiment. However, expression of reference genes varies significantly from one set ofexperiment to the other. Thus, selection of reference genes depends on the experimental conditions. Sometimes the averageexpression of two or three reference genes is taken as standard. This review consolidated the details of about 120 genesattempted for normalization during comparative expression analysis in 16 different plants. Plant species included in thisreview are Arabidopsis thaliana, cotton (Gossypium hirsutum), tobacco (Nicotiana benthamiana and N. tabacum), soybean(Glycine max), rice (Oryza sativa), blueberry (Vaccinium corymbosum), tomato (Solanum lycopersicum), wheat (Triticumaestivum), potato (Solanum tuberosum), sugar cane (Saccharum sp.), carrot (Daucus carota), coffee (Coffea arabica),cucumber (Cucumis sativus), kiwi (Actinidia deliciosa) and grape (Vitis vinifera). The list includes model and cultivatedcrop plants from both monocot and dicot classes. We have categorized plant-wise the reference genes that have been usedfor expression analyses in any or all of the four different conditions such as biotic stress, abiotic stress, developmentalstages and various organs and tissues, reported till date. This review serves as a guide during the reference gene hunt forgene expression analysis studies.

    • Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives


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      In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfishProcambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring thatare genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draftgenome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, Isummarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promisingdata, discuss what this new model could contribute to answering of ‘‘big’’ biological questions. Genome mining is expectedto reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction,moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory,biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigeneticinvestigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation,tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish isfurther suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance ofepigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies,environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratorylineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically editedstrains.

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