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      Volume 32, Issue 2

      March 2007,   pages  181-428

    • Clipboard: Negative databases

      Jayant R Haritsa

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    • Commentary: Who really wants to save the apes?

      Jonathan Marks

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    • Commentary: The value of comparative genomics in understanding mycobacterial virulence: Mycobacterium tuberculosis H37Ra genome sequencing – a worthwhile endeavour

      Deepak Sharma Jaya Sivaswami Tyagi

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    • Commentary: Successful beyond expectation: David Perkins's research with chromosome rearrangements in Neurospora

      Durgadas P Kasbekar

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    • Beadle’s progeny: Innocence rewarded, innocence lost

      Rowland H Davis

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    • Living in a physical world X. Pumping fluids through conduits

      Steven Vogel

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    • What history tells us VIII. The progressive construction of a mechanism for prion diseases

      Michel Morange

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    • BOXTO as a real-time thermal cycling reporter dye

      Ashraf I Ahmad

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      The unsymmetrical cyanine dyes BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-quinolinium chloride) and its positive divalent derivative BOXTO-PRO (4-[(3-methyl-6-(benzoxazole-2-yl)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-(3-trimethylammonium-propyl)-quinolinium dibromide) were studied as real-time PCR reporting fluorescent dyes and compared to SYBR GREEN I (SG) (2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium). Unmodified BOXTO showed no inhibitory effects on real-time PCR, while BOXTO-PRO showed complete inhibition. Sufficient fluorescent signal was acquired when 0.5–1.0 𝜇M BOXTO was used with RotorGene and iCycler platforms. Statistical analysis showed that there is no significant difference between the efficiency and dynamic range of BOXTO and SG. BOXTO stock solution (1.5 mM) was stable at –20°C for more than one year and 40 𝜇M BOXTO solution was more stable than 5x SG when both were stored at 4°C for 45 days.

    • cDNA cloning and expression analysis of a mannose-binding lectin from Pinellia pedatisecta

      Juan Lin Xuanwei Zhou Shi Gao Xiaojun Liu Weisheng Wu Xiaofen Sun Kexuan Tang

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      Pinellia pedatisecta agglutinin (PPA) is a very basic protein that accumulates in the tuber of P. pedatisecta. PPA is a hetero-tetramer protein of 40 kDa, composed of two polypeptide chains A (about 12 kDa) and two polypeptides chains B (about 12 kDa). The full-length cDNA of PPA was cloned from P. pedatisecta using SMART RACE-PCR technology; it was 1146 bp and contained a 771 bp open reading frame (ORF) encoding a lectin precursor of 256 amino acid residues with a 24 amino acid signal peptide. The PPA precursor contained 3 mannose-binding sites (QXDXNXVXY) and two conserved domains of 43% identity, PPA-DOM1 (polypeptides A) and PPA-DOM2 (polypeptides B). PPA shared varying identities, ranging from 40% to 85%, with mannose-binding lectins from other species of plant families such as Araceae, Alliaceae, Iridaceae, Liliaceae, Amaryllidaceae and Bromeliaceae. Southern blot analysis indicated that ppa belonged to a multi-copy gene family. Expression pattern analysis revealed that ppa expressed in most tested tissues, with high expression being found in spadix, spathe and tuber. Cloning of the ppa gene not only provides a basis for further investigation of its structure, expression and regulatory mechanism, but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into plants in the future.

    • Antisense expression of a gene encoding a calcium-binding protein in transgenic tobacco leads to altered morphology and enhanced chlorophyll

      Girdhar K Pandey Amita Pandey Vanga Siva Reddy Renu Deswal Alok Bhattacharya Kailash C Upadhyaya Sudhir K Sopory

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      Entamoeba histolytica contains a novel calcium-binding protein like calmodulin, which was discovered earlier, and we have reported the presence of its homologue(s) and a dependent protein kinase in plants. To understand the functions of these in plants, a cDNA encoding a calcium-binding protein isolated from Entamoeba histolytica (EhCaBP) was cloned into vector pBI121 in antisense orientation and transgenic tobacco plants were raised. These plants showed variation in several phenotypic characters, of which two distinct features, more greenness and leaf thickness, were inherited in subsequent generations. The increase in the level of total chlorophyll in different plants ranged from 60% to 70%. There was no major change in chloroplast structure and in the protein level of D1, D2, LHCP and RuBP carboxylase. These morphological changes were not seen in antisense calmodulin transgenic tobacco plants, nor was the calmodulin level altered in EhCaBP antisense plants.

    • A homologue of the defender against the apoptotic death gene (dad1) in UV-exposed Chlamydomonas cells is downregulated with the onset of programmed cell death

      Swati Moharikar Jacinta S D’souza Basuthkar J Rao

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      We report here the isolation of a homologue of the potential anti-apoptotic gene, defender against apoptotic death (dad1) from Chlamydomonas reinhardtii cells. Using polymerase chain reaction (PCR), we investigated its expression in the execution process of programmed cell death (PCD) in UV-C exposed dying C. reinhardtii cells. Reverse-transcriptase (RT)-PCR showed that C. reinhardtii dad1 amplification was drastically reduced in UV-C exposed dying C. reinhardtii cells. We connect the downregulation of dad1 with the upregulation of apoptosis protease activating factor-1 (APAF-1) and the physiological changes that occur in C. reinhardtii cells upon exposure to 12 J/m2 UV-C in order to show a reciprocal relationship between proapoptotic and inhibitor of apoptosis factors. The temporal changes indicate a correlation between the onset of cell death and dad1 downregulation. The sequence of the PCR product of the cDNA encoding the dad1 homologue was aligned with the annotated dad1 (C_20215) from the Chlamydomonas database (http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=chlre2); Annotation?pDb=chlre2); this sequence was found to show 100% identity, both at the nucleotide and amino acid level. The 327 bp transcript showed an open reading frame of 87 amino acid residues. The deduced amino acid sequence of the putative C. reinhardtii DAD1 homologue showed 54% identity with Oryza sativa, 56% identity with Drosophila melanogaster, 66% identity with Xenopus laevis, and 64% identity with Homo sapiens, Sus scrofa, Gallus gallus, Rattus norvegicus and Mus musculus.

    • Electrochemical investigation of the effect of some organic phosphates on haemoglobin

      S Rezaei-Zarchi A A Saboury H Ghourchian J Hong A Barzegar P Norouzi A A Moosavi-Movahedi M R Ganjali A Javed

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      The effects of DPG, IHP, GTP, GDP and GMP on the structure and stability of haemoglobin were electrochemically investigated with an iodide-modified silver electrode in 0.01 M KNO3 at pH 7.0. Anodic and cathodic peaks of haemoglobin were observed at 250 mV and 12 mV with a formal potential value of 133 mV vs. Ag/AgCl. The effects of different concentrations of DPG, IHP, GTP, GDP and GMP on the anaerobic redox reaction were determined. The results showed that DPG and IHP can lead to a positive shift in the reduction peak of haemoglobin, indicating that the oxidation peak shift of haemoglobin was small as a result of stabilization of the reduced state and destabilization of the R-like state of haemoglobin. GTP elicited a more positive shift in the cathodic and anodic peaks of haemoglobin at a higher concentration, signifying that it has a low-affinity binding site on haemoglobin. The positive shift of the cathodic and anodic peaks revealed a slight variation in the structure and indicated the unfolding of haemoglobin in the presence of high concentrations of GTP. Our study also showed that GDP and GMP did not cause significant shift the cathodic and anodic peaks of haemoglobin even at high concentrations, refuting the existence of specific GDP- and GMP-binding sites on the protein. Moreover, the iodide-modified silver electrode method proved to be easy and useful in investigating the effects of ligands or other effectors on haemoglobin in solution.

    • Dihydroxyoctadecamonoenoate esters inhibit the neutrophil respiratory burst

      David Alan Thompson Bruce D Hammock

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      The leukotoxins [9(10)- and 12(13)-EpOME] are produced by activated inflammatory leukocytes such as neutrophils. High EpOME levels are observed in disorders such as acute respiratory distress syndrome and in patients with extensive burns. Although the physiological significance of the EpOMEs remains poorly understood, in some systems, the EpOMEs act as a protoxin, with their corresponding epoxide hydrolase metabolites, 9,10- and 12,13-DiHOME, specifically exerting toxicity. Both the EpOMEs and the DiHOMEs were also recently shown to have neutrophil chemotactic activity. We evaluated whether the neutrophil respiratory burst, a surge of oxidant production thought to play an important role in limiting certain bacterial and fungal infections, is modulated by members of the EpOME metabolic pathway. We present evidence that the DiHOMEs suppress the neutrophil respiratory burst by a mechanism distinct from that of respiratory burst inhibitors such as cyclosporin H or lipoxin A4, which inhibit multiple aspects of neutrophil activation.

    • Age-related decrease in rod bipolar cell density of the human retina: an immunohistochemical study

      P Aggarwal T C Nag S Wadhwa

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      During normal ageing, the rods (and other neurones) undergo a significant decrease in density in the human retina from the fourth decade of life onward. Since the rods synapse with the rod bipolar cells in the outer plexiform layer, a decline in rod density (mainly due to death) may ultimately cause an associated decline of the neurones which, like the rod bipolar cells, are connected to them. The rod bipolar cells are selectively stained with antibodies to protein kinase C-𝛼. This study examined if rod bipolar cell density changes with ageing of the retina, utilizing donor human eyes (age: 6–91 years). The retinas were fixed and their temporal parts from the macula to the mid-periphery sectioned and processed for protein kinase C-𝛼 immunohistochemistry. The density of the immunopositive rod bipolar cells was estimated in the mid-peripheral retina (eccentricity: 3–5 mm) along the horizontal temporal axis. The results show that while there is little change in the density of the rod bipolar cells from 6 to 35 years (2.2%), the decline during the period from 35 to 62 years is about 21% and between seventh and tenth decades, it is approximately 27%.

    • Chondroprotective potential of root extracts of Withania somnifera in osteoarthritis

      Venil N Sumantran Asavari Kulkarni Sanjay Boddul Trushna Chinchwade Soumya J Koppikar Abhay Harsulkar Bhushan Patwardhan Arvind Chopra Ulhas V Wagh

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      This is the first report describing two novel chondroprotective activities of aqueous extracts of Withania somnifera root powder. First, these extracts had a statistically significant, short-term chondroprotective effect on damaged human osteoarthritic cartilage matrix in 50% of the patients tested. Second, these extracts caused a significant and reproducible inhibition of the gelatinase activity of collagenase type 2 enzyme in vitro.

    • Programmed cell death in the larval salivary glands of Apis mellifera (Hymenoptera, Apidae)

      E C M Silva-Zacarin G A Tomaino M R Brocheto-Braga S R Taboga R L M Silva De Moraes

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      The morphological and histochemical features of degeneration in honeybee (Apis mellifera) salivary glands were investigated in 5th instar larvae and in the pre-pupal period. The distribution and activity patterns of acid phosphatase enzyme were also analysed. As a routine, the larval salivary glands were fixed and processed for light microscopy and transmission electron microscopy. Tissue sections were subsequently stained with haematoxylin–eosin, bromophenol blue, silver, or a variant of the critical electrolyte concentration (CEC) method. Ultrathin sections were contrasted with uranyl acetate and lead citrate. Glands were processed for the histochemical and cytochemical localization of acid phosphatase, as well as biochemical assay to detect its activity pattern. Acid phosphatase activity was histochemically detected in all the salivary glands analysed. The cytochemical results showed acid phosphatase in vesicles, Golgi apparatus and lysosomes during the secretory phase and, additionally, in autophagic structures and luminal secretion during the degenerative phase. These findings were in agreement with the biochemical assay. At the end of the 5th instar, the glandular cells had a vacuolated cytoplasm and pyknotic nuclei, and epithelial cells were shed into the glandular lumen. The transition phase from the 5th instar to the pre-pupal period was characterized by intense vacuolation of the basal cytoplasm and release of parts of the cytoplasm into the lumen by apical blebbing; these blebs contained cytoplasmic RNA, rough endoplasmic reticule and, occasionally, nuclear material. In the pre-pupal phase, the glandular epithelium showed progressive degeneration so that at the end of this phase only nuclei and remnants of the cytoplasm were observed. The nuclei were pyknotic, with peripheral chromatin and blebs. The gland remained in the haemolymph and was recycled during metamorphosis. The programmed cell death in this gland represented a morphological form intermediate between apoptosis and autophagy.

    • A model for cell type localization in the migrating slug of Dictyostelium discoideum based on differential chemotactic sensitivity to cAMP and differential sensitivity to suppression of chemotaxis by ammonia

      Ira N Feit Jeffrey Pawlikowski Caroline Zawilski

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      The three basic cell types in the migrating slug of Dictyostelium discoideum show differential chemotactic response to cyclic AMP (cAMP) and differential sensitivity to suppression of the chemotaxis by ammonia. The values of these parameters indicate a progressive maturation of chemotactic properties during the transdifferentiation of slug cell types. We present a model that explains the localization of the three cell types within the slug based on these chemotactic differences and on the maturation of their chemotactic properties.

    • Electroantennogram responses of the potato tuber moth, Phthorimaea operculella (Lepidoptera; Gelichiidae) to plant volatiles

      P D Das R Raina A R Prasad A Sen

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      Electroantennograms (EAGs) were recorded from males and females of the potato tuber moth, Phthorimaea operculella in response to a broad range of plant volatile compounds belonging to diverse chemical classes. The responses to 27 compounds were evaluated, which indicated significant differences in EAGs between chemicals as well as between sexes. The fatty acid derivatives comprising essentially green leaf volatile components elicited significantly greater responses in females. The response profile of males was, in general, lower than that of females. EAG responses to the oxygenated and hydrocarbon monoterpenes were lower in both males and females. Dose–response studies indicate differences in response between the sexes and concentrations, suggesting the existence of sexual dimorphism. Compounds belonging to the fatty acid derivatives class appear to be important for an oligophagous pest such as the potato tuber moth and the findings are discussed in relation to host plant selection in this species.

    • A mechanical model of wing and theoretical estimate of taper factor for three gliding birds

      Moosarreza Shamsyeh Zahedi Mir Yaseen Ali Khan

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      We tested a mechanical model of wing, which was constructed using the measurements of wingspan and wing area taken from three species of gliding birds. In this model, we estimated the taper factors of the wings for jackdaw (Corrus monedula), Harris’ hawk (Parabuteo unicinctas) and Lagger falcon (Falco jugger) as 1.8, 1.5 and 1.8, respectively. Likewise, by using the data linear regression and curve estimation method, as well as estimating the taper factors and the angle between the humerus and the body, we calculated the relationship between wingspan, wing area and the speed necessary to meet the aerodynamic requirements of sustained flight. In addition, we calculated the relationship between the speed, wing area and wingspan for a specific angle between the humerus and the body over the range of stall speed to maximum speed of gliding flight. We then compared the results for these three species of gliding birds. These comparisons suggest that the aerodynamic characteristics of Harris’ hawk wings are similar to those of the falcon but different from those of the jackdaw. This paper also presents two simple equations to estimate the minimum angle between the humerus and the body as well as the minimum span ratio of a bird in gliding flight.

    • Heterotrophic free-living and particle-bound bacterial cell size in the river Cauvery and its downstream tributaries

      T S Harsha Sadanand M Yamakanamardi M Mahadevaswamy

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      This is the first comprehensive study on planktonic heterotrophic bacterial cell size in the river Cauvery and its important tributaries in Karnataka State, India. The initial hypothesis that the mean cell size of planktonic heterotrophic bacteria in the four tributaries are markedly different from each other and also from that in the main river Cauvery was rejected, because all five watercourses showed similar planktonic heterotrophic bacterial cell size. Examination of the correlation between mean heterotrophic bacterial cell size and environmental variables showed four correlations in the river Arkavathy and two in the river Shimsha. Regression analysis revealed that 18% of the variation in mean heterotrophic free-living bacterial cell size was due to biological oxygen demand (BOD) in the river Arkavathy, 11% due to surface water velocity (SWV) in the river Cauvery and 11% due to temperature in the river Kapila. Heterotrophic particle-bound bacterial cell size variation was 28% due to chloride and BOD in the river Arkavathy, 11% due to conductivity in the river Kapila and 8% due to calcium in the river Cauvery. This type of relationship between heterotrophic bacterial cell size and environmental variables suggests that, though the mean heterotrophic bacterial cell size was similar in all the five water courses, different sets of environmental variables apparently control the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible cause for this environmental (bottom–up) control is discussed.

    • Contribution of root to soil respiration and carbon balance in disturbed and undisturbed grassland communities, northeast China

      Wei Wang Jixun Guo Takehisa Oikawa

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      Changes in the composition of plant species induced by grassland degradation may alter soil respiration rates and decrease carbon sequestration; however, few studies in this area have been conducted. We used net primary productivity (NPP), microbial biomass carbon (MBC), and soil organic carbon (SOC) to examine the changes in soil respiration and carbon balance in two Chinese temperate grassland communities dominated by Leymus chinensis (undisturbed community; Community 1) and Puccinellia tenuiflora (degraded community; Community 2), respectively. Soil respiration varied from 2.5 to 11.9 g CO2 m-2 d-1 and from 1.5 to 9.3 g CO2 m-2 d-1, and the contribution of root respiration to total soil respiration from 38% to 76% and from 25% to 72% in Communities 1 and 2, respectively. During the growing season (May–September), soil respiration, shoot biomass, live root biomass, MBC and SOC in Community 2 decreased by 28%, 39%, 45%, 55% and 29%, respectively, compared to those in Community 1. The considerably lower net ecosystem productivity in Community 2 than in Community 1 (104.56 vs. 224.73 g C m-2 yr-1) suggests that the degradation has significantly decreased carbon sequestration of the ecosystems.

    • Detection without deflection? A hypothesis for direct sensing of sound pressure by hair cells

      Andrew Bell

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      It is widely thought that organisms detect sound by sensing the deflection of hair-like projections, the stereocilia, at the apex of hair cells. In the case of mammals, the standard interpretation is that hair cells in the cochlea respond to deflection of stereocilia induced by motion generated by a hydrodynamic travelling wave. But in the light of persistent anomalies, an alternative hypothesis seems to have some merit: that sensing cells (in particular the outer hair cells) may, at least at low intensities, be reacting to a different stimulus – the rapid pressure wave that sweeps through the cochlear fluids at the speed of sound in water. This would explain why fast responses are sometimes seen before the peak of the travelling wave. Yet how could cells directly sense fluid pressure? Here, a model is constructed of the outer hair cell as a pressure vessel able to sense pressure variations across its cuticular pore, and this ‘fontanelle’ model, based on the sensing action of the basal body at this compliant spot, could explain the observed anomalies. Moreover, the fontanelle model can be applied to a wide range of other organisms, suggesting that direct pressure detection is a general mode of sensing complementary to stereociliar displacement.

    • Molecular mechanism of insulin resistance

      Samir Bhattacharya Debleena Dey Sib Sankar Roy

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      Free fatty acids are known to play a key role in promoting loss of insulin sensitivity, thereby causing insulin resistance and type 2 diabetes. However, the underlying mechanism involved is still unclear. In searching for the cause of the mechanism, it has been found that palmitate inhibits insulin receptor (IR) gene expression, leading to a reduced amount of IR protein in insulin target cells. PDK1-independent phosphorylation of PKCε causes this reduction in insulin receptor gene expression. One of the pathways through which fatty acid can induce insulin resistance in insulin target cells is suggested by these studies. We provide an overview of this important area, emphasizing the current status.

    • Polyphenism in insects and the juvenile hormone

      K K Verma

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    • The stability of ecosystems: A brief overview of the paradox of enrichment

      Shovonlal Roy J Chattopadhyay

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      In theory, enrichment of resource in a predator–prey model leads to desta bilization of the system, thereby collapsing the trophic interaction, a phe nomenon referred to as ``the paradox of enrichment”. After it was first pro posed by Rosenzweig (1971), a number of subsequent studies were carried out on this dilemma over many decades. In this article, we review these the oretical and experimental works and give a brief overview of the proposed solutions to the paradox. The mechanisms that have been discussed are modifications of simple predator–prey models in the presence of prey that is inedible, invulnerable, unpalatable and toxic. Another class of mechanisms includes an incorporation of a ratio-dependent functional form, inducible defence of prey and density-dependent mortality of the predator. Moreover, we find a third set of explanations based on complex population dynamics including chaos in space and time. We conclude that, although any one of the various mechanisms proposed so far might potentially prevent destabilization of the predator–prey dynamics following enrichment, in nature different mechanisms may combine to cause stability, even when a system is enriched. The exact mechanisms, which may differ among systems, need to be disentangled through extensive field studies and labo ratory experiments coupled with realistic theoretical models.

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