• Issue front cover thumbnail

      Volume 35, Issue 4

      December 2010,   pages  497-673

    • Clipboard: Single-neuron encoding of surprise in auditory processing

      Liisa A Tremere Raphael Pinaud

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    • Clipboard: Neural coding of temporal information and its topography in the auditory cortex

      Thomas A Terleph Raphael Pinaud

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    • Commentary: Optineurin, a multifunctional protein involved in glaucoma, amyotrophic lateral sclerosis and antiviral signalling

      Ghanshyam Swarup Ananthamurthy Nagabhushana

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    • Science literacy and natural history museums

      Antonio G Valdecasas Ana M Correas

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      It appears that developed countries, such as the US, the UK and Italy, are losing the race against irrationalism and arbitrary thinking in regard to nature and human interactions. The incidence of misguided beliefs and the detachment from and, in some cases, outright hostility toward science are on the rise. Paradoxically, this is probably the period in the history of advanced countries in which increasing public and personal efforts have been directed toward the dissemination of scientific knowledge to increase public understanding of science. This article vindicates the role of natural history museums in consolidating rational and critical scientific thinking while briefly examining scientific illiteracy in developed countries. It also discusses methods to improve the involvement of natural history museums in the promotion of rational thinking, the only appropriate avenue for objective knowledge.

    • What history tells us XXII. The French neo-Lamarckians

      Michel Morange

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    • Evidence for functional interaction of plasma membrane electron transport, voltage-dependent anion channel and volume-regulated anion channel in frog aorta

      Rashmi P Rao J Prakasa Rao

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      Frog aortic tissue exhibits plasma membrane electron transport (PMET) owing to its ability to reduce ferricyanide even in the presence of mitochondrial poisons, such as cyanide and azide. Exposure to hypotonic solution (108 mOsmol/kg H2O) enhanced the reduction of ferricyanide in excised aortic tissue of frog. Increment in ferricyanide reductase activity was also brought about by the presence of homocysteine (100 𝜇M dissolved in isotonic frog Ringer solution), a redox active compound and a potent modulator of PMET. Two plasma-membrane-bound channels, the volume regulated anion channel (VRAC) and the voltage-dependent anion channel (VDAC), are involved in the response to hypotonic stress. The presence of VRAC and VDAC antagonists–tamoxifen, glibenclamide, fluoxetine and verapamil, and 4,4′-diisothiocyanatostilbene-2,2′-disulphonic acid (DIDS), respectively–inhibited this enhanced activity brought about by either hypotonic stress or homocysteine. The blockers do not affect the ferricyanide reductase activity under isotonic conditions. Taken together, these findings indicate a functional interaction of the three plasma membrane proteins, namely, ferricyanide reductase (PMET), VDAC and VRAC.

    • Demonstration of a visual cell-based assay for screening glucose transporter 4 translocation modulators in real time

      Maleppillil Vavachan Vijayakumar Amrendra Kumar Ajay Manoj Kumar Bhat

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      Insulin-stimulated translocation of glucose transporter 4 (GLUT4) to cell membrane leading to glucose uptake is the rate-limiting step in diabetes. It is also a defined target of antidiabetic drug research. Existing GLUT4 translocation assays are based on time-consuming immunoassays and are hampered by assay variability and low sensitivity. We describe a real-time, visual, cell-based qualitative GLUT4 translocation assay using CHO-HIRc-myc-GLUT4eGFP cells that stably express myc- and eGFP-tagged GLUT4 in addition to human insulin receptor (HIRc). GLUT4 translocation is visualized by live cell imaging based on GFP fluorescence by employing a cooled charge-coupled device camera attached to a fluorescent microscope. This video imaging method and further quantitative analysis of GLUT4 on the cell membrane provide rapid and foolproof visual evidence that this method is suitable for screening GLUT4 translocation modulators.

    • Antibacterial abietane-type diterpenoid, taxodone from Metasequoia glyptostroboides Miki ex Hu

      Vivek K Bajpai Sun Chul Kang

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      In an attempt to isolate bioactive constituents, ethyl acetate cone extract of Metasequoia glyptostroboides was subjected to a column chromatographic analysis that resulted in isolation of an abietane-type diterpenoid, taxodone. Its structure was elucidated by spectroscopic means. Further, taxodone showed potential antibacterial effect as diameters of zones of inhibition against foodborne pathogenic bacteria, such as Listeria monocytogenes ATCC 19166, Salmonella typhimurium KCTC 2515, S. enteritidis KCTC 2021, Escherichia coli ATCC 8739, E. coli O157:H7 ATCC 43888, Enterobacter aerogenes KCTC 2190, Staphylococcus aureus ATCC 6538 and S. aureus KCTC 1916, were found in the range of 9.4 to 14.2 mm. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of taxodone against the employed bacterial pathogens were found in the range of 250 to 1000 and 250 to < 2000 𝜇g/ml, respectively. Also the compound had a strong antibacterial effect on the viable counts of the tested bacteria. These findings indicate that the bioactive compound taxodone present in M. glyptostroboides could be used as an antibacterial agent in food industry to inhibit the growth of certain important foodborne pathogens.

    • Translocations used to generate chromosome segment duplications in Neurospora can disrupt genes and create novel open reading frames

      Parmit K Singh Srividhya V Iyer T Naga Sowjanya B Kranthi Raj Durgadas P Kasbekar

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      In Neurospora crassa, crosses between normal sequence strains and strains bearing some translocations can yield progeny bearing a duplication (Dp) of the translocated chromosome segment. Here, 30 breakpoint junction sequences of 12 Dp-generating translocations were determined. The breakpoints disrupted 13 genes (including predicted genes), and created 10 novel open reading frames. Insertion of sequences from LG III into LG I as translocation T(UK818) disrupts the eat-3 gene, which is the ortholog of the Podospora anserine gene ami1. Since ami1-homozygous Podospora crosses were reported to increase the frequency of repeat-induced point mutation (RIP), we performed crosses homozygous for a deficiency in eat-3 to test for a corresponding increase in RIP frequency. However, our results suggested that, unlike in Podospora, the eat-3 gene might be essential for ascus development in Neurospora. Duplication–heterozygous crosses are generally barren in Neurospora; however, by using molecular probes developed in this study, we could identify Dp segregants from two different translocation–heterozygous crosses, and using these we found that the barren phenotype of at least some duplication–heterozygous crosses was incompletely penetrant.

    • Replacement of the C-terminal tetrapeptide (314PAPV317 to 314SSSM317) in interferon regulatory factor-2 alters its N-terminal DNA-binding activity

      Krishna Prakash Pramod C Rath

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      Interferon regulatory factor-2 (IRF-2) is an important transcription factor involved in cell growth regulation, immune response and cancer. IRF-2 can function as a transcriptional repressor and activator depending on its DNA-binding activity and protein–protein interactions. We compared the amino acid sequences of IRF-2 and found a C-terminal tetrapeptide (314PAPV317) of mouse IRF-2 to be different (314SSSM317) from human IRF-2. Recombinant GST-IRF-2 with 314PAPV317 (wild type) and 314SSSM317 (mutant) expressed in Escherichia coli were assessed for DNA-binding activity with 32P-(GAAAGT)4 by electrophoretic mobility shift assay (EMSA). Wild type- and mutant GST-IRF-2 showed similar expression patterns and immunoreactivities but different DNA-binding activities. Mutant (mt) IRF-2 formed higher-molecular-mass, more and stronger DNA–protein complexes in comparison to wild type (wt) IRF-2. Anti-IRF-2 antibody stabilized the DNA–protein complexes formed by both wt IRF-2 and mt IRF-2, resolving the differences. This suggests that PAPV and SSSM sequences at 314-317 in the C-terminal region of mouse and human IRF-2 contribute to conformation of IRF-2 and influence DNA-binding activity of the N-terminal region, indicating intramolecular interactions. Thus, evolution of IRF-2 from murine to human genome has resulted in subtle differences in C-terminal amino acid motifs, which may contribute to qualitative changes in IRF-2-dependent DNA-binding activity and gene expression.

    • Proteomic analysis of cell lines to identify the irinotecan resistance proteins

      Xing-Chen Peng Feng-Ming Gong Meng Wei X I Chen Y E Chen K E Cheng Feng Gao Feng Xu FENG Bi Ji-Yan Liu

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      Chemotherapeutic drug resistance is a frequent cause of treatment failure in colon cancer patients. Several mechanisms have been implicated in drug resistance. However, they are not sufficient to exhaustively account for this resistance emergence. In this study, two-dimensional gel electrophoresis (2-DE) and the PDQuest software analysis were applied to compare the differential expression of irinotecan-resistance-associated protein in human colon adenocarcinoma LoVo cells and irinotecan-resistant LoVo cells (LoVo/irinotecan). The differential protein dots were excised and analysed by ESI-Q-TOF mass spectrometry (MS). Fifteen proteins were identified, including eight proteins with decreased expression and seven proteins with increased expression. The identified known proteins included those that function in diverse biological processes such as cellular transcription, cell apoptosis, electron transport/redox regulation, cell proliferation/differentiation and retinol metabolism pathways. Identification of such proteins could allow improved understanding of the mechanisms leading to the acquisition of chemoresistance.

    • Antimycobacterial activity of two natural alkaloids, vasicine acetate and 2-acetyl benzylamine, isolated from Indian shrub Adhatoda vasica Ness. leaves

      S Ignacimuthu N Shanmugam

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      In folk medicine, Adhatoda vasica Ness. (Acanthaceae) is used to treat asthma and cough. The leaves of A.vasica were powdered and extracted with hexane, ethyl acetate and methanol. The hexane extract showed 97% reduction in colony-forming units (CFU) at 100 𝜇g/ml. The hexane extract was subjected to column chromatography. Two natural compounds, vasicine acetate and 2-acetyl benzylamine, were isolated from it. They were bioassayed against Mycobacterium tuberculosis. The two compounds showed strong antimycobacterial activity. Vasicine acetate and 2-acetyl benzylamine isolated from hexane extract of A. vasica leaves, significantly inhibited M. tuberculosis and one multi-drug-resistant (MDR) strain and one sensitive strain at 200 and 50 𝜇g/ml, respectively. Our study demonstrated that both the compounds, vasicine acetate and 2-acetyl benzylamine, could be evaluated further for developing a drug to control M. tuberculosis.

    • Temporal phase relation of circadian neural oscillations as the basis of testicular maturation in mice: A test of a coincidence model

      Sumit Sethi Chandra Mohini Chaturvedi

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      To study the underlying mechanism of gonadal growth during the attainment of puberty and to test a coincidence model, 7 experimental groups of 2-week-old male mice, Mus musculus, were administered the serotonin precursor, 5-hydroxytryptophan, followed by the dopamine precursor, L-dihydroxyphenylalanine at hourly intervals of 6, 7, 8, 9, 10, 11 and 12 h (5 mg/100 g body weight per day for 13 days). At 11 days post-treatment, a suppression of gonadal activity was seen in the 7-h mice and a maximum suppression in the 8-h mice, along with a significantly increased degree of gonadal development in the 12-h mice, as compared with the controls. In addition to its known regulation of seasonal gonadal cycles, the relative position of two circadian neural oscillations may also affect the rate of gonadal development during the attainment of puberty in mice. Moreover, the present study provides an experimental paradigm to test the coincidence model of circadian oscillations.

    • Guanidination of notexin alters its membrane-damaging activity in response to sphingomyelin and cholesterol

      Pei-Hsiu Kao Yi-Ling Chiou Shinne-Ren Lin Long-Sen Chang

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      To elucidate the contribution of phospholipase A2 (PLA2) activity of notexin to its ability to perturb membranes, comparative studies on the interaction of notexin and guanidinated notexin (Gu-notexin) with egg yolk phosphatidylcholine (EYPC), EYPC/egg yolk sphingomyelin (EYSM) and EYPC/EYSM/cholesterol vesicles were conducted. EYSM notably reduced the membrane-damaging activity of notexin against EYPC vesicles, but had an insignificant influence on that of Gu-notexin. Unlike the effects noted with notexin, inactivation of PLA2 activity by EDTA led to a reduction in the ability of Gu-notexin to induce EYPC/EYSM vesicle leakage and to increase Gu-notexin-induced membrane permeability of EYPC/EYSM/cholesterol vesicles. The geometrical arrangement of notexin and Gu-notexin in contact with either EYPC/EYSM vesicles or EYPC/EYSM/cholesterol vesicles differed. Moreover, global conformation of notexin and Gu-notexin differed in either Ca2+-bound or metal-free states. These results indicate that notexin and Gu-notexin could induce membrane permeability without the involvement of PLA2 activity, and suggest that guanidination alters the membrane-bound mode of notexin on damaging phospholipid vesicles containing sphingomyelin and cholesterol.

    • The effect of contaminants on the adhesion of the spatulae of a gecko

      Yeau-Ren Jeng Chien-Ping Mao

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      Many researchers have reported that the robust adhesion that enables geckos to move quickly and securely across a range of vertical and horizontal surfaces is provided by the hierarchical structure of their feet (i.e. lamellae, setae, spatulae, etc.). Maintaining this robust adhesion requires an intimate contact between the terminal tips of the spatulae and the surface. The aim of this study was to investigate the effect on the adhesive properties of the spatulae when a particle becomes trapped at the contact surface. Using the Johnson, Kendall and Roberts (JKR) theory, a model was constructed to assist in the analysis of the interactions between the spatula tip, the particle and the surface. The results showed that the keratin (the natural material of the spatula) provides a robust system for adhesion even when there is a particle in the contact area, and the effective contact area of spatulae will be 80%. When the particle is significantly harder than the surface, the adhesion properties of the contact surface influenced by the particle will be more obvious. The results also reveal that the generated adhesion is considerably higher when the spatula is in contact with a softer surface, such as wood or concrete, rather than a hard surface, such as glass or SiO2.

    • Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein

      T Rana V Chandel Y Kumar R Ram V Hallan A A Zaidi

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      The complete sequences of the coat protein (CP) gene of 26 isolates of Apple chlorotic leaf spot virus (ACLSV) from India were determined. The isolates were obtained from various pome (apple, pear and quince) and stone (plum, peach, apricot, almond and wild Himalayan cherry) fruit trees. Other previously characterized ACLSV isolates and Trichoviruses were used for comparative analysis. Indian ACLSV isolates among themselves and with isolates from elsewhere in the world shared 91–100% and 70–98% sequence identities at the amino acid and nucleotide levels, respectively. The highest degree of variability was observed in the middle portion with 9 amino acid substitutions in contrast to the N-terminal and C-terminal ends, which were maximally conserved with only 4 amino acid substitutions. In phylogenetic analysis no reasonable correlation between host species and/or geographic origin of the isolates was observed. Alignment with capsid protein genes of other Trichoviruses revealed the TaTao ACLSV peach isolate to be phylogenetically closest to Peach mosaic virus, Apricot pseudo chlorotic leaf spot virus and Cherry mottle leaf virus. Recombination analysis (RDP3 ver.2.6) done for all the available ACLSV complete CP sequences of the world and Indian isolates indicate no significant evidence of recombination. However, one recombination event among Indian ACLSV-CP isolates was detected. To the best of our knowledge, this is the first report of complete CP sequence variability study from India and also the first evidence of homologous recombination in ACLSV.

    • Self-organizing maps: A tool to ascertain taxonomic relatedness based on features derived from 16S rDNA sequence

      D V Raje H J Purohit Y P Badhe S S Tambe B D Kulkarni

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      Exploitation of microbial wealth, of which almost 95% or more is still unexplored, is a growing need. The taxonomic placements of a new isolate based on phenotypic characteristics are now being supported by information preserved in the 16S rRNA gene. However, the analysis of 16S rDNA sequences retrieved from metagenome, by the available bioinformatics tools, is subject to limitations. In this study, the occurrences of nucleotide features in 16S rDNA sequences have been used to ascertain the taxonomic placement of organisms. The tetra- and penta-nucleotide features were extracted from the training data set of the 16S rDNA sequence, and was subjected to an artificial neural network (ANN) based tool known as self-organizing map (SOM), which helped in visualization of unsupervised classification. For selection of significant features, principal component analysis (PCA) or curvilinear component analysis (CCA) was applied. The SOM along with these techniques could discriminate the sample sequences with more than 90% accuracy, highlighting the relevance of features. To ascertain the confidence level in the developed classification approach, the test data set was specifically evaluated for Thiobacillus, with Acidiphilium, Paracocus and Starkeya, which are taxonomically reassigned. The evaluation proved the excellent generalization capability of the developed tool. The topology of genera in SOM supported the conventional chemo-biochemical classification reported in the Bergey manual.

    • Male mate location behaviour and encounter sites in a community of tropical butterflies: taxonomic and site associations and distinctions

      Ashish D Tiple Sonali V Padwad Leonardo Dapporto Roger L H Dennis

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      Male mate location behaviour and encounter sites have been studied in 72 butterfly species at Nagpur, India, and related to taxonomy, morphology, habitat and population parameters. Species can be placed in three broad classes of mate location behaviour: invariant patrolling, invariant perching, and perch-patrol, the latter associated with increasing site fidelity, territorial defence and male assemblages. Significant taxonomic differences occur, closely related species tending to share mate location behaviours. Morphological differences are found with heavier and larger butterflies displaying greater site fidelity and territorial defence, and differences occur between individuals of species which both perch and patrol. Invariant patrolling is particularly associated with tracks through vegetation, host plant-track distributions, and high female to male numbers observed on transects; invariant perching is linked more to edge features than patrolling, and to lower population counts on transects. Species which perch-patrol, defend territories and establish male assemblages are associated with more complex vegetation structures, and have encounter sites at vegetation edges, landforms and predictable resource (host plant) concentrations. Attention is drawn to the importance of distinctive mate encounter sites for the conservation of butterfly species’ habitats.

    • Epigenetic modulation of host: new insights into immune evasion by viruse

      Dwaipayan Adhya Anirban Basu

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      Viruses have evolved with their hosts, which include all living species. This has been partly responsible for the development of highly advanced immune systems in the hosts. However, viruses too have evolved ways to regulate and evade the host’s immune defence. In addition to mutational mechanisms that viruses employ to mimic the host genome and undergo latency to evade the host’s recognition of the pathogen, they have also developed epigenetic mechanisms by which they can render the host’s immune responses inactive to their antigens. The epigenetic regulation of gene expression is intrinsically active inside the host and is involved in regulating gene expression and cellular differentiation. Viral immune evasion strategies are an area of major concern in modern biomedical research. Immune evasion strategies may involve interference with the host antigen presentation machinery or host immune gene expression capabilities, and viruses, in these manners, introduce and propagate infection. The aim of this review is to elucidate the various epigenetic changes that viruses are capable of bringing about in their host in order to enhance their own survivability and pathogenesis.

    • Glycan changes: cancer metastasis and anti-cancer vaccines

      Min Li Lujun Song Xinyu Qin

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      Complex carbohydrates, which are major components of the cell membrane, perform important functions in cell–cell and cell–extracellular matrix interactions, as well as in signal transduction. They comprise three kinds of biomolecules: glycoproteins, proteoglycans and glycosphingolipids. Recent studies have also shown that glycan changes in malignant cells take a variety of forms and mediate key pathophysiological events during the various stages of tumour progression. Glycosylation changes are universal hallmarks of malignant transformation and tumour progression in human cancer, which take place on the whole cells or some specific molecules. Accordingly, those changes make them prominent candidates for cancer biomarkers in the meantime. This review mainly focuses on the correlation between glycosylation and the metastasis potential of tumour cells from comprehensive aspects to further address the vital roles of glycans in oncogenesising. Moreover, utilizing these glycosylation changes to ward off tumour metastasis by means of anti-adhesion approach or devising anti-cancer vaccine is one of promising targets of future study.

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